CD_NCBI_ID	CDlen	TaxDiv	TaxonList	Description
CDD:214330	1070	EUK	Plants:131	CHL00001, rpoB, RNA polymerase beta subunit.
CDD:214331	504	EUK	Plants:109	CHL00002, matK, maturase K.
CDD:176950	82	EUK	Plants:74	CHL00005, rps16, ribosomal protein S16.
CDD:214332	78	EUK	Plants:87	CHL00010, infA, translation initiation factor 1.
CDD:176954	498	EUK	Plants:117	CHL00011, ndhD, NADH dehydrogenase subunit 4.
CDD:214333	327	EUK	Plants:123	CHL00013, rpoA, RNA polymerase alpha subunit.
CDD:176958	101	EUK	Plants:119	CHL00015, ndhE, NADH dehydrogenase subunit 4L.
CDD:214335	182	EUK	Plants:118	CHL00016, ndhG, NADH dehydrogenase subunit 6.
CDD:214336	663	EUK	Invertebrates:2,Plants:141	CHL00018, rpoC1, RNA polymerase beta' subunit.
CDD:176962	184	EUK	Plants:145	CHL00019, atpF, ATP synthase CF0 B subunit.
CDD:176964	120	EUK	Plants:118	CHL00022, ndhC, NADH dehydrogenase subunit 3.
CDD:214337	225	EUK	Plants:115	CHL00023, ndhK, NADH dehydrogenase subunit K.
CDD:214338	741	EUK	Plants:117	CHL00025, ndhF, NADH dehydrogenase subunit 5.
CDD:214339	90	EUK	Plants:128	CHL00027, rps15, ribosomal protein S15.
CDD:214340	200	EUK	Invertebrates:1,Plants:148	CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
CDD:176970	26	EUK	Invertebrates:1,Plants:157	CHL00029, rpl36, ribosomal protein L36.
CDD:176971	93	EUK	Plants:134	CHL00030, rpl23, ribosomal protein L23.
CDD:214341	363	EUK	Plants:111	CHL00032, ndhA, NADH dehydrogenase subunit 1.
CDD:176974	168	EUK	Invertebrates:2,Plants:160	CHL00033, ycf3, photosystem I assembly protein Ycf3.
CDD:214342	117	EUK	Plants:121	CHL00034, rpl22, ribosomal protein L22.
CDD:176977	184	EUK	Invertebrates:1,Plants:149	CHL00036, ycf4, photosystem I assembly protein Ycf4.
CDD:176978	320	EUK	Invertebrates:3,Plants:163	CHL00037, petA, cytochrome f.
CDD:176982	116	EUK	Invertebrates:3,Plants:165	CHL00041, rps11, ribosomal protein S11.
CDD:214344	132	EUK	Invertebrates:1,Plants:170	CHL00042, rps8, ribosomal protein S8.
CDD:214345	261	EUK	Plants:148	CHL00043, cemA, envelope membrane protein.
CDD:176985	135	EUK	Invertebrates:1,Plants:166	CHL00044, rpl16, ribosomal protein L16.
CDD:214346	319	EUK	Plants:155	CHL00045, ccsA, cytochrome c biogenesis protein.
CDD:176987	228	EUK	Invertebrates:3,Plants:169	CHL00046, atpI, ATP synthase CF0 A subunit.
CDD:214347	58	EUK	Invertebrates:1,Plants:155	CHL00047, psbK, photosystem II protein K.
CDD:214348	214	EUK	Invertebrates:3,Plants:137	CHL00048, rps3, ribosomal protein S3.
CDD:176990	494	EUK	Plants:114	CHL00049, ndhB, NADH dehydrogenase subunit 2.
CDD:176991	92	EUK	Invertebrates:2,Plants:128	CHL00050, rps19, ribosomal protein S19.
CDD:176992	123	EUK	Invertebrates:7,Plants:170	CHL00051, rps12, ribosomal protein S12.
CDD:176993	273	EUK	Invertebrates:5,Plants:164	CHL00052, rpl2, ribosomal protein L2.
CDD:176994	155	EUK	Invertebrates:3,Plants:159	CHL00053, rps7, ribosomal protein S7.
CDD:176997	122	EUK	Invertebrates:5,Plants:173	CHL00057, rpl14, ribosomal protein L14.
CDD:176999	485	EUK	Invertebrates:3,Plants:170	CHL00059, atpA, ATP synthase CF1 alpha subunit.
CDD:214349	494	EUK	Invertebrates:3,Plants:168	CHL00060, atpB, ATP synthase CF1 beta subunit.
CDD:214351	134	EUK	Invertebrates:1,Plants:157	CHL00063, atpE, ATP synthase CF1 epsilon subunit.
CDD:177006	73	EUK	Invertebrates:1,Plants:163	CHL00066, psbH, photosystem II protein H.
CDD:177007	230	EUK	Invertebrates:3,Plants:164	CHL00067, rps2, ribosomal protein S2.
CDD:214352	115	EUK	Invertebrates:1,Plants:158	CHL00068, rpl20, ribosomal protein L20.
CDD:177010	409	EUK	Invertebrates:7,Plants:44	CHL00071, tufA, elongation factor Tu.
CDD:214353	457	EUK	Invertebrates:1,Plants:45	CHL00073, chlN, photochlorophyllide reductase subunit N.
CDD:214354	100	EUK	Invertebrates:1,Plants:165	CHL00074, rps14, ribosomal protein S14.
CDD:177014	108	EUK	Plants:34	CHL00075, rpl21, ribosomal protein L21.
CDD:214355	513	EUK	Invertebrates:1,Plants:44	CHL00076, chlB, photochlorophyllide reductase subunit B.
CDD:177016	86	EUK	Plants:130	CHL00077, rps18, ribosomal protein S18.
CDD:214356	181	EUK	Invertebrates:3,Plants:45	CHL00078, rpl5, ribosomal protein L5.
CDD:214357	130	EUK	Plants:39	CHL00079, rps9, ribosomal protein S9.
CDD:177020	350	EUK	Invertebrates:1,Plants:34	CHL00081, chlI, Mg-protoporyphyrin IX chelatase.
CDD:177021	62	EUK	Plants:131	CHL00082, psbZ, photosystem II protein Z.
CDD:214358	131	EUK	Plants:29	CHL00083, rpl12, ribosomal protein L12.
CDD:177023	117	EUK	Invertebrates:1,Plants:27	CHL00084, rpl19, ribosomal protein L19.
CDD:214359	485	EUK	Invertebrates:3,Plants:19	CHL00085, ycf24, putative ABC transporter.
CDD:214361	821	EUK	Invertebrates:2,Plants:18	CHL00095, clpC, Clp protease ATP binding subunit.
CDD:214366	93	EUK	Plants:13	CHL00102, rps20, ribosomal protein S20.
CDD:177033	66	EUK	Plants:110	CHL00104, rpl33, ribosomal protein L33.
CDD:177038	201	EUK	Invertebrates:2,Plants:133	CHL00113, rps4, ribosomal protein S4; Reviewed.
CDD:214368	1364	EUK	Invertebrates:1,Plants:126	CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
CDD:214369	156	EUK	Plants:19	CHL00118, atpG, ATP synthase CF0 B' subunit; Validated.
CDD:177042	184	EUK	Plants:15	CHL00119, atpD, ATP synthase CF1 delta subunit; Validated.
CDD:214370	86	EUK	Invertebrates:1,Plants:18	CHL00121, rpl27, ribosomal protein L27; Reviewed.
CDD:214371	870	EUK	Invertebrates:2,Plants:16	CHL00122, secA, preprotein translocase subunit SecA; Validated.
CDD:177046	97	EUK	Plants:13	CHL00123, rps6, ribosomal protein S6; Validated.
CDD:177047	82	EUK	Plants:12	CHL00124, acpP, acyl carrier protein; Validated.
CDD:177049	140	EUK	Invertebrates:4,Plants:18	CHL00127, rpl11, ribosomal protein L11; Validated.
CDD:177051	229	EUK	Plants:18	CHL00129, rpl1, ribosomal protein L1; Reviewed.
CDD:177054	185	EUK	Plants:17	CHL00132, psaF, photosystem I subunit III; Validated.
CDD:177055	163	EUK	Invertebrates:2,Plants:18	CHL00133, psbV, photosystem II cytochrome c550; Validated.
CDD:177057	101	EUK	Plants:19	CHL00135, rps10, ribosomal protein S10; Validated.
CDD:177059	122	EUK	Plants:19	CHL00137, rps13, ribosomal protein S13; Validated.
CDD:177060	143	EUK	Invertebrates:2,Plants:19	CHL00138, rps5, ribosomal protein S5; Validated.
CDD:214373	109	EUK	Plants:16	CHL00139, rpl18, ribosomal protein L18; Validated.
CDD:177062	178	EUK	Invertebrates:1,Plants:19	CHL00140, rpl6, ribosomal protein L6; Validated.
CDD:214374	83	EUK	Plants:17	CHL00141, rpl24, ribosomal protein L24; Validated.
CDD:177064	84	EUK	Invertebrates:1,Plants:19	CHL00142, rps17, ribosomal protein S17; Validated.
CDD:177065	207	EUK	Invertebrates:2,Plants:19	CHL00143, rpl3, ribosomal protein L3; Validated.
CDD:214375	215	EUK	Plants:15	CHL00147, rpl4, ribosomal protein L4; Validated.
CDD:214377	53	EUK	Plants:81	CHL00152, rpl32, ribosomal protein L32; Validated.
CDD:177072	143	EUK	Plants:17	CHL00159, rpl13, ribosomal protein L13; Validated.
CDD:214379	417	EUK	Invertebrates:1,Plants:19	CHL00161, secY, preprotein translocase subunit SecY; Validated.
CDD:214381	99	EUK	Plants:13	CHL00163, ycf65, putative ribosomal protein 3; Validated.
CDD:214384	296	EUK	Plants:117	CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
CDD:214386	638	EUK	Plants:16	CHL00176, ftsH, cell division protein; Validated.
CDD:214387	426	EUK	Plants:17	CHL00177, ccs1, c-type cytochrome biogenensis protein; Validated.
CDD:177084	249	EUK	Invertebrates:1,Plants:18	CHL00182, tatC, Sec-independent translocase component C; Provisional.
CDD:177088	36	EUK	Plants:102	CHL00186, psaI, photosystem I subunit VIII; Validated.
CDD:214388	237	EUK	Plants:12	CHL00187, cysT, sulfate transport protein; Provisional.
CDD:177090	30	EUK	Plants:28	CHL00190, psaM, photosystem I subunit XII; Provisional.
CDD:177092	128	EUK	Plants:15	CHL00193, ycf35, Ycf35; Provisional.
CDD:177093	317	EUK	Plants:18	CHL00194, ycf39, Ycf39; Provisional.
CDD:214395	1832	EUK	Plants:37	CHL00204, ycf1, Ycf1; Provisional.
CDD:214397	1077	EUK	Invertebrates:4,Plants:11	CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
CDD:223080	432	EUKprk	Bacteria:47,Plants:1,nodiv:1	COG0001, HemL, Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism].
CDD:223081	349	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0002, ArgC, Acetylglutamate semialdehyde dehydrogenase [Amino acid transport and metabolism].
CDD:223082	322	EUKprk	Bacteria:20,Plants:2	COG0003, ArsA, Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning].
CDD:223083	409	EUKprk	Bacteria:34,Plants:2,nodiv:1	COG0004, AmtB, Ammonia permease [Inorganic ion transport and metabolism].
CDD:223084	262	EUKprk	Bacteria:34,Plants:2,nodiv:1	COG0005, Pnp, Purine nucleoside phosphorylase [Nucleotide transport and metabolism].
CDD:223085	384	EUKprk	Bacteria:62,Plants:4,nodiv:1	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism].
CDD:223086	244	EUKprk	Bacteria:41,Plants:2,nodiv:1	COG0007, CysG, Uroporphyrinogen-III methylase [Coenzyme metabolism].
CDD:223087	472	EUKprk	Bacteria:64,Plants:4,nodiv:2	COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis].
CDD:223088	211	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0009, SUA5, Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis].
CDD:223089	305	EUKprk	Bacteria:36,Plants:2,nodiv:2	COG0010, SpeB, Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism].
CDD:223090	100	EUKprk	Bacteria:20,Plants:1	COG0011, COG0011, Uncharacterized conserved protein [Function unknown].
CDD:223091	372	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0012, COG0012, Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis].
CDD:223092	879	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223093	417	EUKprk	Bacteria:34,Plants:2,nodiv:1	COG0014, ProA, Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism].
CDD:223094	438	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and metabolism].
CDD:223095	335	EUKprk	Bacteria:61,Plants:4,nodiv:1	COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis].
CDD:223096	435	EUKprk	Bacteria:41,Plants:3	COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis].
CDD:223097	577	EUKprk	Bacteria:61,Plants:4,nodiv:1	COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223098	394	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport and metabolism].
CDD:223099	245	EUKprk	Bacteria:56,Plants:3,nodiv:1	COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism].
CDD:223100	663	EUKprk	Bacteria:46,Plants:4,nodiv:1	COG0021, TktA, Transketolase [Carbohydrate transport and metabolism].
CDD:223101	324	EUKprk	Bacteria:31,Plants:3,nodiv:1	COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion].
CDD:223102	104	EUKprk	Bacteria:23,Plants:2,nodiv:1	COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis].
CDD:223103	255	EUKprk	Bacteria:59,Plants:3,nodiv:2	COG0024, Map, Methionine aminopeptidase [Translation, ribosomal structure and biogenesis].
CDD:223104	429	EUKprk	Bacteria:29,Plants:3,nodiv:1	COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism].
CDD:223105	375	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG0026, PurK, Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism].
CDD:223106	394	PRK	Bacteria:17	COG0027, PurT, Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism].
CDD:223107	550	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0028, IlvB, Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223108	518	PRK	Bacteria:27,nodiv:1	COG0029, NadB, Aspartate oxidase [Coenzyme metabolism].
CDD:223109	259	EUKprk	Bacteria:64,Plants:3,nodiv:1	COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis].
CDD:223110	300	EUKprk	Bacteria:49,Plants:2,nodiv:2	COG0031, CysK, Cysteine synthase [Amino acid transport and metabolism].
CDD:223111	524	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG0033, Pgm, Phosphoglucomutase [Carbohydrate transport and metabolism].
CDD:223112	470	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0034, PurF, Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism].
CDD:223113	210	EUKprk	Bacteria:41,Plants:3,nodiv:4	COG0035, Upp, Uracil phosphoribosyltransferase [Nucleotide transport and metabolism].
CDD:223114	220	EUKprk	Bacteria:48,Plants:3,nodiv:1	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism].
CDD:223115	298	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning].
CDD:223116	443	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0038, EriC, Chloride channel protein EriC [Inorganic ion transport and metabolism].
CDD:223117	313	EUKprk	Bacteria:49,Plants:3,nodiv:1	COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and conversion].
CDD:223118	290	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0040, HisG, ATP phosphoribosyltransferase [Amino acid transport and metabolism].
CDD:223119	162	PRK	Bacteria:45,nodiv:1	COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism].
CDD:223120	323	EUKprk	Bacteria:49,Plants:4,nodiv:2	COG0042, COG0042, tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis].
CDD:223121	477	EUKprk	Bacteria:41,Plants:1,nodiv:1	COG0043, UbiD, 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism].
CDD:223122	430	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0044, PyrC, Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism].
CDD:223123	387	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy production and conversion].
CDD:223124	743	EUKprk	Bacteria:46,Plants:2,nodiv:2	COG0046, PurL, Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism].
CDD:223125	231	PRK	Bacteria:31,nodiv:1	COG0047, PurL, Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain [Nucleotide transport and metabolism].
CDD:223126	129	EUKprk	Bacteria:56,Plants:3,nodiv:1	COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal structure and biogenesis].
CDD:223127	148	EUKprk	Bacteria:58,Plants:4,nodiv:2	COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal structure and biogenesis].
CDD:223128	394	EUKprk	Bacteria:49,Plants:2,nodiv:2	COG0050, TufB, GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis].
CDD:223129	104	EUKprk	Bacteria:55,Plants:4	COG0051, RpsJ, Ribosomal protein S10 [Translation, ribosomal structure and biogenesis].
CDD:223130	252	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0052, RpsB, Ribosomal protein S2 [Translation, ribosomal structure and biogenesis].
CDD:223131	304	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism].
CDD:223132	152	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme metabolism].
CDD:223133	468	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy production and conversion].
CDD:223134	504	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy production and conversion].
CDD:223135	335	EUKprk	Bacteria:58,Plants:3,nodiv:2	COG0057, GapA, Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism].
CDD:223136	750	EUKprk	Bacteria:34,Plants:1,nodiv:1	COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and metabolism].
CDD:223137	338	EUKprk	Bacteria:44,Plants:1,nodiv:1	COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223138	933	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223139	281	EUKprk	Bacteria:55,Plants:3,nodiv:1	COG0061, nadF, NAD kinase [Coenzyme metabolism].
CDD:223140	203	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0062, COG0062, Uncharacterized conserved protein [Function unknown].
CDD:223141	284	EUKprk	Bacteria:8,Plants:3	COG0063, COG0063, Predicted sugar kinase [Carbohydrate transport and metabolism].
CDD:223142	483	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG0064, GatB, Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis].
CDD:223143	423	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0065, LeuC, 3-isopropylmalate dehydratase large subunit [Amino acid transport and metabolism].
CDD:223144	191	PRK	Bacteria:43,nodiv:1	COG0066, LeuD, 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism].
CDD:223145	371	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG0067, GltB, Glutamate synthase domain 1 [Amino acid transport and metabolism].
CDD:223146	750	PRK	Bacteria:18	COG0068, HypF, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones].
CDD:223147	485	EUKprk	Bacteria:16,Plants:1,nodiv:1	COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport and metabolism].
CDD:223148	301	PRK	Bacteria:10,nodiv:1	COG0070, GltB, Glutamate synthase domain 3 [Amino acid transport and metabolism].
CDD:223149	146	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0071, IbpA, Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones].
CDD:223150	650	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis].
CDD:223151	123	EUKprk	Bacteria:53,Plants:3,nodiv:1	COG0073, ARC1, EMAP domain [General function prediction only].
CDD:223152	293	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy production and conversion].
CDD:223153	383	EUKprk	Bacteria:31,Plants:1,nodiv:1	COG0075, COG0075, Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism].
CDD:223154	460	EUKprk	Bacteria:24,Plants:1	COG0076, GadB, Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism].
CDD:223155	279	EUKprk	Bacteria:41,Plants:2,nodiv:1	COG0077, PheA, Prephenate dehydratase [Amino acid transport and metabolism].
CDD:223156	310	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0078, ArgF, Ornithine carbamoyltransferase [Amino acid transport and metabolism].
CDD:223157	356	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0079, HisC, Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism].
CDD:223158	141	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal structure and biogenesis].
CDD:223159	228	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal structure and biogenesis].
CDD:223160	369	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0082, AroC, Chorismate synthase [Amino acid transport and metabolism].
CDD:223161	299	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0083, ThrB, Homoserine kinase [Amino acid transport and metabolism].
CDD:223162	256	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0084, TatD, Mg-dependent DNase [DNA replication, recombination, and repair].
CDD:223163	1060	EUKprk	Bacteria:61,Plants:5,nodiv:1	COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription].
CDD:223164	808	EUKprk	Bacteria:58,Plants:4,nodiv:2	COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription].
CDD:223165	218	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal structure and biogenesis].
CDD:223166	214	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal structure and biogenesis].
CDD:223167	94	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal structure and biogenesis].
CDD:223168	275	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal structure and biogenesis].
CDD:223169	120	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0091, RplV, Ribosomal protein L22 [Translation, ribosomal structure and biogenesis].
CDD:223170	233	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal structure and biogenesis].
CDD:223171	122	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0093, RplN, Ribosomal protein L14 [Translation, ribosomal structure and biogenesis].
CDD:223172	180	EUKprk	Bacteria:58,Plants:4,nodiv:2	COG0094, RplE, Ribosomal protein L5 [Translation, ribosomal structure and biogenesis].
CDD:223173	248	EUKprk	Bacteria:30,Plants:2	COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
CDD:223174	132	EUKprk	Bacteria:57,Plants:4,nodiv:1	COG0096, RpsH, Ribosomal protein S8 [Translation, ribosomal structure and biogenesis].
CDD:223175	178	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis].
CDD:223176	181	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal structure and biogenesis].
CDD:223177	121	EUKprk	Bacteria:59,Plants:4,nodiv:1	COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis].
CDD:223178	129	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal structure and biogenesis].
CDD:223179	266	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis].
CDD:223180	148	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis].
CDD:223181	130	EUKprk	Bacteria:55,Plants:3,nodiv:2	COG0103, RpsI, Ribosomal protein S9 [Translation, ribosomal structure and biogenesis].
CDD:223182	430	EUKprk	Bacteria:48,Plants:2,nodiv:2	COG0104, PurA, Adenylosuccinate synthase [Nucleotide transport and metabolism].
CDD:223183	135	EUKprk	Bacteria:48,Plants:3,nodiv:2	COG0105, Ndk, Nucleoside diphosphate kinase [Nucleotide transport and metabolism].
CDD:223184	241	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism].
CDD:223185	256	EUKprk	Bacteria:39,Plants:2,nodiv:2	COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism].
CDD:223186	203	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG0108, RibB, 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism].
CDD:223187	304	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG0109, CyoE, Polyprenyltransferase (cytochrome oxidase assembly factor) [Posttranslational modification, protein turnover, chaperones].
CDD:223188	190	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0110, WbbJ, Acetyltransferase (isoleucine patch superfamily) [General function prediction only].
CDD:223189	324	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0111, SerA, Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism].
CDD:223190	413	EUKprk	Bacteria:58,Plants:4,nodiv:2	COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism].
CDD:223191	330	EUKprk	Bacteria:46,Plants:2,nodiv:2	COG0113, HemB, Delta-aminolevulinic acid dehydratase [Coenzyme metabolism].
CDD:223192	462	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG0114, FumC, Fumarase [Energy production and conversion].
CDD:223193	284	EUKprk	Bacteria:49,Plants:2,nodiv:2	COG0115, IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223194	381	PRK	Bacteria:30	COG0116, COG0116, Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair].
CDD:223195	146	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism].
CDD:223196	204	PRK	Bacteria:42,nodiv:1	COG0118, HisH, Glutamine amidotransferase [Amino acid transport and metabolism].
CDD:223197	409	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism].
CDD:223198	227	EUKprk	Bacteria:41,Plants:3,nodiv:1	COG0120, RpiA, Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism].
CDD:223199	252	EUKprk	Bacteria:27,Plants:1,nodiv:1	COG0121, COG0121, Predicted glutamine amidotransferase [General function prediction only].
CDD:223200	285	EUKprk	Bacteria:28,Plants:3,nodiv:1	COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair].
CDD:223201	340	EUKprk	Bacteria:28,Plants:3,nodiv:1	COG0123, AcuC, Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223202	429	EUKprk	Bacteria:59,Plants:4,nodiv:1	COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223203	208	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0125, Tmk, Thymidylate kinase [Nucleotide transport and metabolism].
CDD:223204	395	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0126, Pgk, 3-phosphoglycerate kinase [Carbohydrate transport and metabolism].
CDD:223205	194	EUKprk	Bacteria:51,Plants:3,nodiv:1	COG0127, COG0127, Xanthosine triphosphate pyrophosphatase [Nucleotide transport and metabolism].
CDD:223206	428	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0128, AroA, 5-enolpyruvylshikimate-3-phosphate synthase [Amino acid transport and metabolism].
CDD:223207	575	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0129, IlvD, Dihydroxyacid dehydratase/phosphogluconate dehydratase [Amino acid transport and metabolism / Carbohydrate transport and metabolism].
CDD:223208	271	EUKprk	Bacteria:55,Plants:3,nodiv:1	COG0130, TruB, Pseudouridine synthase [Translation, ribosomal structure and biogenesis].
CDD:223209	195	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0131, HisB, Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism].
CDD:223210	223	EUKprk	Bacteria:34,Plants:1,nodiv:1	COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism].
CDD:223211	396	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0133, TrpB, Tryptophan synthase beta chain [Amino acid transport and metabolism].
CDD:223212	254	EUKprk	Bacteria:48,Plants:2,nodiv:1	COG0134, TrpC, Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism].
CDD:223213	208	EUKprk	Bacteria:36,Plants:1,nodiv:1	COG0135, TrpF, Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism].
CDD:223214	334	EUKprk	Bacteria:53,Plants:2,nodiv:2	COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid transport and metabolism].
CDD:223215	403	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0137, ArgG, Argininosuccinate synthase [Amino acid transport and metabolism].
CDD:223216	515	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG0138, PurH, AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) [Nucleotide transport and metabolism].
CDD:223217	111	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG0139, HisI, Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism].
CDD:223218	92	PRK	Bacteria:21,nodiv:1	COG0140, HisI, Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism].
CDD:223219	425	EUKprk	Bacteria:41,Plants:1,nodiv:1	COG0141, HisD, Histidinol dehydrogenase [Amino acid transport and metabolism].
CDD:223220	322	EUKprk	Bacteria:62,Plants:3,nodiv:1	COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism].
CDD:223221	558	EUKprk	Bacteria:28,Plants:3,nodiv:1	COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223222	355	EUKprk	Bacteria:44,Plants:4,nodiv:1	COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis].
CDD:223223	674	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG0145, HyuA, N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223224	563	PRK	Bacteria:12,nodiv:1	COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223225	462	EUKprk	Bacteria:53,Plants:3,nodiv:1	COG0147, TrpE, Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223226	423	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0148, Eno, Enolase [Carbohydrate transport and metabolism].
CDD:223227	251	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0149, TpiA, Triosephosphate isomerase [Carbohydrate transport and metabolism].
CDD:223228	345	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0150, PurM, Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism].
CDD:223229	428	PRK	Bacteria:47,nodiv:2	COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism].
CDD:223230	247	EUKprk	Bacteria:46,Plants:2,nodiv:2	COG0152, PurC, Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase [Nucleotide transport and metabolism].
CDD:223231	390	EUKprk	Bacteria:19,Plants:2	COG0153, GalK, Galactokinase [Carbohydrate transport and metabolism].
CDD:223232	475	EUKprk	Bacteria:52,Plants:2,nodiv:1	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis].
CDD:223233	510	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0155, CysI, Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism].
CDD:223234	388	EUKprk	Bacteria:39,Plants:4,nodiv:1	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism].
CDD:223235	280	EUKprk	Bacteria:44,Plants:1,nodiv:1	COG0157, NadC, Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism].
CDD:223236	326	EUKprk	Bacteria:21,Plants:2	COG0158, Fbp, Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism].
CDD:223237	265	PRK	Bacteria:48,nodiv:1	COG0159, TrpA, Tryptophan synthase alpha chain [Amino acid transport and metabolism].
CDD:223238	447	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0160, GabT, 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism].
CDD:223239	449	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG0161, BioA, Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism].
CDD:223240	401	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223241	191	EUKprk	Bacteria:39,Plants:1,nodiv:2	COG0163, UbiX, 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism].
CDD:223242	199	EUKprk	Bacteria:54,Plants:3,nodiv:2	COG0164, RnhB, Ribonuclease HII [DNA replication, recombination, and repair].
CDD:223243	459	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0165, ArgH, Argininosuccinate lyase [Amino acid transport and metabolism].
CDD:223244	446	EUKprk	Bacteria:50,Plants:3,nodiv:1	COG0166, Pgi, Glucose-6-phosphate isomerase [Carbohydrate transport and metabolism].
CDD:223245	310	EUKprk	Bacteria:52,Plants:2,nodiv:1	COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism].
CDD:223246	499	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0168, TrkG, Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism].
CDD:223247	283	PRK	Bacteria:54,nodiv:1	COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and metabolism].
CDD:223248	216	EUKprk	Bacteria:17,Plants:4	COG0170, SEC59, Dolichol kinase [Lipid metabolism].
CDD:223249	268	EUKprk	Bacteria:55,Plants:2,nodiv:1	COG0171, NadE, NAD synthase [Coenzyme metabolism].
CDD:223250	429	EUKprk	Bacteria:60,Plants:3,nodiv:1	COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223251	585	EUKprk	Bacteria:48,Plants:2,nodiv:1	COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223252	443	EUKprk	Bacteria:53,Plants:2,nodiv:1	COG0174, GlnA, Glutamine synthetase [Amino acid transport and metabolism].
CDD:223253	261	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0175, CysH, 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223254	239	EUKprk	Bacteria:44,Plants:2,nodiv:2	COG0176, MipB, Transaldolase [Carbohydrate transport and metabolism].
CDD:223255	211	EUKprk	Bacteria:55,Plants:3,nodiv:1	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair].
CDD:223256	935	PRK	Bacteria:50,nodiv:2	COG0178, UvrA, Excinuclease ATPase subunit [DNA replication, recombination, and repair].
CDD:223257	266	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223258	314	EUKprk	Bacteria:60,Plants:3,nodiv:2	COG0180, TrpS, Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223259	307	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0181, HemC, Porphobilinogen deaminase [Coenzyme metabolism].
CDD:223260	346	EUKprk	Bacteria:22,Plants:2	COG0182, COG0182, Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis].
CDD:223261	392	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0183, PaaJ, Acetyl-CoA acetyltransferase [Lipid metabolism].
CDD:223262	89	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0184, RpsO, Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis].
CDD:223263	93	EUKprk	Bacteria:55,Plants:4,nodiv:2	COG0185, RpsS, Ribosomal protein S19 [Translation, ribosomal structure and biogenesis].
CDD:223264	87	EUKprk	Bacteria:59,Plants:3	COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal structure and biogenesis].
CDD:223265	635	EUKprk	Bacteria:58,Plants:3,nodiv:2	COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair].
CDD:223266	804	PRK	Bacteria:56,nodiv:1	COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].
CDD:223267	318	PRK	Bacteria:34,nodiv:2	COG0189, RimK, Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis].
CDD:223268	283	EUKprk	Bacteria:52,Plants:3,nodiv:1	COG0190, FolD, 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism].
CDD:223269	286	EUKprk	Bacteria:43,Plants:2	COG0191, Fba, Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism].
CDD:223270	388	EUKprk	Bacteria:42,Plants:2,nodiv:2	COG0192, MetK, S-adenosylmethionine synthetase [Coenzyme metabolism].
CDD:223271	190	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis].
CDD:223272	191	EUKprk	Bacteria:46,Plants:3,nodiv:1	COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism].
CDD:223273	190	PRK	Bacteria:59,nodiv:1	COG0195, NusA, Transcription elongation factor [Transcription].
CDD:223274	304	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0196, RibF, FAD synthase [Coenzyme metabolism].
CDD:223275	146	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis].
CDD:223276	104	EUKprk	Bacteria:58,Plants:4,nodiv:1	COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal structure and biogenesis].
CDD:223277	61	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0199, RpsN, Ribosomal protein S14 [Translation, ribosomal structure and biogenesis].
CDD:223278	152	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0200, RplO, Ribosomal protein L15 [Translation, ribosomal structure and biogenesis].
CDD:223279	436	EUKprk	Bacteria:59,Plants:4,nodiv:1	COG0201, SecY, Preprotein translocase subunit SecY [Intracellular trafficking and secretion].
CDD:223280	317	EUKprk	Bacteria:56,Plants:4,nodiv:1	COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription].
CDD:223281	116	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal structure and biogenesis].
CDD:223282	255	EUKprk	Bacteria:49,Plants:3,nodiv:2	COG0204, PlsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism].
CDD:223283	347	EUKprk	Bacteria:36,Plants:3,nodiv:2	COG0205, PfkA, 6-phosphofructokinase [Carbohydrate transport and metabolism].
CDD:223284	338	PRK	Bacteria:54,nodiv:1	COG0206, FtsZ, Cell division GTPase [Cell division and chromosome partitioning].
CDD:223285	268	EUKprk	Bacteria:38,Plants:3,nodiv:2	COG0207, ThyA, Thymidylate synthase [Nucleotide transport and metabolism].
CDD:223286	348	EUKprk	Bacteria:48,Plants:3,nodiv:1	COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism].
CDD:223287	651	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism].
CDD:223288	655	EUKprk	Bacteria:56,Plants:3,nodiv:1	COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair].
CDD:223289	87	EUKprk	Bacteria:44,Plants:2,nodiv:2	COG0211, RpmA, Ribosomal protein L27 [Translation, ribosomal structure and biogenesis].
CDD:223290	191	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism].
CDD:223291	435	PRK	Bacteria:25,nodiv:1	COG0213, DeoA, Thymidine phosphorylase [Nucleotide transport and metabolism].
CDD:223292	296	EUKprk	Bacteria:28,Plants:2	COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme metabolism].
CDD:223293	464	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223294	363	EUKprk	Bacteria:46,Plants:2,nodiv:2	COG0216, PrfA, Protein chain release factor A [Translation, ribosomal structure and biogenesis].
CDD:223295	241	EUKprk	Bacteria:48,Plants:3,nodiv:1	COG0217, COG0217, Uncharacterized conserved protein [Function unknown].
CDD:223296	200	EUKprk	Bacteria:45,Plants:1,nodiv:1	COG0218, COG0218, Predicted GTPase [General function prediction only].
CDD:223297	155	PRK	Bacteria:39,nodiv:1	COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis].
CDD:223298	227	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0220, COG0220, Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only].
CDD:223299	171	EUKprk	Bacteria:47,Plants:4,nodiv:2	COG0221, Ppa, Inorganic pyrophosphatase [Energy production and conversion].
CDD:223300	124	EUKprk	Bacteria:45,Plants:2,nodiv:2	COG0222, RplL, Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis].
CDD:223301	307	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis].
CDD:223302	287	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0224, AtpG, F0F1-type ATP synthase, gamma subunit [Energy production and conversion].
CDD:223303	174	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0225, MsrA, Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones].
CDD:223304	318	PRK	Bacteria:48,nodiv:1	COG0226, PstS, ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:223305	77	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0227, RpmB, Ribosomal protein L28 [Translation, ribosomal structure and biogenesis].
CDD:223306	87	EUKprk	Bacteria:44,Plants:2,nodiv:2	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis].
CDD:223307	140	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG0229, COG0229, Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones].
CDD:223308	44	EUKprk	Bacteria:41,Plants:2	COG0230, RpmH, Ribosomal protein L34 [Translation, ribosomal structure and biogenesis].
CDD:223309	131	EUKprk	Bacteria:63,Plants:3,nodiv:2	COG0231, Efp, Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis].
CDD:223310	412	PRK	Bacteria:22,nodiv:1	COG0232, Dgt, dGTP triphosphohydrolase [Nucleotide transport and metabolism].
CDD:223311	187	EUKprk	Bacteria:44,Plants:2,nodiv:2	COG0233, Frr, Ribosome recycling factor [Translation, ribosomal structure and biogenesis].
CDD:223312	96	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0234, GroS, Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones].
CDD:223313	219	EUKprk	Bacteria:46,Plants:3	COG0235, AraD, Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases [Carbohydrate transport and metabolism].
CDD:223314	80	EUKprk	Bacteria:56,Plants:2,nodiv:1	COG0236, AcpP, Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223315	201	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
CDD:223316	75	EUKprk	Bacteria:45,Plants:2	COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal structure and biogenesis].
CDD:223317	126	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning].
CDD:223318	329	EUKprk	Bacteria:45,Plants:3,nodiv:2	COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion].
CDD:223319	181	EUKprk	Bacteria:25,Plants:3	COG0241, HisB, Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism].
CDD:223320	168	PRK	Bacteria:46,nodiv:1	COG0242, Def, N-formylmethionyl-tRNA deformylase [Translation, ribosomal structure and biogenesis].
CDD:223321	765	PRK	Bacteria:43,nodiv:1	COG0243, BisC, Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion].
CDD:223322	175	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal structure and biogenesis].
CDD:223323	159	PRK	Bacteria:37,nodiv:2	COG0245, IspF, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism].
CDD:223324	473	EUKprk	Bacteria:27,Plants:1,nodiv:1	COG0246, MtlD, Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism].
CDD:223325	388	PRK	Bacteria:42,nodiv:1	COG0247, GlpC, Fe-S oxidoreductase [Energy production and conversion].
CDD:223326	492	EUKprk	Bacteria:36,Plants:1,nodiv:2	COG0248, GppA, Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism].
CDD:223327	843	EUKprk	Bacteria:39,Plants:5,nodiv:2	COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].
CDD:223328	178	EUKprk	Bacteria:59,Plants:1,nodiv:1	COG0250, NusG, Transcription antiterminator [Transcription].
CDD:223329	130	EUKprk	Bacteria:48,Plants:3,nodiv:1	COG0251, TdcF, Putative translation initiation inhibitor, yjgF family [Translation, ribosomal structure and biogenesis].
CDD:223330	351	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0252, AnsB, L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Amino acid transport and metabolism / Translation, ribosomal structure and biogenesis].
CDD:223331	272	PRK	Bacteria:42,nodiv:1	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism].
CDD:223332	75	PRK	Bacteria:46,nodiv:2	COG0254, RpmE, Ribosomal protein L31 [Translation, ribosomal structure and biogenesis].
CDD:223333	69	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0255, RpmC, Ribosomal protein L29 [Translation, ribosomal structure and biogenesis].
CDD:223334	125	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal structure and biogenesis].
CDD:223335	38	EUKprk	Bacteria:45,Plants:2	COG0257, RpmJ, Ribosomal protein L36 [Translation, ribosomal structure and biogenesis].
CDD:223336	310	EUKprk	Bacteria:65,Plants:3,nodiv:1	COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair].
CDD:223337	214	EUKprk	Bacteria:19,Plants:2,nodiv:1	COG0259, PdxH, Pyridoxamine-phosphate oxidase [Coenzyme metabolism].
CDD:223338	485	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and metabolism].
CDD:223339	103	PRK	Bacteria:46,nodiv:1	COG0261, RplU, Ribosomal protein L21 [Translation, ribosomal structure and biogenesis].
CDD:223340	167	EUKprk	Bacteria:38,Plants:3,nodiv:1	COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism].
CDD:223341	369	EUKprk	Bacteria:34,Plants:2,nodiv:2	COG0263, ProB, Glutamate 5-kinase [Amino acid transport and metabolism].
CDD:223342	296	EUKprk	Bacteria:44,Plants:1,nodiv:2	COG0264, Tsf, Translation elongation factor Ts [Translation, ribosomal structure and biogenesis].
CDD:223343	347	EUKprk	Bacteria:52,Plants:2,nodiv:1	COG0265, DegQ, Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones].
CDD:223344	273	PRK	Bacteria:37,nodiv:1	COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair].
CDD:223345	50	EUKprk	Bacteria:46,Plants:2	COG0267, RpmG, Ribosomal protein L33 [Translation, ribosomal structure and biogenesis].
CDD:223346	88	PRK	Bacteria:44,nodiv:2	COG0268, RpsT, Ribosomal protein S20 [Translation, ribosomal structure and biogenesis].
CDD:223347	217	PRK	Bacteria:22,nodiv:1	COG0269, SgbH, 3-hexulose-6-phosphate synthase and related proteins [Carbohydrate transport and metabolism].
CDD:223348	328	EUKprk	Bacteria:35,Plants:1	COG0270, Dcm, Site-specific DNA methylase [DNA replication, recombination, and repair].
CDD:223349	90	EUKprk	Bacteria:23,Plants:2,nodiv:1	COG0271, BolA, Stress-induced morphogen (activity unknown) [Signal transduction mechanisms].
CDD:223350	667	PRK	Bacteria:50,nodiv:1	COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair].
CDD:223351	228	PRK	Bacteria:35,nodiv:1	COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism].
CDD:223352	314	PRK	Bacteria:47,nodiv:1	COG0275, COG0275, Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane].
CDD:223353	320	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0276, HemH, Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism].
CDD:223354	459	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion].
CDD:223355	105	EUKprk	Bacteria:21,Plants:3,nodiv:1	COG0278, COG0278, Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones].
CDD:223356	176	PRK	Bacteria:22	COG0279, GmhA, Phosphoheptose isomerase [Carbohydrate transport and metabolism].
CDD:223357	327	PRK	Bacteria:47,nodiv:1	COG0280, Pta, Phosphotransacetylase [Energy production and conversion].
CDD:223358	432	EUKprk	Bacteria:34,Plants:2	COG0281, SfcA, Malic enzyme [Energy production and conversion].
CDD:223359	396	PRK	Bacteria:43	COG0282, ackA, Acetate kinase [Energy production and conversion].
CDD:223360	222	EUKprk	Bacteria:41,Plants:1,nodiv:1	COG0283, Cmk, Cytidylate kinase [Nucleotide transport and metabolism].
CDD:223361	240	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0284, PyrF, Orotidine-5'-phosphate decarboxylase [Nucleotide transport and metabolism].
CDD:223362	427	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism].
CDD:223363	489	PRK	Bacteria:36	COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms].
CDD:223364	279	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and metabolism].
CDD:223365	207	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0288, CynT, Carbonic anhydrase [Inorganic ion transport and metabolism].
CDD:223366	266	PRK	Bacteria:42,nodiv:1	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism].
CDD:223367	176	PRK	Bacteria:47,nodiv:2	COG0290, InfC, Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis].
CDD:223368	65	EUKprk	Bacteria:42,Plants:1,nodiv:1	COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal structure and biogenesis].
CDD:223369	118	PRK	Bacteria:45,nodiv:1	COG0292, RplT, Ribosomal protein L20 [Translation, ribosomal structure and biogenesis].
CDD:223370	205	EUKprk	Bacteria:28,Plants:3,nodiv:1	COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure and biogenesis].
CDD:223371	274	EUKprk	Bacteria:56,Plants:2,nodiv:1	COG0294, FolP, Dihydropteroate synthase and related enzymes [Coenzyme metabolism].
CDD:223372	134	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0295, Cdd, Cytidine deaminase [Nucleotide transport and metabolism].
CDD:223373	628	EUKprk	Bacteria:26,Plants:1,nodiv:1	COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism].
CDD:223374	487	EUKprk	Bacteria:28,Plants:1,nodiv:1	COG0297, GlgA, Glycogen synthase [Carbohydrate transport and metabolism].
CDD:223375	82	PRK	Bacteria:16	COG0298, HypC, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones].
CDD:223376	200	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0299, PurN, Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism].
CDD:223377	265	EUKprk	Bacteria:23,Plants:3,nodiv:1	COG0300, DltE, Short-chain dehydrogenases of various substrate specificities [General function prediction only].
CDD:223378	383	PRK	Bacteria:34	COG0301, ThiI, Thiamine biosynthesis ATP pyrophosphatase [Coenzyme metabolism].
CDD:223379	195	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG0302, FolE, GTP cyclohydrolase I [Coenzyme metabolism].
CDD:223380	404	PRK	Bacteria:43,nodiv:1	COG0303, MoeA, Molybdopterin biosynthesis enzyme [Coenzyme metabolism].
CDD:223381	412	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0304, FabB, 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223382	435	PRK	Bacteria:48,nodiv:2	COG0305, DnaB, Replicative DNA helicase [DNA replication, recombination, and repair].
CDD:223383	326	EUKprk	Bacteria:46,Plants:1,nodiv:1	COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion transport and metabolism].
CDD:223384	204	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG0307, RibC, Riboflavin synthase alpha chain [Coenzyme metabolism].
CDD:223385	859	EUKprk	Bacteria:32,Plants:3,nodiv:1	COG0308, PepN, Aminopeptidase N [Amino acid transport and metabolism].
CDD:223386	339	PRK	Bacteria:24	COG0309, HypE, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones].
CDD:223387	204	PRK	Bacteria:13	COG0310, CbiM, ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism].
CDD:223388	194	EUKprk	Bacteria:27,Plants:2	COG0311, PDX2, Predicted glutamine amidotransferase involved in pyridoxine biosynthesis [Coenzyme metabolism].
CDD:223389	454	PRK	Bacteria:40,nodiv:1	COG0312, TldD, Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only].
CDD:223390	275	PRK	Bacteria:47,nodiv:1	COG0313, COG0313, Predicted methyltransferases [General function prediction only].
CDD:223391	149	PRK	Bacteria:39,nodiv:2	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism].
CDD:223392	157	PRK	Bacteria:40,nodiv:1	COG0315, MoaC, Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism].
CDD:223393	110	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG0316, sufA, Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones].
CDD:223394	701	PRK	Bacteria:42,nodiv:1	COG0317, SpoT, Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription].
CDD:223395	534	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0318, CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223396	153	PRK	Bacteria:49,nodiv:1	COG0319, COG0319, Predicted metal-dependent hydrolase [General function prediction only].
CDD:223397	306	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
CDD:223398	221	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG0321, LipB, Lipoate-protein ligase B [Coenzyme metabolism].
CDD:223399	581	PRK	Bacteria:52,nodiv:1	COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair].
CDD:223400	638	EUKprk	Bacteria:39,Plants:4,nodiv:1	COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair].
CDD:223401	308	EUKprk	Bacteria:43,Plants:2,nodiv:2	COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis].
CDD:223402	228	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General function prediction only].
CDD:223403	623	EUKprk	Bacteria:30,Plants:3	COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones].
CDD:223404	250	EUKprk	Bacteria:41,Plants:3,nodiv:1	COG0327, COG0327, Uncharacterized conserved protein [Function unknown].
CDD:223405	154	EUKprk	Bacteria:33,Plants:2,nodiv:2	COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair].
CDD:223406	299	PRK	Bacteria:56,nodiv:1	COG0329, DapA, Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane].
CDD:223407	291	EUKprk	Bacteria:54,Plants:3,nodiv:1	COG0330, HflC, Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones].
CDD:223408	310	EUKprk	Bacteria:38,Plants:3,nodiv:1	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism].
CDD:223409	323	PRK	Bacteria:36,nodiv:1	COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
CDD:223410	57	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0333, RpmF, Ribosomal protein L32 [Translation, ribosomal structure and biogenesis].
CDD:223411	411	EUKprk	Bacteria:41,Plants:2	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism].
CDD:223412	115	EUKprk	Bacteria:45,Plants:2,nodiv:2	COG0335, RplS, Ribosomal protein L19 [Translation, ribosomal structure and biogenesis].
CDD:223413	240	PRK	Bacteria:46,nodiv:1	COG0336, TrmD, tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis].
CDD:223414	360	PRK	Bacteria:44,nodiv:1	COG0337, AroB, 3-dehydroquinate synthetase [Amino acid transport and metabolism].
CDD:223415	274	PRK	Bacteria:22,nodiv:1	COG0338, Dam, Site-specific DNA methylase [DNA replication, recombination, and repair].
CDD:223416	683	EUKprk	Bacteria:21,Plants:2,nodiv:1	COG0339, Dcp, Zn-dependent oligopeptidases [Amino acid transport and metabolism].
CDD:223417	238	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0340, BirA, Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism].
CDD:223418	305	PRK	Bacteria:47,nodiv:1	COG0341, SecF, Preprotein translocase subunit SecF [Intracellular trafficking and secretion].
CDD:223419	506	PRK	Bacteria:38	COG0342, SecD, Preprotein translocase subunit SecD [Intracellular trafficking and secretion].
CDD:223420	372	EUKprk	Bacteria:52,Plants:3,nodiv:1	COG0343, Tgt, Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis].
CDD:223421	200	PRK	Bacteria:35,nodiv:1	COG0344, COG0344, Predicted membrane protein [Function unknown].
CDD:223422	266	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism].
CDD:223423	138	EUKprk	Bacteria:47,Plants:2,nodiv:2	COG0346, GloA, Lactoylglutathione lyase and related lyases [Amino acid transport and metabolism].
CDD:223424	112	PRK	Bacteria:30,nodiv:1	COG0347, GlnK, Nitrogen regulatory protein PII [Amino acid transport and metabolism].
CDD:223425	386	PRK	Bacteria:28,nodiv:1	COG0348, NapH, Polyferredoxin [Energy production and conversion].
CDD:223426	361	EUKprk	Bacteria:23,Plants:1,nodiv:1	COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis].
CDD:223427	168	EUKprk	Bacteria:53,Plants:1,nodiv:2	COG0350, Ada, Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair].
CDD:223428	263	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0351, ThiD, Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism].
CDD:223429	211	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme metabolism].
CDD:223430	198	PRK	Bacteria:40,nodiv:2	COG0353, RecR, Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair].
CDD:223431	305	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG0354, COG0354, Predicted aminomethyltransferase related to GcvT [General function prediction only].
CDD:223432	135	EUKprk	Bacteria:42,Plants:2,nodiv:2	COG0355, AtpC, F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion].
CDD:223433	246	EUKprk	Bacteria:43,Plants:1,nodiv:1	COG0356, AtpB, F0F1-type ATP synthase, subunit a [Energy production and conversion].
CDD:223434	215	PRK	Bacteria:43,nodiv:2	COG0357, GidB, Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane].
CDD:223435	568	PRK	Bacteria:60,nodiv:1	COG0358, DnaG, DNA primase (bacterial type) [DNA replication, recombination, and repair].
CDD:223436	148	EUKprk	Bacteria:46,Plants:1,nodiv:1	COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal structure and biogenesis].
CDD:223437	112	EUKprk	Bacteria:48,Plants:2	COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal structure and biogenesis].
CDD:223438	75	EUKprk	Bacteria:55,Plants:3,nodiv:1	COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis].
CDD:223439	473	EUKprk	Bacteria:30,Plants:3,nodiv:1	COG0362, Gnd, 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism].
CDD:223440	238	EUKprk	Bacteria:37,Plants:4,nodiv:1	COG0363, NagB, 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism].
CDD:223441	483	EUKprk	Bacteria:37,Plants:4,nodiv:1	COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism].
CDD:223442	528	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG0365, Acs, Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism].
CDD:223443	505	EUKprk	Bacteria:36,Plants:4,nodiv:2	COG0366, AmyA, Glycosidases [Carbohydrate transport and metabolism].
CDD:223444	542	EUKprk	Bacteria:31,Plants:3	COG0367, AsnB, Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism].
CDD:223445	246	PRK	Bacteria:32,nodiv:1	COG0368, CobS, Cobalamin-5-phosphate synthase [Coenzyme metabolism].
CDD:223446	587	EUKprk	Bacteria:20,Plants:4,nodiv:1	COG0369, CysJ, Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism].
CDD:223447	653	PRK	Bacteria:30	COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism].
CDD:223448	360	EUKprk	Bacteria:31,Plants:1	COG0371, GldA, Glycerol dehydrogenase and related enzymes [Energy production and conversion].
CDD:223449	390	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0372, GltA, Citrate synthase [Energy production and conversion].
CDD:223450	414	PRK	Bacteria:40,nodiv:1	COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
CDD:223451	545	PRK	Bacteria:13	COG0374, HyaB, Ni,Fe-hydrogenase I large subunit [Energy production and conversion].
CDD:223452	115	PRK	Bacteria:17	COG0375, HybF, Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only].
CDD:223453	730	EUKprk	Bacteria:17,Plants:1,nodiv:1	COG0376, KatG, Catalase (peroxidase I) [Inorganic ion transport and metabolism].
CDD:223454	194	PRK	Bacteria:35,nodiv:1	COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion].
CDD:223455	202	EUKprk	Bacteria:30,Plants:1,nodiv:1	COG0378, HypB, Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription].
CDD:223456	324	PRK	Bacteria:37,nodiv:1	COG0379, NadA, Quinolinate synthase [Coenzyme metabolism].
CDD:223457	486	EUKprk	Bacteria:14,Plants:4,nodiv:1	COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism].
CDD:223458	383	PRK	Bacteria:29	COG0381, WecB, UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane].
CDD:223459	289	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0382, UbiA, 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism].
CDD:223460	943	EUKprk	Bacteria:14,Plants:2	COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and metabolism].
CDD:223461	291	EUKprk	Bacteria:23,Plants:2,nodiv:1	COG0384, COG0384, Predicted epimerase, PhzC/PhzF homolog [General function prediction only].
CDD:223462	319	EUKprk	Bacteria:23,Plants:1,nodiv:1	COG0385, COG0385, Predicted Na+-dependent transporter [General function prediction only].
CDD:223463	162	EUKprk	Bacteria:23,Plants:3	COG0386, BtuE, Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones].
CDD:223464	368	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG0387, ChaA, Ca2+/H+ antiporter [Inorganic ion transport and metabolism].
CDD:223465	274	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0388, COG0388, Predicted amidohydrolase [General function prediction only].
CDD:223466	354	EUKprk	Bacteria:40,Plants:3,nodiv:2	COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair].
CDD:223467	256	PRK	Bacteria:15	COG0390, COG0390, ABC-type uncharacterized transport system, permease component [General function prediction only].
CDD:223468	323	EUKprk	Bacteria:31,Plants:1	COG0391, COG0391, Uncharacterized conserved protein [Function unknown].
CDD:223469	322	PRK	Bacteria:34,nodiv:1	COG0392, COG0392, Predicted integral membrane protein [Function unknown].
CDD:223470	108	PRK	Bacteria:24	COG0393, COG0393, Uncharacterized conserved protein [Function unknown].
CDD:223471	139	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0394, Wzb, Protein-tyrosine-phosphatase [Signal transduction mechanisms].
CDD:223472	281	PRK	Bacteria:40,nodiv:1	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism].
CDD:223473	251	PRK	Bacteria:42,nodiv:1	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones].
CDD:223474	488	EUKprk	Bacteria:14,Plants:2,nodiv:1	COG0397, COG0397, Uncharacterized conserved protein [Function unknown].
CDD:223475	223	EUKprk	Bacteria:22,Plants:2	COG0398, COG0398, Uncharacterized conserved protein [Function unknown].
CDD:223476	374	PRK	Bacteria:35	COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane].
CDD:223477	207	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG0400, COG0400, Predicted esterase [General function prediction only].
CDD:223479	421	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0402, SsnA, Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only].
CDD:223480	450	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG0403, GcvP, Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism].
CDD:223481	379	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG0404, GcvT, Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism].
CDD:223482	539	EUKprk	Bacteria:30,Plants:3,nodiv:1	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism].
CDD:223483	208	EUKprk	Bacteria:37,Plants:3,nodiv:1	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only].
CDD:223484	352	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0407, HemE, Uroporphyrinogen-III decarboxylase [Coenzyme metabolism].
CDD:223485	303	EUKprk	Bacteria:17,Plants:2,nodiv:1	COG0408, HemF, Coproporphyrinogen III oxidase [Coenzyme metabolism].
CDD:223486	364	PRK	Bacteria:18	COG0409, HypD, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones].
CDD:223487	237	PRK	Bacteria:23,nodiv:2	COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism].
CDD:223488	250	PRK	Bacteria:19,nodiv:2	COG0411, LivG, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism].
CDD:223489	236	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG0412, COG0412, Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223490	268	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG0413, PanB, Ketopantoate hydroxymethyltransferase [Coenzyme metabolism].
CDD:223491	285	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0414, PanC, Panthothenate synthetase [Coenzyme metabolism].
CDD:223492	461	EUKprk	Bacteria:22,Plants:1,nodiv:1	COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair].
CDD:223493	338	PRK	Bacteria:37,nodiv:2	COG0416, PlsX, Fatty acid/phospholipid biosynthesis enzyme [Lipid metabolism].
CDD:223494	792	EUKprk	Bacteria:22,Plants:3	COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair].
CDD:223495	344	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG0418, PyrC, Dihydroorotase [Nucleotide transport and metabolism].
CDD:223496	908	EUKprk	Bacteria:33,Plants:3	COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair].
CDD:223497	390	EUKprk	Bacteria:37,Plants:3	COG0420, SbcD, DNA repair exonuclease [DNA replication, recombination, and repair].
CDD:223498	282	EUKprk	Bacteria:31,Plants:2	COG0421, SpeE, Spermidine synthase [Amino acid transport and metabolism].
CDD:223499	432	PRK	Bacteria:37,nodiv:1	COG0422, ThiC, Thiamine biosynthesis protein ThiC [Coenzyme metabolism].
CDD:223500	558	EUKprk	Bacteria:25,Plants:3	COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis].
CDD:223501	193	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0424, Maf, Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning].
CDD:223502	78	PRK	Bacteria:37,nodiv:2	COG0425, SirA, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones].
CDD:223503	388	PRK	Bacteria:17	COG0426, FpaA, Uncharacterized flavoproteins [Energy production and conversion].
CDD:223504	501	EUKprk	Bacteria:13,Plants:2,nodiv:1	COG0427, ACH1, Acetyl-CoA hydrolase [Energy production and conversion].
CDD:223505	266	EUKprk	Bacteria:25,Plants:3,nodiv:1	COG0428, COG0428, Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism].
CDD:223506	345	EUKprk	Bacteria:12,Plants:2	COG0429, COG0429, Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only].
CDD:223507	341	EUKprk	Bacteria:19,Plants:3	COG0430, RCL1, RNA 3'-terminal phosphate cyclase [RNA processing and modification].
CDD:223508	184	EUKprk	Bacteria:31,Plants:2,nodiv:1	COG0431, COG0431, Predicted flavoprotein [General function prediction only].
CDD:223509	137	EUKprk	Bacteria:23,Plants:1,nodiv:2	COG0432, COG0432, Uncharacterized conserved protein [Function unknown].
CDD:223510	520	PRK	Bacteria:33,nodiv:1	COG0433, COG0433,  HerA helicase [Replication, recombination, and repair].
CDD:223511	263	PRK	Bacteria:13,nodiv:1	COG0434, SgcQ, Predicted TIM-barrel enzyme [General function prediction only].
CDD:223512	324	EUKprk	Bacteria:13,Plants:2,nodiv:1	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].
CDD:223513	393	EUKprk	Bacteria:60,Plants:2,nodiv:1	COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism].
CDD:223514	203	PRK	Bacteria:22,nodiv:1	COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion].
CDD:223515	381	EUKprk	Bacteria:56,Plants:4,nodiv:1	COG0438, RfaG, Glycosyltransferase [Cell envelope biogenesis, outer membrane].
CDD:223516	449	EUKprk	Bacteria:41,Plants:2,nodiv:1	COG0439, AccC, Biotin carboxylase [Lipid metabolism].
CDD:223517	163	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0440, IlvH, Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism].
CDD:223518	589	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223519	500	EUKprk	Bacteria:62,Plants:3,nodiv:1	COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223520	579	EUKprk	Bacteria:60,Plants:5,nodiv:1	COG0443, DnaK, Molecular chaperone [Posttranslational modification, protein turnover, chaperones].
CDD:223521	316	PRK	Bacteria:48,nodiv:1	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism].
CDD:223522	621	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0445, GidA, Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA    [Cell cycle control, cell division, chromosome partitioning].
CDD:223523	415	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only].
CDD:223525	393	PRK	Bacteria:23,nodiv:1	COG0448, GlgC, ADP-glucose pyrophosphorylase [Carbohydrate transport and metabolism].
CDD:223526	597	EUKprk	Bacteria:53,Plants:3,nodiv:1	COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell envelope biogenesis, outer membrane].
CDD:223527	194	EUKprk	Bacteria:48,Plants:4,nodiv:2	COG0450, AhpC, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones].
CDD:223528	314	EUKprk	Bacteria:54,Plants:2,nodiv:2	COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism].
CDD:223529	392	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0452, Dfp, Phosphopantothenoylcysteine synthetase/decarboxylase [Coenzyme metabolism].
CDD:223530	156	EUKprk	Bacteria:61,Plants:4,nodiv:1	COG0454, WecD, Histone acetyltransferase HPA2 and related acetyltransferases [Transcription / General function prediction only].
CDD:223531	262	PRK	Bacteria:25	COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility].
CDD:223532	177	EUKprk	Bacteria:51,Plants:4,nodiv:1	COG0456, RimI, Acetyltransferases [General function prediction only].
CDD:223533	291	EUKprk	Bacteria:54,Plants:5,nodiv:2	COG0457, NrfG, FOG: TPR repeat [General function prediction only].
CDD:223534	400	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0458, CarB, Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism].
CDD:223535	524	EUKprk	Bacteria:59,Plants:4,nodiv:2	COG0459, GroL, Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].
CDD:223536	333	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and metabolism].
CDD:223537	201	EUKprk	Bacteria:50,Plants:2,nodiv:2	COG0461, PyrE, Orotate phosphoribosyltransferase [Nucleotide transport and metabolism].
CDD:223538	314	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0462, PrsA, Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism].
CDD:223539	291	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0463, WcaA, Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane].
CDD:223540	494	EUKprk	Bacteria:28,Plants:4,nodiv:1	COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones].
CDD:223541	596	EUKprk	Bacteria:47,Plants:2,nodiv:2	COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones].
CDD:223542	782	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].
CDD:223543	260	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms].
CDD:223544	279	EUKprk	Bacteria:58,Plants:3,nodiv:2	COG0468, RecA, RecA/RadA recombinase [DNA replication, recombination, and repair].
CDD:223545	477	EUKprk	Bacteria:53,Plants:4,nodiv:1	COG0469, PykF, Pyruvate kinase [Carbohydrate transport and metabolism].
CDD:223546	230	EUKprk	Bacteria:60,Plants:4,nodiv:1	COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair].
CDD:223547	461	EUKprk	Bacteria:39,Plants:3,nodiv:1	COG0471, CitT, Di- and tricarboxylate transporters [Inorganic ion transport and metabolism].
CDD:223548	319	EUKprk	Bacteria:56,Plants:2,nodiv:1	COG0472, Rfe, UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane].
CDD:223549	348	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism].
CDD:223550	917	EUKprk	Bacteria:33,Plants:4	COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and metabolism].
CDD:223551	397	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0475, KefB, Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism].
CDD:223552	254	EUKprk	Bacteria:48,Plants:4,nodiv:1	COG0476, ThiF, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism].
CDD:223553	338	EUKprk	Bacteria:69,Plants:5,nodiv:2	COG0477, ProP, Permeases of the major facilitator superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / Inorganic ion transport and metabolism / General function prediction only].
CDD:223554	304	EUKprk	Bacteria:10,Plants:3	COG0478, COG0478, RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms].
CDD:223555	234	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion].
CDD:223556	697	EUKprk	Bacteria:59,Plants:4,nodiv:2	COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis].
CDD:223557	603	EUKprk	Bacteria:45,Plants:2,nodiv:2	COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis, outer membrane].
CDD:223558	356	EUKprk	Bacteria:48,Plants:2,nodiv:1	COG0482, TrmU, Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis].
CDD:223559	260	EUKprk	Bacteria:49,Plants:1,nodiv:2	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism].
CDD:223560	371	EUKprk	Bacteria:51,Plants:5,nodiv:2	COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones].
CDD:223561	454	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0486, ThdF, Predicted GTPase [General function prediction only].
CDD:223562	530	EUKprk	Bacteria:46,Plants:4,nodiv:1	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only].
CDD:223563	265	EUKprk	Bacteria:52,Plants:3,nodiv:1	COG0489, Mrp, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning].
CDD:223564	162	PRK	Bacteria:10	COG0490, COG0490, Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism].
CDD:223565	252	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0491, GloB, Zn-dependent hydrolases, including glyoxylases [General function prediction only].
CDD:223566	305	EUKprk	Bacteria:60,Plants:2,nodiv:1	COG0492, TrxB, Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones].
CDD:223567	457	EUKprk	Bacteria:40,Plants:3,nodiv:1	COG0493, GltD, NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only].
CDD:223568	161	EUKprk	Bacteria:55,Plants:3,nodiv:2	COG0494, MutT, NTP pyrophosphohydrolases including oxidative damage repair enzymes [DNA replication, recombination, and repair / General function prediction only].
CDD:223569	814	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223570	252	EUKprk	Bacteria:33,Plants:1,nodiv:2	COG0496, SurE, Predicted acid phosphatase [General function prediction only].
CDD:223571	557	PRK	Bacteria:40,nodiv:1	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair].
CDD:223572	411	EUKprk	Bacteria:50,Plants:2,nodiv:1	COG0498, ThrC, Threonine synthase [Amino acid transport and metabolism].
CDD:223573	420	EUKprk	Bacteria:27,Plants:2,nodiv:1	COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme metabolism].
CDD:223574	257	EUKprk	Bacteria:63,Plants:5,nodiv:1	COG0500, SmtA, SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only].
CDD:223575	302	EUKprk	Bacteria:53,Plants:4,nodiv:1	COG0501, HtpX, Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones].
CDD:223576	335	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG0502, BioB, Biotin synthase and related enzymes [Coenzyme metabolism].
CDD:223577	179	EUKprk	Bacteria:56,Plants:3,nodiv:1	COG0503, Apt, Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism].
CDD:223578	533	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0504, PyrG, CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism].
CDD:223579	368	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0505, CarA, Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism].
CDD:223580	391	EUKprk	Bacteria:25,Plants:2,nodiv:1	COG0506, PutA, Proline dehydrogenase [Amino acid transport and metabolism].
CDD:223581	696	EUKprk	Bacteria:34,Plants:2,nodiv:1	COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair].
CDD:223582	404	EUKprk	Bacteria:48,Plants:2,nodiv:1	COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion].
CDD:223583	131	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG0509, GcvH, Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism].
CDD:223584	269	EUKprk	Bacteria:20,Plants:2	COG0510, ycfN, Thiamine kinase and related kinases [Coenzyme transport and metabolism].
CDD:223585	140	PRK	Bacteria:46,nodiv:1	COG0511, AccB, Biotin carboxyl carrier protein [Lipid metabolism].
CDD:223586	191	PRK	Bacteria:48	COG0512, PabA, Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:223587	513	EUKprk	Bacteria:57,Plants:4,nodiv:2	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].
CDD:223588	590	EUKprk	Bacteria:31,Plants:3,nodiv:1	COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair].
CDD:223589	384	EUKprk	Bacteria:41,Plants:5,nodiv:1	COG0515, SPS1, Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
CDD:223590	170	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0516, GuaB, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism].
CDD:223591	117	EUKprk	Bacteria:56,Plants:3,nodiv:1	COG0517, COG0517, FOG: CBS domain [General function prediction only].
CDD:223592	198	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0518, GuaA, GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism].
CDD:223593	315	PRK	Bacteria:12	COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism].
CDD:223594	405	EUKprk	Bacteria:55,Plants:1,nodiv:1	COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones].
CDD:223595	169	PRK	Bacteria:40,nodiv:1	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism].
CDD:223596	205	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis].
CDD:223597	323	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only].
CDD:223598	311	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0524, RbsK, Sugar kinases, ribokinase family [Carbohydrate transport and metabolism].
CDD:223599	877	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
CDD:223600	127	EUKprk	Bacteria:72,Plants:4,nodiv:2	COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion].
CDD:223601	447	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0527, LysC, Aspartokinases [Amino acid transport and metabolism].
CDD:223602	238	PRK	Bacteria:58,nodiv:2	COG0528, PyrH, Uridylate kinase [Nucleotide transport and metabolism].
CDD:223603	197	EUKprk	Bacteria:23,Plants:2	COG0529, CysC, Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism].
CDD:223604	320	EUKprk	Bacteria:26,Plants:2	COG0530, ECM27, Ca2+/Na+ antiporter [Inorganic ion transport and metabolism].
CDD:223605	466	EUKprk	Bacteria:53,Plants:3,nodiv:2	COG0531, PotE, Amino acid transporters [Amino acid transport and metabolism].
CDD:223606	509	EUKprk	Bacteria:60,Plants:3,nodiv:1	COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis].
CDD:223607	342	EUKprk	Bacteria:61,Plants:4,nodiv:1	COG0533, QRI7, Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones].
CDD:223608	455	EUKprk	Bacteria:53,Plants:2,nodiv:1	COG0534, NorM, Na+-driven multidrug efflux pump [Defense mechanisms].
CDD:223609	347	PRK	Bacteria:28	COG0535, COG0535, Predicted Fe-S oxidoreductases [General function prediction only].
CDD:223610	369	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0536, Obg, Predicted GTPase [General function prediction only].
CDD:223611	138	EUKprk	Bacteria:58,Plants:4,nodiv:1	COG0537, Hit, Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only].
CDD:223612	407	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG0538, Icd, Isocitrate dehydrogenases [Energy production and conversion].
CDD:223613	541	PRK	Bacteria:42,nodiv:1	COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis].
CDD:223614	316	PRK	Bacteria:45,nodiv:2	COG0540, PyrB, Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism].
CDD:223615	451	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0541, Ffh, Signal recognition particle GTPase [Intracellular trafficking and secretion].
CDD:223616	786	EUKprk	Bacteria:49,Plants:3,nodiv:1	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones].
CDD:223617	252	EUKprk	Bacteria:32,Plants:3,nodiv:1	COG0543, UbiB, 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion].
CDD:223618	441	PRK	Bacteria:45,nodiv:2	COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones].
CDD:223619	205	EUKprk	Bacteria:24,Plants:2	COG0545, FkpA, FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones].
CDD:223620	220	EUKprk	Bacteria:44,Plants:1,nodiv:1	COG0546, Gph, Predicted phosphatases [General function prediction only].
CDD:223621	338	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG0547, TrpD, Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism].
CDD:223622	265	PRK	Bacteria:44,nodiv:2	COG0548, ArgB, Acetylglutamate kinase [Amino acid transport and metabolism].
CDD:223623	312	PRK	Bacteria:20	COG0549, ArcC, Carbamate kinase [Amino acid transport and metabolism].
CDD:223624	570	EUKprk	Bacteria:60,Plants:3,nodiv:3	COG0550, TopA, Topoisomerase IA [DNA replication, recombination, and repair].
CDD:223625	140	PRK	Bacteria:12	COG0551, TopA, Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair].
CDD:223626	340	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0552, FtsY, Signal recognition particle GTPase [Intracellular trafficking and secretion].
CDD:223627	866	EUKprk	Bacteria:38,Plants:5	COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
CDD:223628	499	EUKprk	Bacteria:42,Plants:1,nodiv:1	COG0554, GlpK, Glycerol kinase [Energy production and conversion].
CDD:223629	274	PRK	Bacteria:36,nodiv:1	COG0555, CysU, ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones].
CDD:223630	663	PRK	Bacteria:49,nodiv:1	COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair].
CDD:223631	706	EUKprk	Bacteria:45,Plants:4,nodiv:1	COG0557, VacB, Exoribonuclease R [Transcription].
CDD:223632	192	EUKprk	Bacteria:61,Plants:3,nodiv:1	COG0558, PgsA, Phosphatidylglycerophosphate synthase [Lipid metabolism].
CDD:223633	297	PRK	Bacteria:21,nodiv:2	COG0559, LivH, Branched-chain amino acid ABC-type transport system, permease components [Amino acid transport and metabolism].
CDD:223634	212	EUKprk	Bacteria:41,Plants:2,nodiv:1	COG0560, SerB, Phosphoserine phosphatase [Amino acid transport and metabolism].
CDD:223635	264	EUKprk	Bacteria:54,Plants:3,nodiv:1	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only].
CDD:223636	374	PRK	Bacteria:12,nodiv:1	COG0562, Glf, UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane].
CDD:223637	178	EUKprk	Bacteria:52,Plants:3,nodiv:1	COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism].
CDD:223638	289	EUKprk	Bacteria:52,Plants:3,nodiv:1	COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis].
CDD:223639	242	PRK	Bacteria:33,nodiv:2	COG0565, LasT, rRNA methylase [Translation, ribosomal structure and biogenesis].
CDD:223640	260	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0566, SpoU, rRNA methylases [Translation, ribosomal structure and biogenesis].
CDD:223641	906	EUKprk	Bacteria:25,Plants:2,nodiv:1	COG0567, SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes [Energy production and conversion].
CDD:223642	342	PRK	Bacteria:51,nodiv:2	COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription].
CDD:223643	225	PRK	Bacteria:42,nodiv:2	COG0569, TrkA, K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism].
CDD:223644	235	EUKprk	Bacteria:46,Plants:3,nodiv:1	COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
CDD:223645	218	EUKprk	Bacteria:23,Plants:3,nodiv:1	COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
CDD:223646	310	PRK	Bacteria:42,nodiv:1	COG0573, PstC, ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism].
CDD:223647	740	PRK	Bacteria:49,nodiv:1	COG0574, PpsA, Phosphoenolpyruvate synthase/pyruvate phosphate dikinase [Carbohydrate transport and metabolism].
CDD:223648	265	EUKprk	Bacteria:59,Plants:3,nodiv:1	COG0575, CdsA, CDP-diglyceride synthetase [Lipid metabolism].
CDD:223649	193	EUKprk	Bacteria:52,Plants:2,nodiv:1	COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones].
CDD:223650	419	PRK	Bacteria:42,nodiv:1	COG0577, SalY, ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms].
CDD:223651	532	EUKprk	Bacteria:34,Plants:3,nodiv:1	COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion].
CDD:223652	429	PRK	Bacteria:33,nodiv:1	COG0579, COG0579, Predicted dehydrogenase [General function prediction only].
CDD:223653	241	EUKprk	Bacteria:32,Plants:4,nodiv:1	COG0580, GlpF, Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism].
CDD:223654	292	PRK	Bacteria:45,nodiv:1	COG0581, PstA, ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism].
CDD:223655	309	PRK	Bacteria:61,nodiv:1	COG0582, XerC, Integrase [DNA replication, recombination, and repair].
CDD:223656	297	PRK	Bacteria:47,nodiv:4	COG0583, LysR, Transcriptional regulator [Transcription].
CDD:223657	257	EUKprk	Bacteria:43,Plants:3,nodiv:1	COG0584, UgpQ, Glycerophosphoryl diester phosphodiesterase [Energy production and conversion].
CDD:223658	406	EUKprk	Bacteria:27,Plants:3	COG0585, COG0585, Uncharacterized conserved protein [Function unknown].
CDD:223659	208	PRK	Bacteria:39,nodiv:1	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown].
CDD:223660	1139	PRK	Bacteria:50,nodiv:1	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair].
CDD:223661	230	EUKprk	Bacteria:29,Plants:2	COG0588, GpmA, Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism].
CDD:223662	154	EUKprk	Bacteria:52,Plants:2,nodiv:1	COG0589, UspA, Universal stress protein UspA and related nucleotide-binding proteins [Signal transduction mechanisms].
CDD:223663	152	EUKprk	Bacteria:37,Plants:3,nodiv:1	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis].
CDD:223664	493	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0591, PutP, Na+/proline symporter [Amino acid transport and metabolism / General function prediction only].
CDD:223665	364	EUKprk	Bacteria:58,Plants:3,nodiv:1	COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair].
CDD:223666	408	PRK	Bacteria:49,nodiv:1	COG0593, DnaA, ATPase involved in DNA replication initiation [DNA replication, recombination, and repair].
CDD:223667	117	PRK	Bacteria:46,nodiv:1	COG0594, RnpA, RNase P protein component [Translation, ribosomal structure and biogenesis].
CDD:223668	555	PRK	Bacteria:37,nodiv:1	COG0595, COG0595, mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair].
CDD:223669	282	EUKprk	Bacteria:53,Plants:3,nodiv:1	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only].
CDD:223670	167	PRK	Bacteria:48,nodiv:1	COG0597, LspA, Lipoprotein signal peptidase [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].
CDD:223671	322	EUKprk	Bacteria:41,Plants:2,nodiv:2	COG0598, CorA, Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].
CDD:223672	124	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG0599, COG0599, Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown].
CDD:223673	258	PRK	Bacteria:31,nodiv:2	COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism].
CDD:223674	317	PRK	Bacteria:56,nodiv:2	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].
CDD:223675	212	PRK	Bacteria:45,nodiv:1	COG0602, NrdG, Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones].
CDD:223676	222	PRK	Bacteria:42,nodiv:1	COG0603, COG0603, Predicted PP-loop superfamily ATPase [General function prediction only].
CDD:223677	326	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG0604, Qor, NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only].
CDD:223678	204	EUKprk	Bacteria:50,Plants:4,nodiv:2	COG0605, SodA, Superoxide dismutase [Inorganic ion transport and metabolism].
CDD:223679	490	PRK	Bacteria:34,nodiv:1	COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones].
CDD:223680	110	EUKprk	Bacteria:51,Plants:2,nodiv:2	COG0607, PspE, Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism].
CDD:223681	491	PRK	Bacteria:53,nodiv:1	COG0608, RecJ, Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair].
CDD:223682	334	PRK	Bacteria:45,nodiv:1	COG0609, FepD, ABC-type Fe3+-siderophore transport system, permease component [Inorganic ion transport and metabolism].
CDD:223683	962	PRK	Bacteria:27	COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms].
CDD:223684	317	PRK	Bacteria:38	COG0611, ThiL, Thiamine monophosphate kinase [Coenzyme metabolism].
CDD:223685	438	EUKprk	Bacteria:41,Plants:2,nodiv:1	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only].
CDD:223686	258	PRK	Bacteria:26	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only].
CDD:223687	319	PRK	Bacteria:50,nodiv:1	COG0614, FepB, ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:223688	140	EUKprk	Bacteria:18,Plants:5	COG0615, TagD, Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism].
CDD:223689	317	PRK	Bacteria:51,nodiv:1	COG0616, SppA, Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:223690	412	EUKprk	Bacteria:44,Plants:3,nodiv:2	COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis].
CDD:223691	332	PRK	Bacteria:34	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only].
CDD:223692	252	PRK	Bacteria:36,nodiv:1	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism].
CDD:223693	330	EUKprk	Bacteria:42,Plants:2,nodiv:1	COG0620, MetE, Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism].
CDD:223694	437	PRK	Bacteria:51,nodiv:1	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis].
CDD:223695	172	EUKprk	Bacteria:31,Plants:2	COG0622, COG0622, Predicted phosphoesterase [General function prediction only].
CDD:223696	259	PRK	Bacteria:30,nodiv:1	COG0623, FabI, Enoyl-[acyl-carrier-protein].
CDD:223697	409	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0624, ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism].
CDD:223698	211	EUKprk	Bacteria:25,Plants:4,nodiv:1	COG0625, Gst, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].
CDD:223699	396	EUKprk	Bacteria:45,Plants:3,nodiv:1	COG0626, MetC, Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism].
CDD:223700	316	EUKprk	Bacteria:28,Plants:1,nodiv:1	COG0627, COG0627, Predicted esterase [General function prediction only].
CDD:223701	355	PRK	Bacteria:51,nodiv:1	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only].
CDD:223702	167	EUKprk	Bacteria:51,Plants:2,nodiv:2	COG0629, Ssb, Single-stranded DNA-binding protein [DNA replication, recombination, and repair].
CDD:223703	312	PRK	Bacteria:21,nodiv:2	COG0630, VirB11, Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:223704	262	EUKprk	Bacteria:29,Plants:4,nodiv:1	COG0631, PTC1, Serine/threonine protein phosphatase [Signal transduction mechanisms].
CDD:223705	201	PRK	Bacteria:43,nodiv:2	COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair].
CDD:223706	102	EUKprk	Bacteria:29,Plants:3,nodiv:1	COG0633, Fdx, Ferredoxin [Energy production and conversion].
CDD:223707	178	PRK	Bacteria:35,nodiv:1	COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism].
CDD:223708	416	PRK	Bacteria:46,nodiv:2	COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism].
CDD:223709	79	EUKprk	Bacteria:57,Plants:4,nodiv:1	COG0636, AtpE, F0F1-type ATP synthase, subunit c/Archaeal/vacuolar-type H+-ATPase, subunit K [Energy production and conversion].
CDD:223710	221	EUKprk	Bacteria:42,Plants:4,nodiv:1	COG0637, COG0637, Predicted phosphatase/phosphohexomutase [General function prediction only].
CDD:223711	236	EUKprk	Bacteria:17,Plants:5	COG0638, PRE1, 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones].
CDD:223712	155	EUKprk	Bacteria:41,Phages:1,Plants:3,nodiv:2	COG0639, ApaH, Diadenosine tetraphosphatase and related serine/threonine protein phosphatases [Signal transduction mechanisms].
CDD:223713	110	PRK	Bacteria:49,nodiv:1	COG0640, ArsR, Predicted transcriptional regulators [Transcription].
CDD:223714	378	PRK	Bacteria:19	COG0641, AslB, Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only].
CDD:223715	336	EUKprk	Bacteria:57,Plants:3,nodiv:1	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms].
CDD:223716	716	PRK	Bacteria:30,nodiv:1	COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms].
CDD:223717	396	EUKprk	Bacteria:38,Plants:2,nodiv:1	COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production and conversion].
CDD:223718	170	PRK	Bacteria:10	COG0645, COG0645, Predicted kinase [General function prediction only].
CDD:223719	311	PRK	Bacteria:23,nodiv:1	COG0646, MetH, Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism].
CDD:223720	269	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism].
CDD:223721	280	EUKprk	Bacteria:31,Plants:3	COG0648, Nfo, Endonuclease IV [DNA replication, recombination, and repair].
CDD:223722	398	PRK	Bacteria:34,nodiv:2	COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion].
CDD:223723	309	PRK	Bacteria:16	COG0650, HyfC, Formate hydrogenlyase subunit 4 [Energy production and conversion].
CDD:223724	504	PRK	Bacteria:33,nodiv:1	COG0651, HyfB, Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit [Energy production and conversion / Inorganic ion transport and metabolism].
CDD:223725	158	EUKprk	Bacteria:38,Plants:4,nodiv:1	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones].
CDD:223726	822	PRK	Bacteria:48,nodiv:1	COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion].
CDD:223727	387	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion].
CDD:223728	207	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only].
CDD:223729	280	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only].
CDD:223730	312	EUKprk	Bacteria:31,Plants:2,nodiv:1	COG0657, Aes, Esterase/lipase [Lipid metabolism].
CDD:223731	453	PRK	Bacteria:45,nodiv:1	COG0658, ComEC, Predicted membrane metal-binding protein [General function prediction only].
CDD:223732	554	EUKprk	Bacteria:24,Plants:3,nodiv:1	COG0659, SUL1, Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism].
CDD:223733	517	EUKprk	Bacteria:28,Plants:3,nodiv:2	COG0661, AarF, Predicted unusual protein kinase [General function prediction only].
CDD:223734	127	PRK	Bacteria:33,nodiv:1	COG0662, {ManC}, Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism].
CDD:223735	176	PRK	Bacteria:36,nodiv:1	COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only].
CDD:223736	214	EUKprk	Bacteria:39,Plants:3,nodiv:2	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
CDD:223737	387	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism].
CDD:223738	235	EUKprk	Bacteria:29,Plants:4,nodiv:1	COG0666, Arp, FOG: Ankyrin repeat [General function prediction only].
CDD:223739	316	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0667, Tas, Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion].
CDD:223740	316	EUKprk	Bacteria:55,Plants:2,nodiv:1	COG0668, MscS, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].
CDD:223741	159	PRK	Bacteria:38,nodiv:1	COG0669, CoaD, Phosphopantetheine adenylyltransferase [Coenzyme metabolism].
CDD:223742	233	EUKprk	Bacteria:36,Plants:2,nodiv:1	COG0670, COG0670, Integral membrane protein, interacts with FtsH [General function prediction only].
CDD:223743	232	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG0671, PgpB, Membrane-associated phospholipid phosphatase [Lipid metabolism].
CDD:223744	383	EUKprk	Bacteria:22,Plants:2	COG0672, FTR1, High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism].
CDD:223745	342	EUKprk	Bacteria:43,Plants:2,nodiv:1	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only].
CDD:223746	365	EUKprk	Bacteria:31,Plants:1	COG0674, PorA, Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit [Energy production and conversion].
CDD:223747	364	PRK	Bacteria:26	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:223748	287	EUKprk	Bacteria:11,Plants:1	COG0676, COG0676, Uncharacterized enzymes related to aldose 1-epimerase [Carbohydrate transport and metabolism].
CDD:223749	436	PRK	Bacteria:19,nodiv:1	COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane].
CDD:223750	165	EUKprk	Bacteria:12,Plants:2,nodiv:1	COG0678, AHP1, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones].
CDD:223751	311	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0679, COG0679, Predicted permeases [General function prediction only].
CDD:223752	160	PRK	Bacteria:21	COG0680, HyaD, Ni,Fe-hydrogenase maturation factor [Energy production and conversion].
CDD:223753	166	EUKprk	Bacteria:57,Plants:3,nodiv:2	COG0681, LepB, Signal peptidase I [Intracellular trafficking and secretion].
CDD:223754	287	PRK	Bacteria:46,nodiv:2	COG0682, Lgt, Prolipoprotein diacylglyceryltransferase [Cell envelope biogenesis, outer membrane].
CDD:223755	366	PRK	Bacteria:27,nodiv:2	COG0683, LivK, ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
CDD:223756	210	EUKprk	Bacteria:19,Plants:1,nodiv:2	COG0684, MenG, Demethylmenaquinone methyltransferase [Coenzyme metabolism].
CDD:223757	291	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG0685, MetF, 5,10-methylenetetrahydrofolate reductase [Amino acid transport and metabolism].
CDD:223758	371	PRK	Bacteria:17	COG0686, Ald, Alanine dehydrogenase [Amino acid transport and metabolism].
CDD:223759	363	PRK	Bacteria:38,nodiv:2	COG0687, PotD, Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism].
CDD:223760	239	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG0688, Psd, Phosphatidylserine decarboxylase [Lipid metabolism].
CDD:223761	230	EUKprk	Bacteria:35,Plants:4,nodiv:2	COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis].
CDD:223762	73	PRK	Bacteria:46,nodiv:2	COG0690, SecE, Preprotein translocase subunit SecE [Intracellular trafficking and secretion].
CDD:223763	153	PRK	Bacteria:46,nodiv:2	COG0691, SmpB, tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones].
CDD:223764	223	EUKprk	Bacteria:37,Plants:3,nodiv:1	COG0692, Ung, Uracil DNA glycosylase [DNA replication, recombination, and repair].
CDD:223765	188	EUKprk	Bacteria:48,Plants:2,nodiv:1	COG0693, ThiJ, Putative intracellular protease/amidase [General function prediction only].
CDD:223766	93	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG0694, COG0694, Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones].
CDD:223767	80	EUKprk	Bacteria:36,Plants:3,nodiv:2	COG0695, GrxC, Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones].
CDD:223768	509	EUKprk	Bacteria:23,Plants:1,nodiv:1	COG0696, GpmI, Phosphoglyceromutase [Carbohydrate transport and metabolism].
CDD:223769	292	EUKprk	Bacteria:59,Plants:4,nodiv:2	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].
CDD:223770	151	PRK	Bacteria:31	COG0698, RpiB, Ribose 5-phosphate isomerase RpiB [Carbohydrate transport and metabolism].
CDD:223771	546	EUKprk	Bacteria:15,Plants:5	COG0699, COG0699, Predicted GTPases (dynamin-related) [General function prediction only].
CDD:223773	317	PRK	Bacteria:21	COG0701, COG0701, Predicted permeases [General function prediction only].
CDD:223774	275	EUKprk	Bacteria:26,Plants:2,nodiv:1	COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism].
CDD:223775	172	PRK	Bacteria:39,nodiv:1	COG0703, AroK, Shikimate kinase [Amino acid transport and metabolism].
CDD:223776	240	PRK	Bacteria:46,nodiv:1	COG0704, PhoU, Phosphate uptake regulator [Inorganic ion transport and metabolism].
CDD:223777	228	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG0705, COG0705, Membrane associated serine protease [Amino acid transport and metabolism].
CDD:223778	314	EUKprk	Bacteria:49,Plants:2,nodiv:1	COG0706, YidC, Preprotein translocase subunit YidC [Intracellular trafficking and secretion].
CDD:223779	357	PRK	Bacteria:48,nodiv:1	COG0707, MurG, UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane].
CDD:223780	261	EUKprk	Bacteria:41,Plants:3,nodiv:2	COG0708, XthA, Exonuclease III [DNA replication, recombination, and repair].
CDD:223781	346	PRK	Bacteria:13	COG0709, SelD, Selenophosphate synthase [Amino acid transport and metabolism].
CDD:223782	231	PRK	Bacteria:23	COG0710, AroD, 3-dehydroquinate dehydratase [Amino acid transport and metabolism].
CDD:223783	161	PRK	Bacteria:42,nodiv:1	COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production and conversion].
CDD:223784	178	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion].
CDD:223785	100	PRK	Bacteria:28,nodiv:1	COG0713, NuoK, NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Energy production and conversion].
CDD:223786	329	PRK	Bacteria:42,nodiv:1	COG0714, COG0714, MoxR-like ATPases [General function prediction only].
CDD:223787	335	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG0715, TauA, ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism].
CDD:223788	151	PRK	Bacteria:31,nodiv:1	COG0716, FldA, Flavodoxins [Energy production and conversion].
CDD:223789	183	PRK	Bacteria:43,nodiv:2	COG0717, Dcd, Deoxycytidine deaminase [Nucleotide transport and metabolism].
CDD:223790	105	PRK	Bacteria:43,nodiv:1	COG0718, COG0718, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:223791	412	PRK	Bacteria:43,nodiv:1	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones].
CDD:223792	127	PRK	Bacteria:40,nodiv:1	COG0720, COG0720, 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism].
CDD:223793	96	PRK	Bacteria:44,nodiv:1	COG0721, GatC, Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis].
CDD:223794	351	EUKprk	Bacteria:23,Plants:2,nodiv:1	COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism].
CDD:223795	177	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0723, QcrA, Rieske Fe-S protein [Energy production and conversion].
CDD:223796	306	EUKprk	Bacteria:7,Plants:5	COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only].
CDD:223797	258	PRK	Bacteria:41,nodiv:1	COG0725, ModA, ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:223798	267	EUKprk	Bacteria:38,Plants:3,nodiv:1	COG0726, CDA1, Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism].
CDD:223799	132	PRK	Bacteria:24	COG0727, COG0727, Predicted Fe-S-cluster oxidoreductase [General function prediction only].
CDD:223800	518	PRK	Bacteria:34,nodiv:1	COG0728, MviN, Uncharacterized membrane protein, putative virulence factor [General function prediction only].
CDD:223801	594	PRK	Bacteria:18,nodiv:1	COG0729, COG0729, Outer membrane protein [Cell envelope biogenesis, outer membrane].
CDD:223802	258	PRK	Bacteria:47,nodiv:1	COG0730, COG0730, Predicted permeases [General function prediction only].
CDD:223803	296	EUKprk	Bacteria:21,Plants:2	COG0731, COG0731, Fe-S oxidoreductases [Energy production and conversion].
CDD:223804	391	PRK	Bacteria:35	COG0732, HsdS, Restriction endonuclease S subunits [Defense mechanisms].
CDD:223805	439	PRK	Bacteria:25	COG0733, COG0733, Na+-dependent transporters of the SNF family [General function prediction only].
CDD:223806	145	PRK	Bacteria:55,nodiv:1	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism].
CDD:223807	127	EUKprk	Bacteria:42,Plants:1,nodiv:2	COG0736, AcpS, Phosphopantetheinyl transferase (holo-ACP synthase) [Lipid metabolism].
CDD:223808	517	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG0737, UshA, 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism].
CDD:223809	422	EUKprk	Bacteria:14,Plants:1	COG0738, FucP, Fucose permease [Carbohydrate transport and metabolism].
CDD:223810	277	PRK	Bacteria:44,Phages:2,nodiv:1	COG0739, NlpD, Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane].
CDD:223811	200	PRK	Bacteria:46,nodiv:2	COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:223812	296	PRK	Bacteria:38,nodiv:1	COG0741, MltE, Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane].
CDD:223813	187	PRK	Bacteria:45,nodiv:1	COG0742, COG0742, N6-adenine-specific methylase [DNA replication, recombination, and repair].
CDD:223814	385	PRK	Bacteria:35,nodiv:1	COG0743, Dxr, 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Lipid metabolism].
CDD:223815	661	PRK	Bacteria:40,nodiv:1	COG0744, MrcB, Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane].
CDD:223816	229	PRK	Bacteria:50,nodiv:2	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].
CDD:223817	192	PRK	Bacteria:39,nodiv:1	COG0746, MobA, Molybdopterin-guanine dinucleotide biosynthesis protein A [Coenzyme metabolism].
CDD:223818	556	PRK	Bacteria:46,nodiv:1	COG0747, DdpA, ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism].
CDD:223819	245	PRK	Bacteria:11,nodiv:1	COG0748, HugZ, Putative heme iron utilization protein [Inorganic ion transport and metabolism].
CDD:223820	593	EUKprk	Bacteria:3,Plants:1	COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair].
CDD:223821	375	PRK	Bacteria:56,nodiv:1	COG0750, COG0750, Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane].
CDD:223822	691	PRK	Bacteria:36,nodiv:1	COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis].
CDD:223823	298	PRK	Bacteria:35,nodiv:1	COG0752, GlyQ, Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis].
CDD:223824	496	EUKprk	Bacteria:23,Plants:3,nodiv:1	COG0753, KatE, Catalase [Inorganic ion transport and metabolism].
CDD:223825	387	PRK	Bacteria:13,nodiv:1	COG0754, Gsp, Glutathionylspermidine synthase [Amino acid transport and metabolism].
CDD:223826	281	PRK	Bacteria:35,nodiv:1	COG0755, CcmC, ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones].
CDD:223827	148	EUKprk	Bacteria:33,Plants:3,nodiv:2	COG0756, Dut, dUTPase [Nucleotide transport and metabolism].
CDD:223828	146	PRK	Bacteria:26,nodiv:1	COG0757, AroQ, 3-dehydroquinate dehydratase II [Amino acid transport and metabolism].
CDD:223829	350	PRK	Bacteria:41,nodiv:1	COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion].
CDD:223830	92	PRK	Bacteria:36,nodiv:1	COG0759, COG0759, Uncharacterized conserved protein [Function unknown].
CDD:223831	320	EUKprk	Bacteria:40,Plants:3,nodiv:2	COG0760, SurA, Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones].
CDD:223832	294	PRK	Bacteria:31,nodiv:1	COG0761, lytB, 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism].
CDD:223833	96	PRK	Bacteria:34,nodiv:1	COG0762, COG0762, Predicted integral membrane protein [Function unknown].
CDD:223834	381	PRK	Bacteria:27,nodiv:1	COG0763, LpxB, Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane].
CDD:223835	147	PRK	Bacteria:41,nodiv:2	COG0764, FabA, 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Lipid metabolism].
CDD:223836	222	PRK	Bacteria:43,nodiv:1	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism].
CDD:223837	421	PRK	Bacteria:44,nodiv:2	COG0766, MurA, UDP-N-acetylglucosamine enolpyruvyl transferase [Cell envelope biogenesis, outer membrane].
CDD:223838	267	PRK	Bacteria:26,nodiv:1	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223839	599	PRK	Bacteria:45,nodiv:1	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane].
CDD:223840	475	PRK	Bacteria:51,nodiv:1	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane].
CDD:223841	451	PRK	Bacteria:47,nodiv:1	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane].
CDD:223842	448	PRK	Bacteria:47,nodiv:1	COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane].
CDD:223843	381	PRK	Bacteria:42,nodiv:1	COG0772, FtsW, Bacterial cell division membrane protein [Cell division and chromosome partitioning].
CDD:223844	459	PRK	Bacteria:46,nodiv:1	COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane].
CDD:223845	300	PRK	Bacteria:26,nodiv:1	COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane].
CDD:223846	234	PRK	Bacteria:38,nodiv:1	COG0775, Pfs, Nucleoside phosphorylase [Nucleotide transport and metabolism].
CDD:223847	94	PRK	Bacteria:49,nodiv:3	COG0776, HimA, Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair].
CDD:223848	294	PRK	Bacteria:35,nodiv:1	COG0777, AccD, Acetyl-CoA carboxylase beta subunit [Lipid metabolism].
CDD:223849	207	PRK	Bacteria:49,nodiv:1	COG0778, NfnB, Nitroreductase [Energy production and conversion].
CDD:223850	153	PRK	Bacteria:40,nodiv:1	COG0779, COG0779, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:223851	149	PRK	Bacteria:30,nodiv:1	COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General function prediction only].
CDD:223852	151	PRK	Bacteria:47,nodiv:1	COG0781, NusB, Transcription termination factor [Transcription].
CDD:223853	151	PRK	Bacteria:44,nodiv:1	COG0782, COG0782,  Uncharacterized conserved protein, YhbC family [Function unknown].
CDD:223854	156	PRK	Bacteria:32,nodiv:1	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism].
CDD:223855	130	EUKprk	Bacteria:42,Plants:3,nodiv:2	COG0784, CheY, FOG: CheY-like receiver [Signal transduction mechanisms].
CDD:223856	220	PRK	Bacteria:28,nodiv:1	COG0785, CcdA, Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones].
CDD:223857	404	PRK	Bacteria:16	COG0786, GltS, Na+/glutamate symporter [Amino acid transport and metabolism].
CDD:223858	360	EUKprk	Bacteria:43,Plants:1,nodiv:2	COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer membrane].
CDD:223859	287	PRK	Bacteria:25,nodiv:1	COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism].
CDD:223860	124	PRK	Bacteria:51,nodiv:2	COG0789, SoxR, Predicted transcriptional regulators [Transcription].
CDD:223861	292	EUKprk	Bacteria:21,Plants:4,nodiv:1	COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function prediction only].
CDD:223862	197	PRK	Bacteria:37,Phages:1,nodiv:1	COG0791, Spr, Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane].
CDD:223863	114	PRK	Bacteria:32,nodiv:1	COG0792, COG0792, Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair].
CDD:223864	406	PRK	Bacteria:42,nodiv:1	COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer membrane].
CDD:223865	202	PRK	Bacteria:17,nodiv:1	COG0794, GutQ, Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane].
CDD:223866	364	PRK	Bacteria:32,nodiv:1	COG0795, COG0795, Predicted permeases [General function prediction only].
CDD:223867	269	PRK	Bacteria:38,nodiv:1	COG0796, MurI, Glutamate racemase [Cell envelope biogenesis, outer membrane].
CDD:223868	233	PRK	Bacteria:27,nodiv:1	COG0797, RlpA, Lipoproteins [Cell envelope biogenesis, outer membrane].
CDD:223869	342	EUKprk	Bacteria:13,Plants:1,nodiv:1	COG0798, ACR3, Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism].
CDD:223870	115	PRK	Bacteria:42,nodiv:1	COG0799, COG0799, Uncharacterized homolog of plant Iojap protein [Function unknown].
CDD:223871	211	PRK	Bacteria:27,nodiv:1	COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism].
CDD:223872	160	PRK	Bacteria:37,nodiv:1	COG0801, FolK, 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism].
CDD:223873	149	PRK	Bacteria:41,nodiv:1	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only].
CDD:223874	303	PRK	Bacteria:44,nodiv:1	COG0803, LraI, ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism].
CDD:223876	255	PRK	Bacteria:41,nodiv:1	COG0805, TatC, Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion].
CDD:223877	174	PRK	Bacteria:41,nodiv:2	COG0806, RimM, RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis].
CDD:223878	193	EUKprk	Bacteria:16,Plants:2	COG0807, RibA, GTP cyclohydrolase II [Coenzyme metabolism].
CDD:223879	348	PRK	Bacteria:36,nodiv:1	COG0809, QueA, S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis].
CDD:223880	244	PRK	Bacteria:23,nodiv:1	COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane].
CDD:223881	216	PRK	Bacteria:29,nodiv:2	COG0811, TolQ, Biopolymer transport proteins [Intracellular trafficking and secretion].
CDD:223882	291	PRK	Bacteria:43,nodiv:1	COG0812, MurB, UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane].
CDD:223883	236	PRK	Bacteria:24	COG0813, DeoD, Purine-nucleoside phosphorylase [Nucleotide transport and metabolism].
CDD:223884	415	EUKprk	Bacteria:19,Plants:4	COG0814, SdaC, Amino acid permeases [Amino acid transport and metabolism].
CDD:223885	518	PRK	Bacteria:34,nodiv:1	COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope biogenesis, outer membrane].
CDD:223886	141	PRK	Bacteria:45,nodiv:1	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair].
CDD:223887	160	PRK	Bacteria:30,nodiv:2	COG0817, RuvC, Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair].
CDD:223888	123	PRK	Bacteria:30,nodiv:1	COG0818, DgkA, Diacylglycerol kinase [Cell envelope biogenesis, outer membrane].
CDD:223889	218	EUKprk	Bacteria:22,Plants:1	COG0819, TenA, Putative transcription activator [Transcription].
CDD:223890	349	PRK	Bacteria:40,nodiv:1	COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General function prediction only].
CDD:223891	361	PRK	Bacteria:34,nodiv:1	COG0821, gcpE, 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism].
CDD:223892	150	EUKprk	Bacteria:43,Plants:3,nodiv:1	COG0822, IscU, NifU homolog involved in Fe-S cluster formation [Energy production and conversion].
CDD:223893	425	PRK	Bacteria:23,nodiv:1	COG0823, TolB, Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion].
CDD:223894	137	PRK	Bacteria:43,nodiv:1	COG0824, FcbC, Predicted thioesterase [General function prediction only].
CDD:223895	317	PRK	Bacteria:32,nodiv:2	COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid metabolism].
CDD:223896	347	PRK	Bacteria:34,nodiv:1	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones].
CDD:223897	381	PRK	Bacteria:17,nodiv:1	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair].
CDD:223898	67	PRK	Bacteria:37,nodiv:1	COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal structure and biogenesis].
CDD:223899	269	EUKprk	Bacteria:17,Plants:1,nodiv:1	COG0829, UreH, Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones].
CDD:223900	229	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones].
CDD:223901	100	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG0831, UreA, Urea amidohydrolase (urease) gamma subunit [Amino acid transport and metabolism].
CDD:223902	106	PRK	Bacteria:17	COG0832, UreB, Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism].
CDD:223903	541	EUKprk	Bacteria:16,Plants:4	COG0833, LysP, Amino acid transporters [Amino acid transport and metabolism].
CDD:223904	275	PRK	Bacteria:49,nodiv:2	COG0834, HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].
CDD:223905	165	PRK	Bacteria:27,nodiv:1	COG0835, CheW, Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms].
CDD:223906	333	PRK	Bacteria:11	COG0836, {ManC}, Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane].
CDD:223907	320	PRK	Bacteria:16,nodiv:1	COG0837, Glk, Glucokinase [Carbohydrate transport and metabolism].
CDD:223908	123	PRK	Bacteria:32,nodiv:1	COG0838, NuoA, NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Energy production and conversion].
CDD:223909	166	PRK	Bacteria:31,nodiv:1	COG0839, NuoJ, NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion].
CDD:223910	408	PRK	Bacteria:35,nodiv:1	COG0840, Tar, Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms].
CDD:223911	1009	PRK	Bacteria:35,nodiv:1	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].
CDD:223912	286	EUKprk	Bacteria:45,Plants:4,nodiv:1	COG0842, COG0842, ABC-type multidrug transport system, permease component [Defense mechanisms].
CDD:223913	566	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG0843, CyoB, Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion].
CDD:223914	372	PRK	Bacteria:42,nodiv:1	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane].
CDD:223915	250	EUKprk	Bacteria:35,Plants:4,nodiv:1	COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family [Transcription].
CDD:223916	243	EUKprk	Bacteria:45,Plants:3,nodiv:2	COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair].
CDD:223917	137	PRK	Bacteria:28,nodiv:1	COG0848, ExbD, Biopolymer transport protein [Intracellular trafficking and secretion].
CDD:223918	418	PRK	Bacteria:37,nodiv:1	COG0849, ftsA, Cell division ATPase FtsA [Cell division and chromosome partitioning].
CDD:223919	219	PRK	Bacteria:28,nodiv:1	COG0850, MinC, Septum formation inhibitor [Cell division and chromosome partitioning].
CDD:223920	88	PRK	Bacteria:19,nodiv:1	COG0851, MinE, Septum formation topological specificity factor [Cell division and chromosome partitioning].
CDD:223921	176	PRK	Bacteria:27,nodiv:1	COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion].
CDD:223922	126	PRK	Bacteria:25,nodiv:2	COG0853, PanD, Aspartate 1-decarboxylase [Coenzyme metabolism].
CDD:223923	243	PRK	Bacteria:20,nodiv:1	COG0854, PdxJ, Pyridoxal phosphate biosynthesis protein [Coenzyme metabolism].
CDD:223924	696	PRK	Bacteria:25,nodiv:1	COG0855, Ppk, Polyphosphate kinase [Inorganic ion transport and metabolism].
CDD:223926	354	PRK	Bacteria:5	COG0857, Pta, BioD-like N-terminal domain of phosphotransacetylase [General function prediction only].
CDD:223927	118	PRK	Bacteria:46,nodiv:1	COG0858, RbfA, Ribosome-binding factor A [Translation, ribosomal structure and biogenesis].
CDD:223928	334	PRK	Bacteria:23	COG0859, RfaF, ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane].
CDD:223929	231	PRK	Bacteria:41,nodiv:1	COG0860, AmiC, N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane].
CDD:223930	254	PRK	Bacteria:36,nodiv:1	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism].
CDD:223931	302	PRK	Bacteria:29,nodiv:1	COG0863, COG0863, DNA modification methylase [DNA replication, recombination, and repair].
CDD:223932	136	PRK	Bacteria:20,nodiv:1	COG0864, NikR, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription].
CDD:223933	584	PRK	Bacteria:18,nodiv:1	COG1001, AdeC, Adenine deaminase [Nucleotide transport and metabolism].
CDD:223934	786	PRK	Bacteria:20	COG1002, COG1002, Type II restriction enzyme, methylase subunits [Defense mechanisms].
CDD:223935	496	PRK	Bacteria:14	COG1003, GcvP, Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism].
CDD:223936	414	PRK	Bacteria:33,nodiv:1	COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane].
CDD:223937	332	PRK	Bacteria:31,nodiv:1	COG1005, NuoH, NADH:ubiquinone oxidoreductase subunit 1 (chain H) [Energy production and conversion].
CDD:223938	115	PRK	Bacteria:23,nodiv:1	COG1006, MnhC, Multisubunit Na+/H+ antiporter, MnhC subunit [Inorganic ion transport and metabolism].
CDD:223939	475	PRK	Bacteria:33,nodiv:1	COG1007, NuoN, NADH:ubiquinone oxidoreductase subunit 2 (chain N) [Energy production and conversion].
CDD:223940	497	PRK	Bacteria:29,nodiv:1	COG1008, NuoM, NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion].
CDD:223941	606	PRK	Bacteria:41,nodiv:1	COG1009, NuoL, NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit [Energy production and conversion / Inorganic ion transport and metabolism].
CDD:223942	249	PRK	Bacteria:22,nodiv:1	COG1010, CobJ, Precorrin-3B methylase [Coenzyme metabolism].
CDD:223943	229	EUKprk	Bacteria:42,Plants:3,nodiv:1	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only].
CDD:223944	472	EUKprk	Bacteria:53,Plants:2,nodiv:1	COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy production and conversion].
CDD:223945	294	PRK	Bacteria:25	COG1013, PorB, Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion].
CDD:223946	203	PRK	Bacteria:22	COG1014, PorG, Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion].
CDD:223947	397	PRK	Bacteria:21,nodiv:1	COG1015, DeoB, Phosphopentomutase [Carbohydrate transport and metabolism].
CDD:223948	150	EUKprk	Bacteria:16,Plants:2	COG1017, Hmp, Hemoglobin-like flavoprotein [Energy production and conversion].
CDD:223949	266	PRK	Bacteria:22,nodiv:1	COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion].
CDD:223950	158	EUKprk	Bacteria:11,Plants:2	COG1019, COG1019, Predicted nucleotidyltransferase [General function prediction only].
CDD:223951	642	EUKprk	Bacteria:24,Plants:2,nodiv:1	COG1020, EntF, Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:223953	613	EUKprk	Bacteria:17,Plants:3	COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism].
CDD:223955	257	EUKprk	Bacteria:40,Plants:3,nodiv:1	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism].
CDD:223956	937	EUKprk	Bacteria:9,Plants:4	COG1025, Ptr, Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones].
CDD:223957	978	EUKprk	Bacteria:6,Plants:2	COG1026, COG1026, Predicted Zn-dependent peptidases, insulinase-like [General function prediction only].
CDD:223958	471	PRK	Bacteria:23,nodiv:1	COG1027, AspA, Aspartate ammonia-lyase [Amino acid transport and metabolism].
CDD:223959	251	EUKprk	Bacteria:58,Plants:4,nodiv:2	COG1028, FabG, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only].
CDD:223961	436	PRK	Bacteria:16	COG1030, NfeD, Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones].
CDD:223963	490	PRK	Bacteria:30	COG1032, COG1032, Fe-S oxidoreductase [Energy production and conversion].
CDD:223964	727	PRK	Bacteria:13	COG1033, COG1033, Predicted exporters of the RND superfamily [General function prediction only].
CDD:223965	693	PRK	Bacteria:28,nodiv:1	COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion].
CDD:223966	332	PRK	Bacteria:8	COG1035, FrhB, Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion].
CDD:223968	1149	EUKprk	Bacteria:12,Plants:2,nodiv:1	COG1038, PycA, Pyruvate carboxylase [Energy production and conversion].
CDD:223969	297	PRK	Bacteria:13	COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination, and repair].
CDD:223970	225	PRK	Bacteria:39,nodiv:1	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only].
CDD:223971	347	EUKprk	Bacteria:13,Plants:2	COG1041, COG1041, Predicted DNA modification methylase [DNA replication, recombination, and repair].
CDD:223972	598	PRK	Bacteria:15	COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy production and conversion].
CDD:223973	260	PRK	Bacteria:27,nodiv:1	COG1043, LpxA, Acyl-[acyl carrier protein].
CDD:223974	338	PRK	Bacteria:26,nodiv:2	COG1044, LpxD, UDP-3-O-[3-hydroxymyristoyl].
CDD:223975	194	EUKprk	Bacteria:37,Plants:1,nodiv:1	COG1045, CysE, Serine acetyltransferase [Amino acid transport and metabolism].
CDD:223976	174	PRK	Bacteria:30	COG1047, SlpA, FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones].
CDD:223977	861	EUKprk	Bacteria:36,Plants:3,nodiv:1	COG1048, AcnA, Aconitase A [Energy production and conversion].
CDD:223979	145	PRK	Bacteria:34,nodiv:1	COG1051, COG1051, ADP-ribose pyrophosphatase [Nucleotide transport and metabolism].
CDD:223980	324	EUKprk	Bacteria:37,Plants:3,nodiv:1	COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only].
CDD:223981	562	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG1053, SdhA, Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [Energy production and conversion].
CDD:223982	308	PRK	Bacteria:28,nodiv:1	COG1054, COG1054, Predicted sulfurtransferase [General function prediction only].
CDD:223983	424	PRK	Bacteria:32,nodiv:1	COG1055, ArsB, Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism].
CDD:223984	172	PRK	Bacteria:20	COG1056, NadR, Nicotinamide mononucleotide adenylyltransferase [Coenzyme metabolism].
CDD:223985	197	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG1057, NadD, Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism].
CDD:223986	255	EUKprk	Bacteria:37,Plants:1,nodiv:1	COG1058, CinA, Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only].
CDD:223988	370	PRK	Bacteria:33	COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only].
CDD:223989	442	EUKprk	Bacteria:29,Plants:3	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair].
CDD:223990	366	EUKprk	Bacteria:22,Plants:2,nodiv:1	COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion].
CDD:223991	350	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only].
CDD:223992	339	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General function prediction only].
CDD:223993	456	PRK	Bacteria:40,nodiv:1	COG1066, Sms, Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones].
CDD:223994	647	PRK	Bacteria:24	COG1067, LonB, Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones].
CDD:223995	544	EUKprk	Bacteria:10,Plants:1,nodiv:1	COG1069, AraB, Ribulose kinase [Energy production and conversion].
CDD:223996	502	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism].
CDD:223997	358	EUKprk	Bacteria:31,Plants:3,nodiv:1	COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion].
CDD:223998	283	EUKprk	Bacteria:22,Plants:2,nodiv:1	COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
CDD:223999	299	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG1073, COG1073, Hydrolases of the alpha/beta superfamily [General function prediction only].
CDD:224000	1139	PRK	Bacteria:37,nodiv:1	COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair].
CDD:224001	336	EUKprk	Bacteria:15,Plants:1	COG1075, LipA, Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only].
CDD:224002	174	EUKprk	Bacteria:22,Plants:3,nodiv:1	COG1076, DjlA, DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones].
CDD:224003	342	PRK	Bacteria:35	COG1077, MreB, Actin-like ATPase involved in cell morphogenesis [Cell division and chromosome partitioning].
CDD:224004	421	EUKprk	Bacteria:26,Plants:1	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only].
CDD:224005	304	PRK	Bacteria:26,nodiv:1	COG1079, COG1079, Uncharacterized ABC-type transport system, permease component [General function prediction only].
CDD:224006	574	PRK	Bacteria:33,nodiv:1	COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism].
CDD:224007	274	PRK	Bacteria:33,nodiv:1	COG1082, IolE, Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism].
CDD:224008	228	PRK	Bacteria:8	COG1083, NeuA, CMP-N-acetylneuraminic acid synthetase [Cell envelope biogenesis, outer membrane].
CDD:224009	346	EUKprk	Bacteria:13,Plants:3	COG1084, COG1084, Predicted GTPase [General function prediction only].
CDD:224010	338	EUKprk	Bacteria:15,Plants:2	COG1085, GalT, Galactose-1-phosphate uridylyltransferase [Energy production and conversion].
CDD:224011	588	PRK	Bacteria:27	COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism].
CDD:224012	329	EUKprk	Bacteria:31,Plants:2,nodiv:1	COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane].
CDD:224013	340	EUKprk	Bacteria:36,Plants:1,nodiv:1	COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane].
CDD:224014	345	PRK	Bacteria:21,nodiv:1	COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane].
CDD:224015	297	PRK	Bacteria:21	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only].
CDD:224016	281	PRK	Bacteria:35,nodiv:1	COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane].
CDD:224017	393	PRK	Bacteria:32,nodiv:1	COG1092, COG1092, Predicted SAM-dependent methyltransferases [General function prediction only].
CDD:224018	269	EUKprk	Bacteria:13,Plants:3	COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis].
CDD:224019	194	EUKprk	Bacteria:13,Plants:4	COG1094, COG1094, Predicted RNA-binding protein (contains KH domains) [General function prediction only].
CDD:224020	183	EUKprk	Bacteria:13,Plants:3	COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription].
CDD:224021	188	EUKprk	Bacteria:11,Plants:2	COG1096, COG1096, Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis].
CDD:224022	239	EUKprk	Bacteria:11,Plants:3	COG1097, RRP4, RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis].
CDD:224023	129	PRK	Bacteria:10	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis].
CDD:224025	219	EUKprk	Bacteria:18,Plants:5	COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only].
CDD:224026	263	PRK	Bacteria:12,nodiv:1	COG1101, PhnK, ABC-type uncharacterized transport system, ATPase component [General function prediction only].
CDD:224027	179	PRK	Bacteria:15	COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism].
CDD:224029	386	EUKprk	Bacteria:45,Plants:3,nodiv:1	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism].
CDD:224030	310	PRK	Bacteria:28	COG1105, FruK, Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism].
CDD:224031	371	PRK	Bacteria:8	COG1106, COG1106, Predicted ATPases [General function prediction only].
CDD:224033	274	PRK	Bacteria:47,nodiv:1	COG1108, ZnuB, ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism].
CDD:224034	464	EUKprk	Bacteria:64,Plants:4,nodiv:1	COG1109, {ManB}, Phosphomannomutase [Carbohydrate transport and metabolism].
CDD:224035	1187	PRK	Bacteria:10	COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair].
CDD:224036	542	EUKprk	Bacteria:10,Plants:2	COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair].
CDD:224037	767	EUKprk	Bacteria:30,Plants:3	COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair].
CDD:224038	462	PRK	Bacteria:23,nodiv:2	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism].
CDD:224039	431	PRK	Bacteria:16,nodiv:1	COG1114, BrnQ, Branched-chain amino acid permeases [Amino acid transport and metabolism].
CDD:224040	452	PRK	Bacteria:29	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism].
CDD:224041	248	PRK	Bacteria:34,nodiv:1	COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:224042	253	PRK	Bacteria:45,nodiv:2	COG1117, PstB, ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:224043	345	PRK	Bacteria:25,nodiv:1	COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism].
CDD:224044	257	EUKprk	Bacteria:17,Plants:2	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism].
CDD:224045	258	PRK	Bacteria:43,nodiv:1	COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism].
CDD:224046	254	PRK	Bacteria:48,nodiv:1	COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism].
CDD:224047	235	PRK	Bacteria:41,nodiv:1	COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:224048	539	PRK	Bacteria:26,nodiv:1	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].
CDD:224049	252	PRK	Bacteria:19,nodiv:1	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism].
CDD:224050	309	PRK	Bacteria:24,nodiv:1	COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism].
CDD:224051	240	PRK	Bacteria:43,nodiv:1	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism].
CDD:224052	263	PRK	Bacteria:26,nodiv:1	COG1127, Ttg2A, ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224053	500	PRK	Bacteria:24,nodiv:1	COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism].
CDD:224054	293	EUKprk	Bacteria:54,Plants:2,nodiv:1	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms].
CDD:224055	567	EUKprk	Bacteria:57,Plants:4,nodiv:1	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
CDD:224057	249	PRK	Bacteria:30	COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane].
CDD:224058	339	PRK	Bacteria:35,nodiv:1	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:224059	226	PRK	Bacteria:59,nodiv:1	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms].
CDD:224060	243	PRK	Bacteria:29,nodiv:1	COG1137, YhbG, ABC-type (unclassified) transport system, ATPase component [General function prediction only].
CDD:224061	648	PRK	Bacteria:22,nodiv:1	COG1138, CcmF, Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones].
CDD:224062	459	PRK	Bacteria:21	COG1139, COG1139, Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion].
CDD:224064	68	PRK	Bacteria:19	COG1141, Fer, Ferredoxin [Energy production and conversion].
CDD:224065	165	PRK	Bacteria:17	COG1142, HycB, Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion].
CDD:224066	172	PRK	Bacteria:38,nodiv:1	COG1143, NuoI, Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion].
CDD:224067	91	PRK	Bacteria:15	COG1144, COG1144, Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion].
CDD:224068	99	PRK	Bacteria:39,nodiv:1	COG1145, NapF, Ferredoxin [Energy production and conversion].
CDD:224069	68	PRK	Bacteria:35,nodiv:1	COG1146, COG1146, Ferredoxin [Energy production and conversion].
CDD:224070	622	PRK	Bacteria:8	COG1148, HdrA, Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion].
CDD:224071	284	PRK	Bacteria:8	COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion].
CDD:224072	195	PRK	Bacteria:7	COG1150, HdrC, Heterodisulfide reductase, subunit C [Energy production and conversion].
CDD:224073	576	PRK	Bacteria:14	COG1151, COG1151, 6Fe-6S prismane cluster-containing protein [Energy production and conversion].
CDD:224076	627	PRK	Bacteria:38,nodiv:1	COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme metabolism / Lipid metabolism].
CDD:224077	588	EUKprk	Bacteria:21,Plants:3	COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion].
CDD:224078	463	EUKprk	Bacteria:21,Plants:3	COG1156, NtpB, Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion].
CDD:224079	441	PRK	Bacteria:26,nodiv:2	COG1157, FliI, Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224080	422	PRK	Bacteria:37,nodiv:2	COG1158, Rho, Transcription termination factor [Transcription].
CDD:224081	298	PRK	Bacteria:45,nodiv:1	COG1159, Era, GTPase [General function prediction only].
CDD:224082	444	PRK	Bacteria:47,nodiv:1	COG1160, COG1160, Predicted GTPases [General function prediction only].
CDD:224083	322	EUKprk	Bacteria:28,Plants:3	COG1161, COG1161, Predicted GTPases [General function prediction only].
CDD:224084	301	PRK	Bacteria:37	COG1162, COG1162, Predicted GTPases [General function prediction only].
CDD:224085	365	EUKprk	Bacteria:13,Plants:4	COG1163, DRG, Predicted GTPase [General function prediction only].
CDD:224086	598	PRK	Bacteria:29,nodiv:1	COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and metabolism].
CDD:224087	566	PRK	Bacteria:19	COG1165, MenD, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [Coenzyme metabolism].
CDD:224088	652	PRK	Bacteria:17	COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism].
CDD:224089	459	EUKprk	Bacteria:35,Plants:2,nodiv:1	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism].
CDD:224090	388	PRK	Bacteria:19	COG1168, MalY, Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism].
CDD:224091	423	PRK	Bacteria:22	COG1169, MenF, Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224092	347	EUKprk	Bacteria:40,Plants:3,nodiv:1	COG1171, IlvA, Threonine dehydratase [Amino acid transport and metabolism].
CDD:224093	316	PRK	Bacteria:23,nodiv:2	COG1172, AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism].
CDD:224094	289	PRK	Bacteria:53,nodiv:1	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].
CDD:224095	221	PRK	Bacteria:26,nodiv:1	COG1174, OpuBB, ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism].
CDD:224096	295	PRK	Bacteria:43,nodiv:1	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism].
CDD:224097	287	PRK	Bacteria:37,nodiv:2	COG1176, PotB, ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism].
CDD:224098	267	PRK	Bacteria:37,nodiv:1	COG1177, PotC, ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism].
CDD:224099	540	PRK	Bacteria:29,nodiv:1	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism].
CDD:224100	263	EUKprk	Bacteria:20,Plants:2	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism].
CDD:224101	260	PRK	Bacteria:35	COG1180, PflA, Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones].
CDD:224102	317	PRK	Bacteria:42,nodiv:2	COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane].
CDD:224103	202	PRK	Bacteria:18,nodiv:2	COG1182, AcpD, Acyl carrier protein phosphodiesterase [Lipid metabolism].
CDD:224104	234	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG1183, PssA, Phosphatidylserine synthase [Lipid metabolism].
CDD:224105	301	EUKprk	Bacteria:11,Plants:2	COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis].
CDD:224106	692	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis].
CDD:224107	239	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG1186, PrfB, Protein chain release factor B [Translation, ribosomal structure and biogenesis].
CDD:224108	248	PRK	Bacteria:49,nodiv:1	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis].
CDD:224109	100	PRK	Bacteria:27,nodiv:1	COG1188, COG1188, Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis].
CDD:224110	245	PRK	Bacteria:30,nodiv:1	COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis].
CDD:224111	502	EUKprk	Bacteria:44,Plants:3,nodiv:1	COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis].
CDD:224112	247	PRK	Bacteria:22,nodiv:1	COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription].
CDD:224113	259	PRK	Bacteria:48,nodiv:1	COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning].
CDD:224114	753	PRK	Bacteria:23	COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].
CDD:224115	342	EUKprk	Bacteria:41,Plants:1,nodiv:1	COG1194, MutY, A/G-specific DNA glycosylase [DNA replication, recombination, and repair].
CDD:224116	363	PRK	Bacteria:33,nodiv:1	COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair].
CDD:224117	1163	EUKprk	Bacteria:40,Plants:3,nodiv:1	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning].
CDD:224118	1139	PRK	Bacteria:43,nodiv:1	COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription].
CDD:224119	730	PRK	Bacteria:45,nodiv:1	COG1198, PriA, Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair].
CDD:224120	654	EUKprk	Bacteria:36,Plants:3	COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair].
CDD:224121	677	PRK	Bacteria:41,nodiv:1	COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription].
CDD:224122	814	PRK	Bacteria:25,nodiv:1	COG1201, Lhr, Lhr-like helicases [General function prediction only].
CDD:224124	733	PRK	Bacteria:20	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms].
CDD:224125	766	EUKprk	Bacteria:16,Plants:3,nodiv:1	COG1204, COG1204, Superfamily II helicase [General function prediction only].
CDD:224126	851	EUKprk	Bacteria:19,Plants:2	COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only].
CDD:224127	439	PRK	Bacteria:17,nodiv:1	COG1206, Gid, NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis].
CDD:224128	460	PRK	Bacteria:39,nodiv:1	COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane].
CDD:224129	358	EUKprk	Bacteria:35,Plants:3,nodiv:1	COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure and biogenesis].
CDD:224130	286	PRK	Bacteria:37,Synthetic:1,nodiv:1	COG1209, RfbA, dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane].
CDD:224131	291	PRK	Bacteria:41,nodiv:2	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane].
CDD:224132	230	PRK	Bacteria:33	COG1211, IspD, 4-diphosphocytidyl-2-methyl-D-erithritol synthase [Lipid metabolism].
CDD:224133	247	PRK	Bacteria:25,nodiv:1	COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane].
CDD:224134	239	PRK	Bacteria:6	COG1213, COG1213, Predicted sugar nucleotidyltransferases [Cell envelope biogenesis, outer membrane].
CDD:224135	220	PRK	Bacteria:48,nodiv:1	COG1214, COG1214, Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones].
CDD:224136	439	EUKprk	Bacteria:34,Plants:3,nodiv:1	COG1215, COG1215, Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane].
CDD:224137	305	PRK	Bacteria:25,nodiv:1	COG1216, COG1216, Predicted glycosyltransferases [General function prediction only].
CDD:224138	603	PRK	Bacteria:38,nodiv:1	COG1217, TypA, Predicted membrane GTPase involved in stress response [Signal transduction mechanisms].
CDD:224139	276	EUKprk	Bacteria:27,Plants:2,nodiv:1	COG1218, CysQ, 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase [Inorganic ion transport and metabolism].
CDD:224140	408	EUKprk	Bacteria:43,Plants:1,nodiv:1	COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones].
CDD:224141	444	PRK	Bacteria:26,nodiv:2	COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones].
CDD:224142	403	PRK	Bacteria:14	COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms].
CDD:224143	406	EUKprk	Bacteria:10,Plants:4	COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones].
CDD:224145	450	EUKprk	Bacteria:7,Plants:3	COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription].
CDD:224146	157	EUKprk	Bacteria:40,Plants:2,nodiv:1	COG1225, Bcp, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones].
CDD:224147	212	EUKprk	Bacteria:43,Plants:1	COG1226, Kch, Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism].
CDD:224148	311	EUKprk	Bacteria:13,Plants:3	COG1227, PPX1, Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion].
CDD:224149	406	EUKprk	Bacteria:27,Plants:1,nodiv:1	COG1228, HutI, Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224151	296	EUKprk	Bacteria:33,Plants:4,nodiv:1	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].
CDD:224152	450	PRK	Bacteria:11	COG1231, COG1231, Monoamine oxidase [Amino acid transport and metabolism].
CDD:224153	444	EUKprk	Bacteria:20,Plants:2	COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
CDD:224154	487	PRK	Bacteria:19	COG1233, COG1233, Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224155	292	EUKprk	Bacteria:43,Plants:3	COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only].
CDD:224156	269	EUKprk	Bacteria:39,Plants:1,nodiv:1	COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only].
CDD:224157	427	EUKprk	Bacteria:19,Plants:4,nodiv:1	COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis].
CDD:224158	259	PRK	Bacteria:10	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only].
CDD:224159	161	PRK	Bacteria:24,nodiv:1	COG1238, COG1238, Predicted membrane protein [Function unknown].
CDD:224160	423	PRK	Bacteria:17	COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
CDD:224161	261	PRK	Bacteria:4	COG1240, ChlD, Mg-chelatase subunit ChlD [Coenzyme metabolism].
CDD:224162	682	EUKprk	Bacteria:13,Plants:5	COG1241, MCM2, Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair].
CDD:224163	312	PRK	Bacteria:16	COG1242, COG1242, Predicted Fe-S oxidoreductase [General function prediction only].
CDD:224164	515	EUKprk	Bacteria:15,Plants:3	COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin structure and dynamics].
CDD:224165	358	PRK	Bacteria:11	COG1244, COG1244, Predicted Fe-S oxidoreductase [General function prediction only].
CDD:224166	591	EUKprk	Bacteria:13,Plants:3	COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only].
CDD:224167	153	PRK	Bacteria:10	COG1246, ArgA, N-acetylglutamate synthase and related acetyltransferases [Amino acid transport and metabolism].
CDD:224168	169	PRK	Bacteria:25,nodiv:1	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane].
CDD:224169	454	EUKprk	Bacteria:57,Plants:2,nodiv:2	COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion].
CDD:224170	307	PRK	Bacteria:22,nodiv:1	COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism].
CDD:224171	793	PRK	Bacteria:18,nodiv:1	COG1251, NirB, NAD(P)H-nitrite reductase [Energy production and conversion].
CDD:224172	405	EUKprk	Bacteria:26,Plants:2,nodiv:1	COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy production and conversion].
CDD:224173	429	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only].
CDD:224174	92	PRK	Bacteria:31	COG1254, AcyP, Acylphosphatases [Energy production and conversion].
CDD:224176	552	PRK	Bacteria:23,nodiv:2	COG1256, FlgK, Flagellar hook-associated protein [Cell motility and secretion].
CDD:224177	436	EUKprk	Bacteria:20,Plants:3	COG1257, HMG1, Hydroxymethylglutaryl-CoA reductase [Lipid metabolism].
CDD:224178	398	EUKprk	Bacteria:13,Plants:1	COG1258, COG1258, Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis].
CDD:224179	151	PRK	Bacteria:15	COG1259, COG1259, Uncharacterized conserved protein [Function unknown].
CDD:224180	362	EUKprk	Bacteria:14,Plants:1	COG1260, INO1, Myo-inositol-1-phosphate synthase [Lipid metabolism].
CDD:224181	220	PRK	Bacteria:18,nodiv:1	COG1261, FlgA, Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones].
CDD:224182	314	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG1262, COG1262, Uncharacterized conserved protein [Function unknown].
CDD:224183	393	PRK	Bacteria:31	COG1263, PtsG, Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism].
CDD:224184	88	PRK	Bacteria:14	COG1264, PtsG, Phosphotransferase system IIB components [Carbohydrate transport and metabolism].
CDD:224185	226	PRK	Bacteria:37	COG1266, COG1266, Predicted metal-dependent membrane protease [General function prediction only].
CDD:224186	160	PRK	Bacteria:30	COG1267, PgpA, Phosphatidylglycerophosphatase A and related proteins [Lipid metabolism].
CDD:224187	184	PRK	Bacteria:27,nodiv:1	COG1268, BioY, Uncharacterized conserved protein [General function prediction only].
CDD:224188	660	EUKprk	Bacteria:21,Plants:3	COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion].
CDD:224189	320	PRK	Bacteria:29,nodiv:1	COG1270, CbiB, Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism].
CDD:224190	457	PRK	Bacteria:35,nodiv:1	COG1271, CydA, Cytochrome bd-type quinol oxidase, subunit 1 [Energy production and conversion].
CDD:224191	226	EUKprk	Bacteria:26,Plants:4,nodiv:1	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only].
CDD:224192	278	PRK	Bacteria:8,nodiv:1	COG1273, COG1273, Ku-homolog [Replication, recombination, and repair].
CDD:224194	329	EUKprk	Bacteria:20,Plants:2	COG1275, TehA, Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism].
CDD:224195	289	PRK	Bacteria:13	COG1276, PcoD, Putative copper export protein [Inorganic ion transport and metabolism].
CDD:224196	278	PRK	Bacteria:28	COG1277, NosY, ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only].
CDD:224197	67	PRK	Bacteria:42,nodiv:2	COG1278, CspC, Cold shock proteins [Transcription].
CDD:224198	202	PRK	Bacteria:19,nodiv:1	COG1279, COG1279, Lysine efflux permease [General function prediction only].
CDD:224199	208	PRK	Bacteria:33,nodiv:1	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism].
CDD:224200	286	PRK	Bacteria:32,nodiv:1	COG1281, COG1281, Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones].
CDD:224201	463	PRK	Bacteria:21,nodiv:1	COG1282, PntB, NAD/NADP transhydrogenase beta subunit [Energy production and conversion].
CDD:224202	533	PRK	Bacteria:20,nodiv:2	COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and metabolism].
CDD:224203	289	PRK	Bacteria:22,nodiv:1	COG1284, COG1284, Uncharacterized conserved protein [Function unknown].
CDD:224204	221	PRK	Bacteria:23,nodiv:1	COG1285, SapB, Uncharacterized membrane protein [Function unknown].
CDD:224205	182	PRK	Bacteria:31,nodiv:1	COG1286, CvpA, Uncharacterized membrane protein, required for colicin V production [General function prediction only].
CDD:224206	773	EUKprk	Bacteria:12,Plants:2	COG1287, COG1287, Uncharacterized membrane protein, required for N-linked glycosylation [General function prediction only].
CDD:224207	481	PRK	Bacteria:13	COG1288, COG1288, Predicted membrane protein [Function unknown].
CDD:224208	674	PRK	Bacteria:23,nodiv:1	COG1289, COG1289, Predicted membrane protein [Function unknown].
CDD:224209	381	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG1290, QcrB, Cytochrome b subunit of the bc complex [Energy production and conversion].
CDD:224210	266	PRK	Bacteria:22,nodiv:1	COG1291, MotA, Flagellar motor component [Cell motility and secretion].
CDD:224211	537	PRK	Bacteria:21	COG1292, BetT, Choline-glycine betaine transporter [Cell envelope biogenesis, outer membrane].
CDD:224212	564	EUKprk	Bacteria:30,Plants:3	COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].
CDD:224213	346	PRK	Bacteria:33,nodiv:1	COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy production and conversion].
CDD:224214	303	PRK	Bacteria:44,nodiv:1	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair].
CDD:224215	238	PRK	Bacteria:28,nodiv:1	COG1296, AzlC, Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism].
CDD:224216	624	EUKprk	Bacteria:12,Plants:1	COG1297, COG1297, Predicted membrane protein [Function unknown].
CDD:224217	696	PRK	Bacteria:26,nodiv:1	COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224218	343	PRK	Bacteria:27	COG1299, FruA, Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism].
CDD:224219	207	PRK	Bacteria:19	COG1300, SpoIIM, Uncharacterized membrane protein [Function unknown].
CDD:224220	415	PRK	Bacteria:38,nodiv:1	COG1301, GltP, Na+/H+-dicarboxylate symporters [Energy production and conversion].
CDD:224221	131	PRK	Bacteria:14	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224222	179	PRK	Bacteria:12	COG1303, COG1303, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224223	360	EUKprk	Bacteria:46,Plants:2,nodiv:1	COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism].
CDD:224224	319	PRK	Bacteria:29,nodiv:1	COG1305, COG1305, Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism].
CDD:224226	282	PRK	Bacteria:19	COG1307, DegV, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224227	122	EUKprk	Bacteria:12,Plants:3	COG1308, EGD2, Transcription factor homologous to NACalpha-BTF3 [Transcription].
CDD:224228	201	PRK	Bacteria:48,nodiv:1	COG1309, AcrR, Transcriptional regulator [Transcription].
CDD:224229	134	EUKprk	Bacteria:21,Plants:4	COG1310, COG1310, Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only].
CDD:224230	481	EUKprk	Bacteria:10,Plants:3	COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [DNA replication, recombination, and repair].
CDD:224231	362	PRK	Bacteria:15,nodiv:2	COG1312, UxuA, D-mannonate dehydratase [Carbohydrate transport and metabolism].
CDD:224232	335	PRK	Bacteria:12	COG1313, PflX, Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only].
CDD:224233	86	PRK	Bacteria:45,nodiv:1	COG1314, SecG, Preprotein translocase subunit SecG [Intracellular trafficking and secretion].
CDD:224235	307	PRK	Bacteria:18	COG1316, LytR, Transcriptional regulator [Transcription].
CDD:224236	234	PRK	Bacteria:22	COG1317, FliH, Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224238	284	PRK	Bacteria:18,nodiv:1	COG1319, CoxM, Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion].
CDD:224239	113	PRK	Bacteria:19,nodiv:1	COG1320, MnhG, Multisubunit Na+/H+ antiporter, MnhG subunit [Inorganic ion transport and metabolism].
CDD:224240	154	PRK	Bacteria:33,nodiv:1	COG1321, TroR, Mn-dependent transcriptional regulator [Transcription].
CDD:224241	448	PRK	Bacteria:22,nodiv:2	COG1322, COG1322, Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].
CDD:224242	358	PRK	Bacteria:14	COG1323, COG1323, Predicted nucleotidyltransferase [General function prediction only].
CDD:224243	104	EUKprk	Bacteria:22,Plants:1	COG1324, CutA, Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism].
CDD:224244	149	PRK	Bacteria:11	COG1325, COG1325, Predicted exosome subunit [Translation, ribosomal structure and biogenesis].
CDD:224245	201	PRK	Bacteria:8	COG1326, COG1326, Uncharacterized archaeal Zn-finger protein [General function prediction only].
CDD:224246	156	PRK	Bacteria:32,nodiv:1	COG1327, COG1327, Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription].
CDD:224247	700	PRK	Bacteria:24	COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism].
CDD:224248	166	PRK	Bacteria:15,nodiv:1	COG1329, COG1329, Transcriptional regulators, similar to M. xanthus CarD [Transcription].
CDD:224249	1078	PRK	Bacteria:18	COG1330, RecC, Exonuclease V gamma subunit [DNA replication, recombination, and repair].
CDD:224250	667	PRK	Bacteria:20	COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones].
CDD:224251	369	PRK	Bacteria:8	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms].
CDD:224252	478	PRK	Bacteria:12	COG1333, ResB, ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones].
CDD:224253	120	PRK	Bacteria:9	COG1334, FlaG, Uncharacterized flagellar protein FlaG [Cell motility and secretion].
CDD:224254	205	EUKprk	Bacteria:47,Plants:2,nodiv:1	COG1335, PncA, Amidases related to nicotinamidase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224255	298	PRK	Bacteria:7	COG1336, COG1336, CRISPR system related protein, RAMP superfamily [Defense mechanisms].
CDD:224256	249	PRK	Bacteria:12	COG1337, COG1337, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:224257	248	PRK	Bacteria:24,nodiv:1	COG1338, FliP, Flagellar biosynthesis pathway, component FliP [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224258	214	PRK	Bacteria:13	COG1339, COG1339, Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism].
CDD:224259	294	PRK	Bacteria:11	COG1340, COG1340, Uncharacterized archaeal coiled-coil protein [Function unknown].
CDD:224260	398	EUKprk	Bacteria:8,Plants:2	COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only].
CDD:224261	99	PRK	Bacteria:8	COG1342, COG1342, Predicted DNA-binding proteins [General function prediction only].
CDD:224262	89	PRK	Bacteria:15	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms].
CDD:224263	360	PRK	Bacteria:25,nodiv:1	COG1344, FlgL, Flagellin and related hook-associated proteins [Cell motility and secretion].
CDD:224264	483	PRK	Bacteria:17	COG1345, FliD, Flagellar capping protein [Cell motility and secretion].
CDD:224265	230	PRK	Bacteria:24	COG1346, LrgB, Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane].
CDD:224267	278	PRK	Bacteria:10	COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism].
CDD:224268	253	PRK	Bacteria:31,nodiv:1	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism].
CDD:224270	273	PRK	Bacteria:25	COG1351, THY1, Predicted alternative thymidylate synthase [Nucleotide transport and metabolism].
CDD:224271	268	PRK	Bacteria:24,nodiv:1	COG1352, CheR, Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms].
CDD:224272	799	PRK	Bacteria:14	COG1353, COG1353, Predicted CRISPR-associated polymerase [Defense mechanisms].
CDD:224273	248	PRK	Bacteria:38,nodiv:1	COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family) [Replication,    recombination, and repair].
CDD:224274	279	EUKprk	Bacteria:15,Plants:2	COG1355, COG1355, Predicted dioxygenase [General function prediction only].
CDD:224276	238	PRK	Bacteria:26,nodiv:1	COG1357, COG1357, Pentapeptide repeats containing protein [Function unknown].
CDD:224277	116	EUKprk	Bacteria:24,Plants:4	COG1358, RPL8A, Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis].
CDD:224278	100	PRK	Bacteria:25,nodiv:1	COG1359, COG1359, Uncharacterized conserved protein [Function unknown].
CDD:224279	244	PRK	Bacteria:25,nodiv:1	COG1360, MotB, Flagellar motor protein [Cell motility and secretion].
CDD:224280	500	PRK	Bacteria:11	COG1361, COG1361, S-layer domain [Cell envelope biogenesis, outer membrane].
CDD:224281	437	EUKprk	Bacteria:10,Plants:2	COG1362, LAP4, Aspartyl aminopeptidase [Amino acid transport and metabolism].
CDD:224282	355	PRK	Bacteria:30	COG1363, FrvX, Cellulase M and related proteins [Carbohydrate transport and metabolism].
CDD:224283	404	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG1364, ArgJ, N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism].
CDD:224285	117	PRK	Bacteria:23,nodiv:1	COG1366, SpoIIAA, Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms].
CDD:224287	650	PRK	Bacteria:23,nodiv:1	COG1368, MdoB, Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane].
CDD:224288	124	EUKprk	Bacteria:10,Plants:2	COG1369, POP5, RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis].
CDD:224289	155	PRK	Bacteria:7	COG1370, COG1370, tRNA modification protein, contains pre-PUA and PUA domains [Translation, ribosomal structure and biogenesis].
CDD:224290	137	PRK	Bacteria:17	COG1371, COG1371, SHS2 domain protein implicated in nucleic acid metabolism [General function prediction    only].
CDD:224291	420	EUKprk	Bacteria:6,Plants:2	COG1372, COG1372, Intein/homing endonuclease [DNA replication, recombination, and repair].
CDD:224292	398	PRK	Bacteria:20	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only].
CDD:224293	176	EUKprk	Bacteria:6,Plants:3	COG1374, NIP7, Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis].
CDD:224294	232	PRK	Bacteria:24,nodiv:1	COG1376, ErfK, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224295	363	PRK	Bacteria:26,nodiv:1	COG1377, FlhB, Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224296	247	PRK	Bacteria:16	COG1378, COG1378, Predicted transcriptional regulators [Transcription].
CDD:224298	128	PRK	Bacteria:23	COG1380, COG1380, Putative effector of murein hydrolase LrgA [General function prediction only].
CDD:224299	251	PRK	Bacteria:36,nodiv:2	COG1381, RecO, Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair].
CDD:224300	119	EUKprk	Bacteria:13,Plants:2	COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones].
CDD:224301	74	EUKprk	Bacteria:13,Plants:3	COG1383, RPS17A, Ribosomal protein S17E [Translation, ribosomal structure and biogenesis].
CDD:224302	521	PRK	Bacteria:18	COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis].
CDD:224303	246	PRK	Bacteria:44,nodiv:1	COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224304	184	PRK	Bacteria:36,nodiv:1	COG1386, scpB, Chromosome segregation and condensation protein B [DNA replication, recombination and repair].
CDD:224305	237	EUKprk	Bacteria:28,Plants:2	COG1387, HIS2, Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only].
CDD:224306	124	PRK	Bacteria:11	COG1388, LytE, FOG: LysM repeat [Cell envelope biogenesis, outer membrane].
CDD:224307	538	PRK	Bacteria:11	COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair].
CDD:224308	194	EUKprk	Bacteria:18,Plants:3	COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion].
CDD:224309	963	PRK	Bacteria:21,nodiv:1	COG1391, GlnE, Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms].
CDD:224310	217	PRK	Bacteria:22,nodiv:1	COG1392, COG1392, Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism].
CDD:224311	117	PRK	Bacteria:38,nodiv:1	COG1393, ArsC, Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism].
CDD:224312	211	EUKprk	Bacteria:21,Plants:3	COG1394, NtpD, Archaeal/vacuolar-type H+-ATPase subunit D [Energy production and conversion].
CDD:224313	313	PRK	Bacteria:13	COG1395, COG1395, Predicted transcriptional regulator [Transcription].
CDD:224314	120	PRK	Bacteria:45,Phages:2,nodiv:1	COG1396, HipB, Predicted transcriptional regulators [Transcription].
CDD:224315	314	PRK	Bacteria:13	COG1397, DraG, ADP-ribosylglycohydrolase [Posttranslational modification, protein turnover, chaperones].
CDD:224316	289	EUKprk	Bacteria:6,Plants:2	COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].
CDD:224317	176	PRK	Bacteria:27,nodiv:1	COG1399, COG1399, Predicted metal-binding, possibly nucleic acid-binding protein [General function prediction only].
CDD:224318	93	EUKprk	Bacteria:13,Plants:3	COG1400, SEC65, Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion].
CDD:224319	601	PRK	Bacteria:15	COG1401, McrB, GTPase subunit of restriction endonuclease [Defense mechanisms].
CDD:224320	250	PRK	Bacteria:18,nodiv:1	COG1402, COG1402, Uncharacterized protein, putative amidase [General function prediction only].
CDD:224321	146	PRK	Bacteria:24,nodiv:1	COG1403, McrA, Restriction endonuclease [Defense mechanisms].
CDD:224322	508	EUKprk	Bacteria:32,Plants:3	COG1404, AprE, Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones].
CDD:224323	285	EUKprk	Bacteria:13,Plants:3	COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription].
CDD:224325	235	PRK	Bacteria:17,nodiv:1	COG1407, COG1407, Predicted ICC-like phosphoesterases [General function prediction only].
CDD:224326	284	PRK	Bacteria:25	COG1408, COG1408, Predicted phosphohydrolases [General function prediction only].
CDD:224327	301	EUKprk	Bacteria:34,Plants:2,nodiv:1	COG1409, Icc, Predicted phosphohydrolases [General function prediction only].
CDD:224328	842	PRK	Bacteria:8,nodiv:1	COG1410, MetH, Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism].
CDD:224330	136	EUKprk	Bacteria:13,Plants:3	COG1412, COG1412, Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only].
CDD:224331	335	EUKprk	Bacteria:16,Plants:3	COG1413, COG1413, FOG: HEAT repeat [Energy production and conversion].
CDD:224332	246	PRK	Bacteria:25,nodiv:1	COG1414, IclR, Transcriptional regulator [Transcription].
CDD:224333	373	PRK	Bacteria:12	COG1415, COG1415, Uncharacterized conserved protein [Function unknown].
CDD:224334	112	PRK	Bacteria:9	COG1416, COG1416, Uncharacterized conserved protein [Function unknown].
CDD:224336	222	PRK	Bacteria:33,nodiv:1	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only].
CDD:224337	407	PRK	Bacteria:14	COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion].
CDD:224338	346	PRK	Bacteria:30,nodiv:1	COG1420, HrcA, Transcriptional regulator of heat shock gene [Transcription].
CDD:224340	201	PRK	Bacteria:10	COG1422, COG1422, Predicted membrane protein [Function unknown].
CDD:224341	382	PRK	Bacteria:9	COG1423, COG1423, ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair].
CDD:224343	284	PRK	Bacteria:26	COG1426, COG1426, Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown].
CDD:224344	252	PRK	Bacteria:13	COG1427, COG1427, Predicted periplasmic solute-binding protein [General function prediction only].
CDD:224345	216	PRK	Bacteria:12	COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and metabolism].
CDD:224346	1388	PRK	Bacteria:14,nodiv:1	COG1429, CobN, Cobalamin biosynthesis protein CobN and related Mg-chelatases [Coenzyme metabolism].
CDD:224347	126	PRK	Bacteria:18,nodiv:1	COG1430, COG1430, Uncharacterized conserved protein [Function unknown].
CDD:224349	181	PRK	Bacteria:24,nodiv:1	COG1432, COG1432, Uncharacterized conserved protein [Function unknown].
CDD:224350	121	PRK	Bacteria:14	COG1433, COG1433, Uncharacterized conserved protein [Function unknown].
CDD:224351	223	PRK	Bacteria:29,nodiv:1	COG1434, COG1434, Uncharacterized conserved protein [Function unknown].
CDD:224352	201	EUKprk	Bacteria:28,Plants:1,nodiv:1	COG1435, Tdk, Thymidine kinase [Nucleotide transport and metabolism].
CDD:224353	104	EUKprk	Bacteria:17,Plants:3	COG1436, NtpG, Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion].
CDD:224354	178	PRK	Bacteria:15	COG1437, CyaB, Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism].
CDD:224355	150	PRK	Bacteria:22,nodiv:1	COG1438, ArgR, Arginine repressor [Transcription].
CDD:224356	177	EUKprk	Bacteria:13,Plants:3	COG1439, COG1439, Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only].
CDD:224357	102	PRK	Bacteria:12	COG1440, CelA, Phosphotransferase system cellobiose-specific component IIB [Carbohydrate transport and metabolism].
CDD:224359	325	PRK	Bacteria:13	COG1442, RfaJ, Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].
CDD:224360	185	EUKprk	Bacteria:6,Plants:3	COG1443, Idi, Isopentenyldiphosphate isomerase [Lipid metabolism].
CDD:224361	758	EUKprk	Bacteria:16,Plants:3	COG1444, COG1444, Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only].
CDD:224362	122	PRK	Bacteria:11	COG1445, FrwB, Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism].
CDD:224363	307	EUKprk	Bacteria:16,Plants:1,nodiv:1	COG1446, COG1446, Asparaginase [Amino acid transport and metabolism].
CDD:224364	105	PRK	Bacteria:13	COG1447, CelC, Phosphotransferase system cellobiose-specific component IIA [Carbohydrate transport and metabolism].
CDD:224365	396	EUKprk	Bacteria:17,Plants:3	COG1448, TyrB, Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism].
CDD:224366	615	PRK	Bacteria:12	COG1449, COG1449, Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism].
CDD:224367	587	PRK	Bacteria:16	COG1450, PulD, Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224368	223	PRK	Bacteria:33,nodiv:1	COG1451, COG1451, Predicted metal-dependent hydrolase [General function prediction only].
CDD:224369	784	PRK	Bacteria:25,nodiv:1	COG1452, Imp, Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane].
CDD:224370	391	PRK	Bacteria:6	COG1453, COG1453, Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only].
CDD:224371	377	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG1454, EutG, Alcohol dehydrogenase, class IV [Energy production and conversion].
CDD:224372	432	PRK	Bacteria:15	COG1455, CelB, Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism].
CDD:224374	442	EUKprk	Bacteria:16,Plants:1	COG1457, CodB, Purine-cytosine permease and related proteins [Nucleotide transport and metabolism].
CDD:224376	397	PRK	Bacteria:32	COG1459, PulF, Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224377	114	PRK	Bacteria:12	COG1460, COG1460, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224378	542	PRK	Bacteria:17	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only].
CDD:224379	252	PRK	Bacteria:11,nodiv:1	COG1462, CsgG, Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane].
CDD:224380	359	PRK	Bacteria:26,nodiv:1	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:224381	268	PRK	Bacteria:34,nodiv:1	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism].
CDD:224383	334	PRK	Bacteria:47,nodiv:1	COG1466, HolA, DNA polymerase III, delta subunit [DNA replication, recombination, and repair].
CDD:224384	341	EUKprk	Bacteria:14,Plants:3	COG1467, PRI1, Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair].
CDD:224385	190	PRK	Bacteria:15	COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense    mechanisms].
CDD:224386	289	PRK	Bacteria:20	COG1469, COG1469, Uncharacterized conserved protein [Function unknown].
CDD:224388	241	EUKprk	Bacteria:13,Plants:3	COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis].
CDD:224389	397	EUKprk	Bacteria:36,Plants:1,nodiv:1	COG1472, BglX, Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism].
CDD:224390	392	PRK	Bacteria:37,nodiv:1	COG1473, AbgB, Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only].
CDD:224391	366	EUKprk	Bacteria:11,Plants:3	COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones].
CDD:224392	240	PRK	Bacteria:43,nodiv:1	COG1475, Spo0J, Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription].
CDD:224393	68	PRK	Bacteria:18	COG1476, COG1476, Predicted transcriptional regulators [Transcription].
CDD:224394	337	PRK	Bacteria:28	COG1477, ApbE, Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism].
CDD:224395	257	PRK	Bacteria:9	COG1478, COG1478, GTP and metal dependent enzyme involved F420 coenzyme biosynthesis (catalyzes addition of two    l-glutamates to F420 precursor) [Coenzyme transport and metabolism].
CDD:224396	409	PRK	Bacteria:21	COG1479, COG1479, Uncharacterized conserved protein [Function unknown].
CDD:224397	700	PRK	Bacteria:10	COG1480, COG1480, Predicted membrane-associated HD superfamily hydrolase [General function prediction only].
CDD:224398	308	PRK	Bacteria:18	COG1481, COG1481, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224399	312	EUKprk	Bacteria:24,Plants:2	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism].
CDD:224400	774	PRK	Bacteria:7	COG1483, COG1483, Predicted ATPase (AAA+ superfamily) [General function prediction only].
CDD:224401	254	PRK	Bacteria:25,nodiv:1	COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair].
CDD:224402	367	EUKprk	Bacteria:18,Plants:2,nodiv:1	COG1485, COG1485, Predicted ATPase [General function prediction only].
CDD:224403	442	PRK	Bacteria:13,nodiv:1	COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism].
CDD:224404	133	PRK	Bacteria:21,nodiv:1	COG1487, VapC, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only].
CDD:224405	405	EUKprk	Bacteria:51,Plants:2,nodiv:1	COG1488, PncB, Nicotinic acid phosphoribosyltransferase [Coenzyme metabolism].
CDD:224406	235	PRK	Bacteria:23,nodiv:1	COG1489, SfsA, DNA-binding protein, stimulates sugar fermentation [General function prediction only].
CDD:224407	145	EUKprk	Bacteria:25,Plants:2	COG1490, Dtd, D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis].
CDD:224408	202	PRK	Bacteria:13	COG1491, COG1491, Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis].
CDD:224409	486	PRK	Bacteria:25,nodiv:1	COG1492, CobQ, Cobyric acid synthase [Coenzyme metabolism].
CDD:224410	308	PRK	Bacteria:23,nodiv:1	COG1493, HprK, Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms].
CDD:224411	332	PRK	Bacteria:23	COG1494, GlpX, Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism].
CDD:224412	170	PRK	Bacteria:27,nodiv:1	COG1495, DsbB, Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones].
CDD:224413	249	PRK	Bacteria:36,nodiv:1	COG1496, yfiH, Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism].
CDD:224414	260	PRK	Bacteria:8	COG1497, COG1497, Predicted transcriptional regulator [Transcription].
CDD:224415	395	EUKprk	Bacteria:13,Plants:3	COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis].
CDD:224416	355	EUKprk	Bacteria:13,Plants:3	COG1499, NMD3, NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis].
CDD:224417	234	EUKprk	Bacteria:13,Plants:3	COG1500, COG1500, Predicted exosome subunit [Translation, ribosomal structure and biogenesis].
CDD:224418	772	EUKprk	Bacteria:19,Plants:3,nodiv:1	COG1501, COG1501, Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism].
CDD:224419	438	EUKprk	Bacteria:45,Plants:3,nodiv:1	COG1502, Cls, Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism].
CDD:224420	411	EUKprk	Bacteria:14,Plants:3	COG1503, eRF1, Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis].
CDD:224422	648	PRK	Bacteria:13	COG1505, COG1505, Serine proteases of the peptidase family S9A [Amino acid transport and metabolism].
CDD:224423	620	EUKprk	Bacteria:19,Plants:3,nodiv:1	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism].
CDD:224425	444	PRK	Bacteria:27,nodiv:1	COG1508, RpoN, DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription].
CDD:224426	369	PRK	Bacteria:21,nodiv:1	COG1509, KamA, Lysine 2,3-aminomutase [Amino acid transport and metabolism].
CDD:224427	177	PRK	Bacteria:7,nodiv:1	COG1510, COG1510, Predicted transcriptional regulators [Transcription].
CDD:224428	780	PRK	Bacteria:14	COG1511, COG1511, Predicted membrane protein [Function unknown].
CDD:224429	271	PRK	Bacteria:17	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only].
CDD:224431	180	PRK	Bacteria:32,nodiv:1	COG1514, LigT, 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis].
CDD:224432	212	EUKprk	Bacteria:18,Plants:1,nodiv:1	COG1515, Nfi, Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair].
CDD:224433	132	PRK	Bacteria:18	COG1516, FliS, Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones].
CDD:224434	406	PRK	Bacteria:6	COG1517, COG1517, CRISPR system related protein [Defense mechanisms].
CDD:224435	327	PRK	Bacteria:28	COG1518, COG1518, CRISPR-associated protein Cas1 [Defense mechanisms].
CDD:224436	419	PRK	Bacteria:24,nodiv:1	COG1519, KdtA, 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane].
CDD:224437	370	PRK	Bacteria:26	COG1520, COG1520, FOG: WD40-like repeat [Function unknown].
CDD:224438	251	PRK	Bacteria:23	COG1521, COG1521, Pantothenate kinase type III (Bvg accessory factor family protein) [Transcription].
CDD:224439	154	PRK	Bacteria:36,nodiv:2	COG1522, Lrp, Transcriptional regulators [Transcription].
CDD:224440	697	PRK	Bacteria:28,nodiv:1	COG1523, PulA, Type II secretory pathway, pullulanase PulA and related glycosidases [Carbohydrate transport and metabolism].
CDD:224441	450	EUKprk	Bacteria:18,Plants:4	COG1524, COG1524, Uncharacterized proteins of the AP superfamily [General function prediction only].
CDD:224442	192	EUKprk	Bacteria:23,Plants:2,nodiv:1	COG1525, COG1525, Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair].
CDD:224443	266	PRK	Bacteria:29,nodiv:1	COG1526, FdhD, Uncharacterized protein required for formate dehydrogenase activity [Energy production and conversion].
CDD:224444	346	EUKprk	Bacteria:15,Plants:3	COG1527, NtpC, Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion].
CDD:224445	167	EUKprk	Bacteria:20,Plants:1	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism].
CDD:224446	731	PRK	Bacteria:17,nodiv:1	COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion].
CDD:224447	487	PRK	Bacteria:43,nodiv:1	COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis].
CDD:224448	77	PRK	Bacteria:8	COG1531, COG1531, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224450	297	PRK	Bacteria:24,nodiv:1	COG1533, SplB, DNA repair photolyase [DNA replication, recombination, and repair].
CDD:224451	97	PRK	Bacteria:30	COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis].
CDD:224453	339	PRK	Bacteria:24,nodiv:2	COG1536, FliG, Flagellar motor switch protein [Cell motility and secretion].
CDD:224454	352	EUKprk	Bacteria:13,Plants:3	COG1537, PelA, Predicted RNA-binding proteins [General function prediction only].
CDD:224455	457	PRK	Bacteria:27,nodiv:1	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].
CDD:224456	121	PRK	Bacteria:35,nodiv:1	COG1539, FolB, Dihydroneopterin aldolase [Coenzyme metabolism].
CDD:224457	252	PRK	Bacteria:21,nodiv:1	COG1540, COG1540, Uncharacterized proteins, homologs of lactam utilization protein B [General function prediction only].
CDD:224458	438	PRK	Bacteria:13	COG1541, PaaK, Coenzyme F390 synthetase [Coenzyme metabolism].
CDD:224460	504	PRK	Bacteria:9	COG1543, COG1543, Uncharacterized conserved protein [Function unknown].
CDD:224461	110	PRK	Bacteria:35,nodiv:1	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis].
CDD:224462	140	PRK	Bacteria:16	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only].
CDD:224463	162	PRK	Bacteria:27,nodiv:1	COG1546, CinA, Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only].
CDD:224464	156	PRK	Bacteria:13	COG1547, COG1547, Predicted metal-dependent hydrolase [General function prediction only].
CDD:224466	519	PRK	Bacteria:11	COG1549, COG1549, Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis].
CDD:224468	73	PRK	Bacteria:17	COG1551, CsrA, RNA-binding global regulator CsrA [Signal transduction mechanisms].
CDD:224470	126	PRK	Bacteria:16	COG1553, DsrE, Uncharacterized conserved protein involved in intracellular sulfur reduction [Inorganic ion transport and metabolism].
CDD:224471	772	EUKprk	Bacteria:14,Plants:1	COG1554, ATH1, Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism].
CDD:224472	149	PRK	Bacteria:31	COG1555, ComEA, DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair].
CDD:224473	218	PRK	Bacteria:17	COG1556, COG1556, Uncharacterized conserved protein [Function unknown].
CDD:224474	137	PRK	Bacteria:21,nodiv:2	COG1558, FlgC, Flagellar basal body rod protein [Cell motility and secretion].
CDD:224475	342	PRK	Bacteria:38,nodiv:1	COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport and metabolism].
CDD:224476	308	PRK	Bacteria:31,nodiv:1	COG1560, HtrB, Lauroyl/myristoyl acyltransferase [Cell envelope biogenesis, outer membrane].
CDD:224477	290	PRK	Bacteria:25,nodiv:1	COG1561, COG1561, Uncharacterized stress-induced protein [Function unknown].
CDD:224478	288	EUKprk	Bacteria:19,Plants:2,nodiv:1	COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism].
CDD:224480	212	EUKprk	Bacteria:16,Plants:1,nodiv:1	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism].
CDD:224481	370	PRK	Bacteria:16,nodiv:1	COG1565, COG1565, Uncharacterized conserved protein [Function unknown].
CDD:224482	352	PRK	Bacteria:22,nodiv:1	COG1566, EmrA, Multidrug resistance efflux pump [Defense mechanisms].
CDD:224483	313	PRK	Bacteria:8	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:224485	142	PRK	Bacteria:7	COG1569, COG1569, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only].
CDD:224486	440	PRK	Bacteria:39,nodiv:1	COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair].
CDD:224487	421	PRK	Bacteria:13	COG1571, COG1571, Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only].
CDD:224488	606	PRK	Bacteria:4	COG1572, COG1572, Uncharacterized conserved protein [Function unknown].
CDD:224489	202	PRK	Bacteria:38,nodiv:1	COG1573, COG1573, Uracil-DNA glycosylase [DNA replication, recombination, and repair].
CDD:224490	535	PRK	Bacteria:23,nodiv:1	COG1574, COG1574, Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only].
CDD:224491	303	PRK	Bacteria:20	COG1575, MenA, 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism].
CDD:224492	155	PRK	Bacteria:31,nodiv:1	COG1576, COG1576, Uncharacterized conserved protein [Function unknown].
CDD:224493	307	EUKprk	Bacteria:17,Plants:3	COG1577, ERG12, Mevalonate kinase [Lipid metabolism].
CDD:224494	285	PRK	Bacteria:10	COG1578, COG1578, Uncharacterized conserved protein [Function unknown].
CDD:224495	239	PRK	Bacteria:13	COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].
CDD:224496	159	PRK	Bacteria:16	COG1580, FliL, Flagellar basal body-associated protein [Cell motility and secretion].
CDD:224499	240	PRK	Bacteria:9	COG1583, COG1583, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:224500	207	EUKprk	Bacteria:10,Plants:2	COG1584, COG1584, Predicted membrane protein [Function unknown].
CDD:224501	140	PRK	Bacteria:32,nodiv:1	COG1585, COG1585, Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:224502	136	PRK	Bacteria:22	COG1586, SpeD, S-adenosylmethionine decarboxylase [Amino acid transport and metabolism].
CDD:224503	248	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG1587, HemD, Uroporphyrinogen-III synthase [Coenzyme metabolism].
CDD:224504	95	PRK	Bacteria:11	COG1588, POP4, RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis].
CDD:224505	269	PRK	Bacteria:35,nodiv:1	COG1589, FtsQ, Cell division septal protein [Cell envelope biogenesis, outer membrane].
CDD:224506	208	EUKprk	Bacteria:8,Plants:2	COG1590, COG1590, Uncharacterized conserved protein [Function unknown].
CDD:224507	137	PRK	Bacteria:11	COG1591, COG1591, Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair].
CDD:224508	166	PRK	Bacteria:13	COG1592, COG1592, Rubrerythrin [Energy production and conversion].
CDD:224509	379	PRK	Bacteria:15,nodiv:1	COG1593, DctQ, TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism].
CDD:224510	113	EUKprk	Bacteria:12,Plants:4	COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription].
CDD:224511	182	PRK	Bacteria:33,nodiv:2	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription].
CDD:224512	239	PRK	Bacteria:18,nodiv:1	COG1596, Wza, Periplasmic protein involved in polysaccharide export, contains    SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis].
CDD:224513	301	EUKprk	Bacteria:26,Plants:2,nodiv:1	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].
CDD:224514	73	PRK	Bacteria:19	COG1598, COG1598, Predicted nuclease of the RNAse H fold, HicB family [General    function prediction only].
CDD:224515	407	EUKprk	Bacteria:12,Plants:3	COG1599, RFA1, Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair].
CDD:224516	337	PRK	Bacteria:24,nodiv:1	COG1600, COG1600, Uncharacterized Fe-S protein [Energy production and conversion].
CDD:224517	151	EUKprk	Bacteria:13,Plants:4	COG1601, GCD7, Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis].
CDD:224518	402	PRK	Bacteria:12	COG1602, COG1602, Uncharacterized conserved protein [Function unknown].
CDD:224519	229	EUKprk	Bacteria:10,Plants:2	COG1603, RPP1, RNase P/RNase MRP subunit p30 [Translation, ribosomal structure and biogenesis].
CDD:224520	257	PRK	Bacteria:5	COG1604, COG1604, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:224521	101	EUKprk	Bacteria:37,Plants:2,nodiv:1	COG1605, PheA, Chorismate mutase [Amino acid transport and metabolism].
CDD:224522	269	PRK	Bacteria:9	COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only].
CDD:224523	157	PRK	Bacteria:32,nodiv:2	COG1607, COG1607, Acyl-CoA hydrolase [Lipid metabolism].
CDD:224524	252	PRK	Bacteria:13	COG1608, COG1608, Predicted archaeal kinase [General function prediction only].
CDD:224525	333	PRK	Bacteria:34,nodiv:2	COG1609, PurR, Transcriptional regulators [Transcription].
CDD:224526	148	EUKprk	Bacteria:18,Plants:1,nodiv:1	COG1610, COG1610, Uncharacterized conserved protein [Function unknown].
CDD:224527	205	EUKprk	Bacteria:39,Plants:1,nodiv:1	COG1611, COG1611, Predicted Rossmann fold nucleotide-binding protein [General function prediction only].
CDD:224528	323	EUKprk	Bacteria:23,Plants:1,nodiv:1	COG1612, CtaA, Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones].
CDD:224529	348	PRK	Bacteria:20,nodiv:1	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:224531	885	PRK	Bacteria:8	COG1615, COG1615, Uncharacterized conserved protein [Function unknown].
CDD:224533	179	PRK	Bacteria:14	COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport and metabolism].
CDD:224534	313	PRK	Bacteria:26	COG1619, LdcA, Uncharacterized proteins, homologs of microcin C7 resistance protein MccF [Defense mechanisms].
CDD:224535	522	PRK	Bacteria:24	COG1620, LldP, L-lactate permease [Energy production and conversion].
CDD:224536	486	EUKprk	Bacteria:14,Plants:3,nodiv:1	COG1621, SacC, Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism].
CDD:224537	247	EUKprk	Bacteria:30,Plants:1,nodiv:1	COG1622, CyoA, Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion].
CDD:224539	247	PRK	Bacteria:26	COG1624, COG1624, Uncharacterized conserved protein [Function unknown].
CDD:224540	414	PRK	Bacteria:10	COG1625, COG1625, Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion].
CDD:224541	558	EUKprk	Bacteria:9,Plants:3	COG1626, TreA, Neutral trehalase [Carbohydrate transport and metabolism].
CDD:224543	185	PRK	Bacteria:14	COG1628, COG1628, Endonuclease V homolog [Replication, recombination, and repair].
CDD:224544	768	PRK	Bacteria:27,nodiv:1	COG1629, CirA, Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism].
CDD:224545	379	PRK	Bacteria:9	COG1630, COG1630, NurA 5'-3' nuclease [Replication, recombination, and repair].
CDD:224546	94	EUKprk	Bacteria:13,Plants:3	COG1631, RPL42A, Ribosomal protein L44E [Translation, ribosomal structure and biogenesis].
CDD:224547	195	EUKprk	Bacteria:13,Plants:3	COG1632, RPL15A, Ribosomal protein L15E [Translation, ribosomal structure and biogenesis].
CDD:224548	176	PRK	Bacteria:14,nodiv:1	COG1633, COG1633, Uncharacterized conserved protein [Function unknown].
CDD:224549	232	PRK	Bacteria:13	COG1634, COG1634, Uncharacterized Rossmann fold enzyme [General function prediction only].
CDD:224550	262	EUKprk	Bacteria:12,Plants:2	COG1635, THI4, Ribulose 1,5-bisphosphate synthetase, converts PRPP to RuBP, flavoprotein [Carbohydrate    transport and metabolism].
CDD:224551	204	PRK	Bacteria:17	COG1636, COG1636, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224552	253	PRK	Bacteria:14	COG1637, COG1637, Predicted nuclease of the RecB family [DNA replication, recombination, and repair].
CDD:224553	332	PRK	Bacteria:17,nodiv:1	COG1638, DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism].
CDD:224554	289	PRK	Bacteria:5	COG1639, COG1639, Predicted signal transduction protein [Signal transduction mechanisms].
CDD:224555	520	PRK	Bacteria:24	COG1640, MalQ, 4-alpha-glucanotransferase [Carbohydrate transport and metabolism].
CDD:224556	387	PRK	Bacteria:10	COG1641, COG1641, Uncharacterized conserved protein [Function unknown].
CDD:224557	845	EUKprk	Bacteria:21,Plants:3,nodiv:1	COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair].
CDD:224558	63	EUKprk	Bacteria:13,Plants:3	COG1644, RPB10, DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription].
CDD:224559	131	PRK	Bacteria:10	COG1645, COG1645, Uncharacterized Zn-finger containing protein [General function prediction only].
CDD:224560	240	PRK	Bacteria:17	COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only].
CDD:224561	243	PRK	Bacteria:6	COG1647, COG1647, Esterase/lipase [General function prediction only].
CDD:224562	210	EUKprk	Bacteria:17,Plants:2,nodiv:1	COG1648, CysG, Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism].
CDD:224563	418	PRK	Bacteria:9	COG1649, COG1649, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224564	266	PRK	Bacteria:12	COG1650, COG1650, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224565	244	PRK	Bacteria:39,nodiv:1	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones].
CDD:224566	269	PRK	Bacteria:22,nodiv:1	COG1652, XkdP, Uncharacterized protein containing LysM domain [Function unknown].
CDD:224567	433	PRK	Bacteria:38,nodiv:1	COG1653, UgpB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism].
CDD:224568	79	PRK	Bacteria:1	COG1654, BirA, Biotin operon repressor [Transcription].
CDD:224570	165	PRK	Bacteria:15	COG1656, COG1656, Uncharacterized conserved protein [Function unknown].
CDD:224571	517	EUKprk	Bacteria:5,Plants:2	COG1657, SqhC, Squalene cyclase [Lipid metabolism].
CDD:224572	127	PRK	Bacteria:22	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair].
CDD:224574	286	PRK	Bacteria:24	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only].
CDD:224575	141	PRK	Bacteria:17,nodiv:1	COG1661, COG1661, Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only].
CDD:224576	121	PRK	Bacteria:9	COG1662, InsB, Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair].
CDD:224577	336	PRK	Bacteria:25,nodiv:1	COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane].
CDD:224578	146	PRK	Bacteria:16	COG1664, CcmA, Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane].
CDD:224580	165	PRK	Bacteria:14	COG1666, COG1666, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224582	407	PRK	Bacteria:22	COG1668, NatB, ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism].
CDD:224583	97	PRK	Bacteria:8,nodiv:1	COG1669, COG1669, Predicted nucleotidyltransferases [General function prediction only].
CDD:224584	187	EUKprk	Bacteria:45,Plants:2,nodiv:1	COG1670, RimL, Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis].
CDD:224585	150	PRK	Bacteria:18,nodiv:1	COG1671, COG1671, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224586	359	PRK	Bacteria:14	COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General function prediction only].
CDD:224587	151	PRK	Bacteria:8	COG1673, COG1673, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224588	858	PRK	Bacteria:42,nodiv:1	COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning].
CDD:224589	176	EUKprk	Bacteria:11,Plants:3	COG1675, TFA1, Transcription initiation factor IIE, alpha subunit [Transcription].
CDD:224590	181	EUKprk	Bacteria:13,Plants:3	COG1676, SEN2, tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis].
CDD:224591	105	PRK	Bacteria:21,nodiv:1	COG1677, FliE, Flagellar hook-basal body protein [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224592	194	PRK	Bacteria:25,nodiv:1	COG1678, COG1678, Putative transcriptional regulator [Transcription].
CDD:224593	403	PRK	Bacteria:12,nodiv:1	COG1679, COG1679, Predicted aconitase [General function prediction only].
CDD:224594	390	PRK	Bacteria:36,nodiv:1	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms].
CDD:224595	209	PRK	Bacteria:10	COG1681, FlaB, Archaeal flagellins [Cell motility and secretion].
CDD:224596	263	PRK	Bacteria:30	COG1682, TagG, ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane].
CDD:224597	156	PRK	Bacteria:15,nodiv:1	COG1683, COG1683, Uncharacterized conserved protein [Function unknown].
CDD:224598	258	PRK	Bacteria:23,nodiv:1	COG1684, FliR, Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224599	278	PRK	Bacteria:12	COG1685, COG1685, Archaeal shikimate kinase [Amino acid transport and metabolism / Coenzyme metabolism].
CDD:224600	389	PRK	Bacteria:37,nodiv:1	COG1686, DacC, D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane].
CDD:224602	240	PRK	Bacteria:12	COG1688, COG1688, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:224604	432	EUKprk	Bacteria:25,Plants:1	COG1690, RtcB, Uncharacterized conserved protein [Function unknown].
CDD:224605	254	PRK	Bacteria:10	COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General function prediction only].
CDD:224606	266	PRK	Bacteria:16,nodiv:1	COG1692, COG1692, Calcineurin-like phosphoesterase [General function prediction only].
CDD:224608	102	PRK	Bacteria:40,nodiv:1	COG1694, MazG, Predicted pyrophosphatase [General function prediction only].
CDD:224609	138	PRK	Bacteria:36	COG1695, COG1695, Predicted transcriptional regulators [Transcription].
CDD:224610	425	EUKprk	Bacteria:16,Plants:2	COG1696, DltB, Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane].
CDD:224611	356	EUKprk	Bacteria:11,Plants:3	COG1697, COG1697, DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair].
CDD:224612	93	PRK	Bacteria:11	COG1698, COG1698, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224613	146	PRK	Bacteria:9	COG1699, COG1699, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224616	348	PRK	Bacteria:33,nodiv:1	COG1702, PhoH, Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms].
CDD:224617	323	PRK	Bacteria:18	COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism].
CDD:224618	185	PRK	Bacteria:20,nodiv:1	COG1704, LemA, Uncharacterized conserved protein [Function unknown].
CDD:224619	201	PRK	Bacteria:13	COG1705, FlgJ, Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224620	365	PRK	Bacteria:19,nodiv:1	COG1706, FlgI, Flagellar basal-body P-ring protein [Cell motility and secretion].
CDD:224622	128	PRK	Bacteria:19,nodiv:1	COG1708, COG1708, Predicted nucleotidyltransferases [General function prediction only].
CDD:224623	241	PRK	Bacteria:12	COG1709, COG1709, Predicted transcriptional regulator [Transcription].
CDD:224625	223	PRK	Bacteria:8	COG1711, COG1711, DNA replication initiation complex subunit, GINS family    [Replication, recombination, and repair].
CDD:224626	255	PRK	Bacteria:8	COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General function prediction only].
CDD:224627	187	PRK	Bacteria:13	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism].
CDD:224628	172	PRK	Bacteria:26,nodiv:1	COG1714, COG1714, Predicted membrane protein/domain [Function unknown].
CDD:224629	308	PRK	Bacteria:9	COG1715, Mrr, Restriction endonuclease [Defense mechanisms].
CDD:224630	191	EUKprk	Bacteria:17,Plants:2	COG1716, COG1716, FOG: FHA domain [Signal transduction mechanisms].
CDD:224631	133	EUKprk	Bacteria:12,Plants:3	COG1717, RPL32, Ribosomal protein L32E [Translation, ribosomal structure and biogenesis].
CDD:224632	268	EUKprk	Bacteria:16,Plants:3	COG1718, RIO1, Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning].
CDD:224633	158	PRK	Bacteria:6	COG1719, COG1719, Predicted hydrocarbon binding protein (contains V4R domain) [General function prediction only].
CDD:224634	156	PRK	Bacteria:25	COG1720, COG1720, Uncharacterized conserved protein [Function unknown].
CDD:224635	416	PRK	Bacteria:29,nodiv:1	COG1721, COG1721, Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only].
CDD:224636	81	PRK	Bacteria:35,nodiv:2	COG1722, XseB, Exonuclease VII small subunit [DNA replication, recombination, and repair].
CDD:224637	331	EUKprk	Bacteria:5,Plants:4	COG1723, COG1723, Uncharacterized conserved protein [Function unknown].
CDD:224638	66	PRK	Bacteria:9	COG1724, COG1724, Predicted RNA binding protein (dsRBD-like fold), HicA family    [General function prediction only].
CDD:224639	125	PRK	Bacteria:15	COG1725, COG1725, Predicted transcriptional regulators [Transcription].
CDD:224641	122	EUKprk	Bacteria:13,Plants:3	COG1727, RPL18A, Ribosomal protein L18E [Translation, ribosomal structure and biogenesis].
CDD:224643	262	PRK	Bacteria:18,nodiv:1	COG1729, COG1729, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224644	145	EUKprk	Bacteria:14,Plants:2	COG1730, GIM5, Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones].
CDD:224646	300	PRK	Bacteria:18,nodiv:1	COG1732, OpuBC, Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane].
CDD:224647	120	PRK	Bacteria:38,nodiv:1	COG1733, COG1733, Predicted transcriptional regulators [Transcription].
CDD:224648	120	PRK	Bacteria:31,nodiv:2	COG1734, DksA, DnaK suppressor protein [Signal transduction mechanisms].
CDD:224649	316	PRK	Bacteria:11,nodiv:1	COG1735, Php, Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only].
CDD:224650	347	EUKprk	Bacteria:13,Plants:3	COG1736, DPH2, Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis].
CDD:224651	281	PRK	Bacteria:27,nodiv:1	COG1737, RpiR, Transcriptional regulators [Transcription].
CDD:224652	233	PRK	Bacteria:28,nodiv:1	COG1738, yhhQ, Uncharacterized member of the PurR regulon [General function prediction only].
CDD:224653	203	EUKprk	Bacteria:33,Plants:3,nodiv:1	COG1739, COG1739, Uncharacterized conserved protein [Function unknown].
CDD:224654	355	PRK	Bacteria:12	COG1740, HyaA, Ni,Fe-hydrogenase I small subunit [Energy production and conversion].
CDD:224655	276	PRK	Bacteria:21,nodiv:1	COG1741, COG1741, Pirin-related protein [General function prediction only].
CDD:224656	109	PRK	Bacteria:14,nodiv:1	COG1742, COG1742, Uncharacterized conserved protein [Function unknown].
CDD:224657	875	PRK	Bacteria:7	COG1743, COG1743, Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair].
CDD:224658	345	PRK	Bacteria:29,nodiv:1	COG1744, Med, Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only].
CDD:224659	94	PRK	Bacteria:6	COG1745, COG1745, Predicted metal-binding protein [General function prediction only].
CDD:224660	443	PRK	Bacteria:13	COG1746, CCA1, tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis].
CDD:224662	389	EUKprk	Bacteria:19,Plants:2,nodiv:1	COG1748, LYS9, Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism].
CDD:224663	423	PRK	Bacteria:20,nodiv:2	COG1749, FlgE, Flagellar hook protein FlgE [Cell motility and secretion].
CDD:224664	579	PRK	Bacteria:8	COG1750, COG1750, Archaeal serine proteases [General function prediction only].
CDD:224666	306	EUKprk	Bacteria:26,Plants:3,nodiv:1	COG1752, RssA, Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only].
CDD:224668	298	miss	miss	COG1754, COG1754, Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only].
CDD:224669	172	PRK	Bacteria:12	COG1755, COG1755, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224670	223	EUKprk	Bacteria:10,Plants:3	COG1756, Mra1, Uncharacterized conserved protein [Function unknown].
CDD:224671	485	PRK	Bacteria:20	COG1757, NhaC, Na+/H+ antiporter [Energy production and conversion].
CDD:224672	74	EUKprk	Bacteria:49,Plants:3,nodiv:1	COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription].
CDD:224673	361	PRK	Bacteria:9	COG1759, COG1759, 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl    5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and    metabolism].
CDD:224674	262	PRK	Bacteria:32,nodiv:1	COG1760, SdaA, L-serine deaminase [Amino acid transport and metabolism].
CDD:224675	99	EUKprk	Bacteria:13,Plants:5	COG1761, RPB11, DNA-directed RNA polymerase, subunit L [Transcription].
CDD:224676	152	PRK	Bacteria:33,nodiv:1	COG1762, PtsN, Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism / Signal transduction mechanisms].
CDD:224677	161	PRK	Bacteria:28,nodiv:1	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism].
CDD:224678	143	PRK	Bacteria:22,nodiv:1	COG1764, osmC, Organic hydroperoxide reductase [Secondary metabolites biosynthesis, transport and catabolism].
CDD:224679	137	PRK	Bacteria:30,nodiv:1	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones].
CDD:224680	545	PRK	Bacteria:24,nodiv:1	COG1766, fliF, Flagellar basal body M-ring protein [Cell motility and secretion].
CDD:224681	288	PRK	Bacteria:17	COG1767, CitG, Triphosphoribosyl-dephospho-CoA synthetase [Coenzyme metabolism].
CDD:224684	682	PRK	Bacteria:20,nodiv:1	COG1770, PtrB, Protease II [Amino acid transport and metabolism].
CDD:224687	55	PRK	Bacteria:19	COG1773, COG1773, Rubredoxin [Energy production and conversion].
CDD:224688	265	EUKprk	Bacteria:11,Plants:3	COG1774, COG1774, Uncharacterized homolog of PSP1 [Function unknown].
CDD:224689	379	PRK	Bacteria:8	COG1775, HgdB, Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism].
CDD:224690	203	PRK	Bacteria:16	COG1776, CheC, Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms].
CDD:224691	217	PRK	Bacteria:8	COG1777, COG1777, Predicted transcriptional regulators [Transcription].
CDD:224692	170	PRK	Bacteria:16	COG1778, COG1778, Low specificity phosphatase (HAD superfamily) [General function prediction only].
CDD:224693	201	EUKprk	Bacteria:12,Plants:2	COG1779, COG1779, C4-type Zn-finger protein [General function prediction only].
CDD:224694	141	PRK	Bacteria:17,nodiv:1	COG1780, NrdI, Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism].
CDD:224695	153	PRK	Bacteria:21	COG1781, PyrI, Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism].
CDD:224696	637	PRK	Bacteria:13	COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only].
CDD:224699	482	EUKprk	Bacteria:19,Plants:2	COG1785, PhoA, Alkaline phosphatase [Inorganic ion transport and metabolism].
CDD:224700	131	PRK	Bacteria:10	COG1786, COG1786, Swiveling domain associated with predicted aconitase [Energy    production and conversion].
CDD:224702	220	PRK	Bacteria:21,nodiv:1	COG1788, AtoD, Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism].
CDD:224705	284	PRK	Bacteria:31	COG1792, MreC, Cell shape-determining protein [Cell envelope biogenesis, outer membrane].
CDD:224706	444	EUKprk	Bacteria:28,Plants:4,nodiv:1	COG1793, CDC9, ATP-dependent DNA ligase [DNA replication, recombination, and repair].
CDD:224707	230	PRK	Bacteria:16,nodiv:1	COG1794, RacX, Aspartate racemase [Cell envelope biogenesis, outer membrane].
CDD:224709	326	EUK	Plants:2	COG1796, POL4, DNA polymerase IV (family X) [DNA replication, recombination, and repair].
CDD:224710	451	PRK	Bacteria:24,nodiv:1	COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism].
CDD:224711	260	EUKprk	Bacteria:13,Plants:3	COG1798, DPH5, Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis].
CDD:224712	167	PRK	Bacteria:15	COG1799, COG1799, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224713	335	PRK	Bacteria:3	COG1800, COG1800, Predicted transglutaminase-like proteases [General function prediction only].
CDD:224714	263	PRK	Bacteria:28,nodiv:1	COG1801, COG1801, Uncharacterized conserved protein [Function unknown].
CDD:224715	230	PRK	Bacteria:31,nodiv:1	COG1802, GntR, Transcriptional regulators [Transcription].
CDD:224716	142	PRK	Bacteria:16,nodiv:2	COG1803, MgsA, Methylglyoxal synthase [Carbohydrate transport and metabolism].
CDD:224717	396	PRK	Bacteria:19,nodiv:1	COG1804, CaiB, Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion].
CDD:224719	273	PRK	Bacteria:20,nodiv:1	COG1806, COG1806, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224720	535	PRK	Bacteria:24,nodiv:1	COG1807, ArnT, 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane].
CDD:224721	334	PRK	Bacteria:8	COG1808, COG1808, Predicted membrane protein [Function unknown].
CDD:224723	224	PRK	Bacteria:5	COG1810, COG1810, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224724	228	PRK	Bacteria:12	COG1811, COG1811, Uncharacterized membrane protein, possible Na+ channel or pump [General function prediction only].
CDD:224725	400	PRK	Bacteria:15	COG1812, MetK, Archaeal S-adenosylmethionine synthetase [Amino acid transport and metabolism].
CDD:224726	165	EUKprk	Bacteria:13,Plants:3	COG1813, COG1813, Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription].
CDD:224727	229	EUKprk	Bacteria:19,Plants:2	COG1814, COG1814, Uncharacterized membrane protein [Function unknown].
CDD:224728	133	PRK	Bacteria:24,nodiv:1	COG1815, FlgB, Flagellar basal body protein [Cell motility and secretion].
CDD:224729	345	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG1816, Add, Adenosine deaminase [Nucleotide transport and metabolism].
CDD:224731	175	EUKprk	Bacteria:10,Plants:1	COG1818, COG1818, Predicted RNA-binding protein, contains THUMP domain [General function prediction only].
CDD:224732	406	EUKprk	Bacteria:18,Plants:1	COG1819, COG1819, Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms].
CDD:224733	380	PRK	Bacteria:32,nodiv:1	COG1820, NagA, N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism].
CDD:224735	349	PRK	Bacteria:4	COG1822, COG1822, Predicted archaeal membrane protein [Function unknown].
CDD:224737	203	PRK	Bacteria:8	COG1824, COG1824, Permease, similar to cation transporters [Inorganic ion transport and metabolism].
CDD:224738	93	PRK	Bacteria:37,nodiv:1	COG1825, RplY, Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis].
CDD:224739	94	PRK	Bacteria:45,nodiv:2	COG1826, TatA, Sec-independent protein secretion pathway components [Intracellular trafficking and secretion].
CDD:224740	168	PRK	Bacteria:10	COG1827, COG1827, Predicted small molecule binding protein (contains 3H domain) [General function prediction only].
CDD:224741	83	PRK	Bacteria:31	COG1828, PurS, Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component [Nucleotide transport and metabolism].
CDD:224742	283	PRK	Bacteria:11	COG1829, COG1829, Predicted archaeal kinase (sugar kinase superfamily) [General function prediction only].
CDD:224743	265	PRK	Bacteria:23,nodiv:1	COG1830, FbaB, DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism].
CDD:224744	285	PRK	Bacteria:12	COG1831, COG1831, Predicted metal-dependent hydrolase (urease superfamily) [General function prediction only].
CDD:224745	140	PRK	Bacteria:26,nodiv:1	COG1832, COG1832, Predicted CoA-binding protein [General function prediction only].
CDD:224746	132	PRK	Bacteria:11	COG1833, COG1833, Uri superfamily endonuclease [Replication, recombination, and    repair].
CDD:224747	267	PRK	Bacteria:12	COG1834, COG1834, N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism].
CDD:224748	386	PRK	Bacteria:28,nodiv:1	COG1835, COG1835, Predicted acyltransferases [Lipid metabolism].
CDD:224749	247	PRK	Bacteria:13	COG1836, COG1836, Predicted membrane protein [Function unknown].
CDD:224750	76	PRK	Bacteria:23	COG1837, COG1837, Predicted RNA-binding protein (contains KH domain) [General function prediction only].
CDD:224751	184	PRK	Bacteria:26	COG1838, FumA, Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion].
CDD:224753	299	PRK	Bacteria:29,nodiv:2	COG1840, AfuA, ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:224754	55	EUKprk	Bacteria:47,Plants:3,nodiv:1	COG1841, RpmD, Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis].
CDD:224755	225	PRK	Bacteria:22	COG1842, PspA, Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms].
CDD:224756	222	PRK	Bacteria:23,nodiv:2	COG1843, FlgD, Flagellar hook capping protein [Cell motility and secretion].
CDD:224758	209	EUKprk	Bacteria:25,Plants:1,nodiv:1	COG1845, CyoC, Heme/copper-type cytochrome/quinol oxidase, subunit 3 [Energy production and conversion].
CDD:224759	126	PRK	Bacteria:46,nodiv:3	COG1846, MarR, Transcriptional regulators [Transcription].
CDD:224760	208	PRK	Bacteria:17	COG1847, Jag, Predicted RNA-binding protein [General function prediction only].
CDD:224761	140	PRK	Bacteria:12	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only].
CDD:224762	90	PRK	Bacteria:10	COG1849, COG1849, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224763	429	PRK	Bacteria:10	COG1850, RbcL, Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism].
CDD:224766	176	EUKprk	Bacteria:44,Plants:1,nodiv:1	COG1853, COG1853, Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only].
CDD:224767	161	PRK	Bacteria:22	COG1854, LuxS, LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms].
CDD:224768	604	PRK	Bacteria:13	COG1855, COG1855, ATPase (PilT family) [General function prediction only].
CDD:224770	334	PRK	Bacteria:11	COG1857, COG1857, CRISPR system related protein [Defense mechanisms].
CDD:224771	364	PRK	Bacteria:16,nodiv:1	COG1858, MauG, Cytochrome c peroxidase [Inorganic ion transport and metabolism].
CDD:224772	211	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG1859, KptA, RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis].
CDD:224773	147	PRK	Bacteria:9	COG1860, COG1860, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224775	97	PRK	Bacteria:38,nodiv:1	COG1862, YajC, Preprotein translocase subunit YajC [Intracellular trafficking and secretion].
CDD:224776	158	PRK	Bacteria:19,nodiv:1	COG1863, MnhE, Multisubunit Na+/H+ antiporter, MnhE subunit [Inorganic ion transport and metabolism].
CDD:224777	281	EUKprk	Bacteria:9,Plants:2	COG1864, NUC1, DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism].
CDD:224778	200	PRK	Bacteria:9	COG1865, cbiZ, Adenosylcobinamide amidohydrolase [Coenzyme metabolism].
CDD:224779	529	EUKprk	Bacteria:17,Plants:1,nodiv:1	COG1866, PckA, Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion].
CDD:224780	380	EUKprk	Bacteria:14,Plants:3	COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis].
CDD:224781	332	PRK	Bacteria:23,nodiv:1	COG1868, FliM, Flagellar motor switch protein [Cell motility and secretion].
CDD:224782	135	PRK	Bacteria:15	COG1869, RbsD, ABC-type ribose transport system, auxiliary component [Carbohydrate transport and metabolism].
CDD:224783	164	PRK	Bacteria:15,nodiv:1	COG1871, CheD, Chemotaxis protein; stimulates methylation of MCP proteins [Cell motility and secretion / Signal transduction mechanisms].
CDD:224784	102	PRK	Bacteria:22,nodiv:1	COG1872, COG1872, Uncharacterized conserved protein [Function unknown].
CDD:224785	87	PRK	Bacteria:13	COG1873, COG1873, Protein implicated in RNA metabolism, contains PRC-barrel domain [General    function prediction only].
CDD:224786	673	PRK	Bacteria:11	COG1874, LacA, Beta-galactosidase [Carbohydrate transport and metabolism].
CDD:224787	436	PRK	Bacteria:13	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only].
CDD:224788	241	PRK	Bacteria:16	COG1876, VanY, D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane].
CDD:224789	266	PRK	Bacteria:10	COG1877, OtsB, Trehalose-6-phosphatase [Carbohydrate transport and metabolism].
CDD:224790	218	PRK	Bacteria:24,nodiv:1	COG1878, COG1878, Kynurenine formamidase [Amino acid transport and metabolism].
CDD:224791	322	PRK	Bacteria:26,nodiv:2	COG1879, RbsB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism].
CDD:224793	174	EUKprk	Bacteria:36,Plants:1,nodiv:1	COG1881, COG1881, Phospholipid-binding protein [General function prediction only].
CDD:224794	755	PRK	Bacteria:20	COG1882, PflD, Pyruvate-formate lyase [Energy production and conversion].
CDD:224796	548	PRK	Bacteria:19,nodiv:1	COG1884, Sbm, Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism].
CDD:224798	136	PRK	Bacteria:23,nodiv:1	COG1886, FliN, Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224799	388	PRK	Bacteria:8	COG1887, TagB, Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane].
CDD:224801	231	EUKprk	Bacteria:13,Plants:3	COG1889, NOP1, Fibrillarin-like rRNA methylase [Translation, ribosomal structure and biogenesis].
CDD:224802	214	EUKprk	Bacteria:13,Plants:3	COG1890, RPS1A, Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis].
CDD:224804	488	PRK	Bacteria:9	COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate transport and    metabolism; Energy production and conversion].
CDD:224805	307	EUKprk	Bacteria:27,Plants:3	COG1893, ApbA, Ketopantoate reductase [Coenzyme metabolism].
CDD:224806	424	EUKprk	Bacteria:23,Plants:1,nodiv:1	COG1894, NuoF, NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion].
CDD:224808	193	EUKprk	Bacteria:25,Plants:2,nodiv:1	COG1896, COG1896, Predicted hydrolases of HD superfamily [General function prediction only].
CDD:224809	307	PRK	Bacteria:14,nodiv:1	COG1897, MetA, Homoserine trans-succinylase [Amino acid transport and metabolism].
CDD:224810	173	PRK	Bacteria:33,nodiv:1	COG1898, RfbC, dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane].
CDD:224811	318	EUKprk	Bacteria:15,Plants:3	COG1899, DYS1, Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones].
CDD:224813	197	PRK	Bacteria:10	COG1901, COG1901, Uncharacterized conserved protein [Function unknown].
CDD:224814	363	EUKprk	Bacteria:31,Plants:2,nodiv:1	COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion].
CDD:224815	367	PRK	Bacteria:18,nodiv:1	COG1903, CbiD, Cobalamin biosynthesis protein CbiD [Coenzyme metabolism].
CDD:224816	463	PRK	Bacteria:15	COG1904, UxaC, Glucuronate isomerase [Carbohydrate transport and metabolism].
CDD:224817	160	EUKprk	Bacteria:23,Plants:1,nodiv:2	COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion].
CDD:224819	312	PRK	Bacteria:9	COG1907, COG1907, Predicted archaeal sugar kinases [General function prediction only].
CDD:224821	167	PRK	Bacteria:12	COG1909, COG1909, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224822	223	PRK	Bacteria:5	COG1910, COG1910, Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism].
CDD:224823	100	EUKprk	Bacteria:10,Plants:3	COG1911, RPL30, Ribosomal protein L30E [Translation, ribosomal structure and biogenesis].
CDD:224824	268	PRK	Bacteria:20	COG1912, COG1912, Uncharacterized conserved protein [Function unknown].
CDD:224825	181	PRK	Bacteria:10	COG1913, COG1913, Predicted Zn-dependent proteases [General function prediction only].
CDD:224826	416	EUKprk	Bacteria:32,Plants:2,nodiv:1	COG1914, MntH, Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism].
CDD:224828	388	PRK	Bacteria:11	COG1916, COG1916, Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown].
CDD:224829	131	PRK	Bacteria:33,nodiv:1	COG1917, COG1917, Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown].
CDD:224830	75	PRK	Bacteria:23	COG1918, FeoA, Fe2+ transport system protein A [Inorganic ion transport and metabolism].
CDD:224831	210	PRK	Bacteria:9	COG1920, COG1920, Predicted nucleotidyltransferase, CobY/MobA/RfbA family [General function prediction only].
CDD:224832	395	PRK	Bacteria:16,nodiv:1	COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism].
CDD:224833	253	PRK	Bacteria:18,nodiv:1	COG1922, WecG, Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane].
CDD:224834	77	PRK	Bacteria:21,nodiv:1	COG1923, Hfq, Uncharacterized host factor I protein [General function prediction only].
CDD:224835	396	PRK	Bacteria:14	COG1924, COG1924, Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism].
CDD:224836	88	PRK	Bacteria:37,nodiv:1	COG1925, FruB, Phosphotransferase system, HPr-related proteins [Carbohydrate transport and metabolism].
CDD:224837	220	PRK	Bacteria:12	COG1926, COG1926, Predicted phosphoribosyltransferases [General function prediction only].
CDD:224839	699	EUKprk	Bacteria:5,Plants:4	COG1928, PMT1, Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones].
CDD:224840	378	PRK	Bacteria:24	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism].
CDD:224842	140	PRK	Bacteria:10	COG1931, COG1931, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224843	365	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG1932, SerC, Phosphoserine aminotransferase [Coenzyme metabolism / Amino acid transport and metabolism].
CDD:224845	173	PRK	Bacteria:21,nodiv:1	COG1934, COG1934, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224847	180	EUKprk	Bacteria:13,Plants:3	COG1936, COG1936, Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism].
CDD:224848	89	PRK	Bacteria:22,nodiv:1	COG1937, COG1937, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224849	244	PRK	Bacteria:13	COG1938, COG1938, Archaeal enzymes of ATP-grasp superfamily [General function prediction only].
CDD:224850	132	PRK	Bacteria:12	COG1939, COG1939, Ribonuclease III family protein [Replication, recombination, and    repair].
CDD:224851	314	PRK	Bacteria:43,nodiv:1	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism].
CDD:224852	247	PRK	Bacteria:9	COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion].
CDD:224853	69	PRK	Bacteria:25,nodiv:1	COG1942, COG1942, Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only].
CDD:224854	136	PRK	Bacteria:28,nodiv:1	COG1943, COG1943, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:224855	398	PRK	Bacteria:16,nodiv:1	COG1944, COG1944, Uncharacterized conserved protein [Function unknown].
CDD:224856	163	PRK	Bacteria:12	COG1945, COG1945, Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid    transport and metabolism].
CDD:224857	289	EUKprk	Bacteria:16,Plants:2,nodiv:1	COG1946, TesB, Acyl-CoA thioesterase [Lipid metabolism].
CDD:224858	289	PRK	Bacteria:37,nodiv:1	COG1947, IspE, 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase [Lipid metabolism].
CDD:224859	254	EUKprk	Bacteria:4,Plants:3	COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair].
CDD:224860	184	EUKprk	Bacteria:16,Plants:2,nodiv:1	COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification].
CDD:224861	120	PRK	Bacteria:11	COG1950, COG1950, Predicted membrane protein [Function unknown].
CDD:224862	297	PRK	Bacteria:15	COG1951, TtdA, Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion].
CDD:224863	157	PRK	Bacteria:19,nodiv:1	COG1952, SecB, Preprotein translocase subunit SecB [Intracellular trafficking and secretion].
CDD:224864	497	EUKprk	Bacteria:14,Plants:2	COG1953, FUI1, Cytosine/uracil/thiamine/allantoin permeases [Nucleotide transport and metabolism / Coenzyme metabolism].
CDD:224865	181	PRK	Bacteria:10	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription].
CDD:224866	527	PRK	Bacteria:10	COG1955, FlaJ, Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224867	163	EUKprk	Bacteria:25,Plants:1	COG1956, COG1956, GAF domain-containing protein [Signal transduction mechanisms].
CDD:224868	311	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG1957, URH1, Inosine-uridine nucleoside N-ribohydrolase [Nucleotide transport and metabolism].
CDD:224869	79	EUKprk	Bacteria:14,Plants:4	COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription].
CDD:224870	150	PRK	Bacteria:34,nodiv:1	COG1959, COG1959, Predicted transcriptional regulator [Transcription].
CDD:224871	393	EUKprk	Bacteria:35,Plants:1,nodiv:1	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism].
CDD:224872	222	PRK	Bacteria:31,nodiv:2	COG1961, PinR, Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair].
CDD:224874	153	PRK	Bacteria:10	COG1963, COG1963, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224875	475	PRK	Bacteria:11	COG1964, COG1964, Predicted Fe-S oxidoreductases [General function prediction only].
CDD:224876	106	EUKprk	Bacteria:14,Plants:3	COG1965, CyaY, Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism].
CDD:224877	575	PRK	Bacteria:28	COG1966, CstA, Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms].
CDD:224878	271	PRK	Bacteria:7	COG1967, COG1967, Predicted membrane protein [Function unknown].
CDD:224879	270	PRK	Bacteria:38,nodiv:1	COG1968, BacA, Undecaprenyl pyrophosphate phosphatase [Lipid transport and metabolism].
CDD:224881	130	PRK	Bacteria:25,nodiv:2	COG1970, MscL, Large-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].
CDD:224882	190	PRK	Bacteria:17	COG1971, COG1971, Predicted membrane protein [Function unknown].
CDD:224883	404	PRK	Bacteria:18	COG1972, NupC, Nucleoside permease [Nucleotide transport and metabolism].
CDD:224885	201	PRK	Bacteria:28,nodiv:2	COG1974, LexA, SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms].
CDD:224886	278	PRK	Bacteria:17,nodiv:1	COG1975, XdhC, Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones].
CDD:224887	222	EUKprk	Bacteria:13,Plants:3	COG1976, TIF6, Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis].
CDD:224888	84	PRK	Bacteria:35,nodiv:1	COG1977, MoaD, Molybdopterin converting factor, small subunit [Coenzyme metabolism].
CDD:224890	384	PRK	Bacteria:14	COG1979, COG1979, Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion].
CDD:224892	149	PRK	Bacteria:16,nodiv:1	COG1981, COG1981, Predicted membrane protein [Function unknown].
CDD:224893	557	PRK	Bacteria:25,nodiv:1	COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism].
CDD:224894	70	PRK	Bacteria:16	COG1983, PspC, Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms].
CDD:224895	314	PRK	Bacteria:23,nodiv:1	COG1984, DUR1, Allophanate hydrolase subunit 2 [Amino acid transport and metabolism].
CDD:224896	218	EUKprk	Bacteria:18,Plants:2	COG1985, RibD, Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism].
CDD:224897	175	PRK	Bacteria:14	COG1986, COG1986, Inosine/xanthosine triphosphatase [Nucleotide transport and    metabolism].
CDD:224898	89	PRK	Bacteria:20,nodiv:2	COG1987, FliQ, Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224899	190	PRK	Bacteria:22	COG1988, COG1988, Predicted membrane-bound metal-dependent hydrolases [General function prediction only].
CDD:224900	254	PRK	Bacteria:41	COG1989, PulO, Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:224901	122	EUKprk	Bacteria:14,Plants:3	COG1990, pth2, Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis].
CDD:224902	131	PRK	Bacteria:5	COG1991, COG1991, Uncharacterized conserved protein [Function unknown].
CDD:224903	181	PRK	Bacteria:7	COG1992, COG1992, Uncharacterized conserved protein [Function unknown].
CDD:224904	109	PRK	Bacteria:11	COG1993, COG1993, PII-like signaling protein [Signal transduction mechanisms].
CDD:224905	230	PRK	Bacteria:28	COG1994, SpoIVFB, Zn-dependent proteases [General function prediction only].
CDD:224906	332	PRK	Bacteria:23,nodiv:1	COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme metabolism].
CDD:224907	49	EUKprk	Bacteria:14,Plants:2	COG1996, RPC10, DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription].
CDD:224908	89	EUKprk	Bacteria:13,Plants:3	COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis].
CDD:224909	51	EUKprk	Bacteria:13,Plants:2	COG1998, RPS31, Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis].
CDD:224910	207	EUKprk	Bacteria:20,Plants:2,nodiv:1	COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only].
CDD:224912	146	PRK	Bacteria:29	COG2001, COG2001, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:224913	89	PRK	Bacteria:21,nodiv:1	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription].
CDD:224914	224	PRK	Bacteria:31,nodiv:1	COG2003, RadC, DNA repair proteins [DNA replication, recombination, and repair].
CDD:224915	107	EUKprk	Bacteria:13,Plants:3	COG2004, RPS24A, Ribosomal protein S24E [Translation, ribosomal structure and biogenesis].
CDD:224916	130	PRK	Bacteria:17,nodiv:1	COG2005, ModE, N-terminal domain of molybdenum-binding protein [General function prediction only].
CDD:224917	293	PRK	Bacteria:4	COG2006, COG2006, Uncharacterized conserved protein [Function unknown].
CDD:224918	127	EUKprk	Bacteria:13,Plants:3	COG2007, RPS8A, Ribosomal protein S8E [Translation, ribosomal structure and biogenesis].
CDD:224919	342	EUKprk	Bacteria:21,Plants:2,nodiv:1	COG2008, GLY1, Threonine aldolase [Amino acid transport and metabolism].
CDD:224920	132	EUKprk	Bacteria:32,Plants:2,nodiv:2	COG2009, SdhC, Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion].
CDD:224921	150	PRK	Bacteria:23,nodiv:1	COG2010, CccA, Cytochrome c, mono- and diheme variants [Energy production and conversion].
CDD:224922	222	PRK	Bacteria:33,nodiv:1	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism].
CDD:224923	80	EUKprk	Bacteria:13,Plants:3	COG2012, RPB5, DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription].
CDD:224924	227	PRK	Bacteria:19	COG2013, COG2013, Uncharacterized conserved protein [Function unknown].
CDD:224927	161	EUKprk	Bacteria:13,Plants:3	COG2016, COG2016, Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis].
CDD:224928	308	EUKprk	Bacteria:31,Plants:1,nodiv:1	COG2017, GalM, Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism].
CDD:224929	119	PRK	Bacteria:10	COG2018, COG2018, Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only].
CDD:224930	189	PRK	Bacteria:11	COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and metabolism].
CDD:224931	187	EUKprk	Bacteria:17,Plants:3	COG2020, STE14, Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones].
CDD:224932	368	EUKprk	Bacteria:18,Plants:2	COG2021, MET2, Homoserine acetyltransferase [Amino acid transport and metabolism].
CDD:224933	262	PRK	Bacteria:26,nodiv:1	COG2022, ThiG, Uncharacterized enzyme of thiazole biosynthesis [Nucleotide transport and metabolism].
CDD:224934	105	EUKprk	Bacteria:12,Plants:3	COG2023, RPR2, RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis].
CDD:224936	313	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion].
CDD:224937	90	PRK	Bacteria:17,nodiv:1	COG2026, RelE, Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning].
CDD:224938	470	PRK	Bacteria:22	COG2027, DacB, D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane].
CDD:224941	159	PRK	Bacteria:20,nodiv:1	COG2030, MaoC, Acyl dehydratase [Lipid metabolism].
CDD:224942	446	PRK	Bacteria:11	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism].
CDD:224943	179	EUKprk	Bacteria:21,Plants:2	COG2032, SodC, Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism].
CDD:224944	126	PRK	Bacteria:9	COG2033, COG2033, Desulfoferrodoxin [Energy production and conversion].
CDD:224945	85	PRK	Bacteria:11	COG2034, COG2034, Predicted membrane protein [Function unknown].
CDD:224946	276	PRK	Bacteria:12	COG2035, COG2035, Predicted membrane protein [Function unknown].
CDD:224947	91	EUKprk	Bacteria:10,Plants:4	COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics].
CDD:224949	347	PRK	Bacteria:33,nodiv:1	COG2038, CobT, NaMN:DMB phosphoribosyltransferase [Coenzyme metabolism].
CDD:224950	207	PRK	Bacteria:14	COG2039, Pcp, Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones].
CDD:224951	300	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG2040, MHT1, Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism].
CDD:224952	271	PRK	Bacteria:28,nodiv:2	COG2041, COG2041, Sulfite oxidase and related enzymes [General function prediction only].
CDD:224953	179	EUKprk	Bacteria:8,Plants:3	COG2042, COG2042, Uncharacterized conserved protein [Function unknown].
CDD:224954	237	PRK	Bacteria:5	COG2043, COG2043, Uncharacterized protein conserved in archaea [Function unknown].
CDD:224955	120	PRK	Bacteria:5	COG2044, COG2044, Predicted peroxiredoxins [General function prediction only].
CDD:224956	230	PRK	Bacteria:12	COG2045, COG2045, Phosphosulfolactate phosphohydrolase and related enzymes [Coenzyme metabolism / General function prediction only].
CDD:224957	397	EUKprk	Bacteria:11,Plants:2	COG2046, MET3, ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism].
CDD:224959	293	PRK	Bacteria:10	COG2048, HdrB, Heterodisulfide reductase, subunit B [Energy production and conversion].
CDD:224960	223	PRK	Bacteria:19,nodiv:1	COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid transport and metabolism].
CDD:224961	141	EUKprk	Bacteria:41,Plants:1,nodiv:1	COG2050, PaaI, HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis,    transport, and catabolism].
CDD:224962	67	EUKprk	Bacteria:13,Plants:3	COG2051, RPS27A, Ribosomal protein S27E [Translation, ribosomal structure and biogenesis].
CDD:224966	349	PRK	Bacteria:18,nodiv:1	COG2055, COG2055, Malate/L-lactate dehydrogenases [Energy production and conversion].
CDD:224967	444	PRK	Bacteria:12	COG2056, COG2056, Predicted permease [General function prediction only].
CDD:224968	225	PRK	Bacteria:20,nodiv:1	COG2057, AtoA, Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit [Lipid metabolism].
CDD:224969	109	EUKprk	Bacteria:13,Plants:3	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis].
CDD:224970	195	PRK	Bacteria:17,nodiv:1	COG2059, ChrA, Chromate transport protein ChrA [Inorganic ion transport and metabolism].
CDD:224971	560	PRK	Bacteria:20,nodiv:1	COG2060, KdpA, K+-transporting ATPase, A chain [Inorganic ion transport and metabolism].
CDD:224973	163	PRK	Bacteria:27,nodiv:1	COG2062, SixA, Phosphohistidine phosphatase SixA [Signal transduction mechanisms].
CDD:224974	230	PRK	Bacteria:15,nodiv:2	COG2063, FlgH, Flagellar basal body L-ring protein [Cell motility and secretion].
CDD:224975	320	PRK	Bacteria:23,nodiv:1	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:224976	179	PRK	Bacteria:17,nodiv:1	COG2065, PyrR, Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism].
CDD:224977	309	PRK	Bacteria:20,nodiv:1	COG2066, GlsA, Glutaminase [Amino acid transport and metabolism].
CDD:224978	440	PRK	Bacteria:20,nodiv:1	COG2067, FadL, Long-chain fatty acid transport protein [Lipid metabolism].
CDD:224979	199	PRK	Bacteria:15,nodiv:1	COG2068, COG2068, Uncharacterized MobA-related protein [General function prediction only].
CDD:224981	336	EUKprk	Bacteria:27,Plants:1,nodiv:1	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only].
CDD:224982	243	EUKprk	Bacteria:20,Plants:1,nodiv:1	COG2071, COG2071, Predicted glutamine amidotransferases [General function prediction only].
CDD:224983	443	EUKprk	Bacteria:13,Plants:2,nodiv:2	COG2072, TrkA, Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism].
CDD:224984	298	PRK	Bacteria:19,nodiv:1	COG2073, CbiG, Cobalamin biosynthesis protein CbiG [Coenzyme metabolism].
CDD:224985	299	PRK	Bacteria:8	COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport and metabolism].
CDD:224986	66	EUKprk	Bacteria:13,Plants:3	COG2075, RPL24A, Ribosomal protein L24E [Translation, ribosomal structure and biogenesis].
CDD:224987	106	PRK	Bacteria:27,nodiv:1	COG2076, EmrE, Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism].
CDD:224988	158	PRK	Bacteria:22	COG2077, Tpx, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones].
CDD:224989	203	EUKprk	Bacteria:16,Plants:2	COG2078, AMMECR1, Uncharacterized conserved protein [Function unknown].
CDD:224990	453	EUKprk	Bacteria:18,Plants:1,nodiv:1	COG2079, PrpD, Uncharacterized protein involved in propionate catabolism [General function prediction only].
CDD:224991	156	PRK	Bacteria:17,nodiv:1	COG2080, CoxS, Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion].
CDD:224992	408	PRK	Bacteria:23,nodiv:1	COG2081, COG2081, Predicted flavoproteins [General function prediction only].
CDD:224993	210	PRK	Bacteria:22,nodiv:1	COG2082, CobH, Precorrin isomerase [Coenzyme metabolism].
CDD:224995	286	PRK	Bacteria:37,nodiv:1	COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism].
CDD:224996	211	PRK	Bacteria:14,nodiv:1	COG2085, COG2085, Predicted dinucleotide-binding enzymes [General function prediction only].
CDD:224997	260	EUKprk	Bacteria:29,Plants:2,nodiv:1	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion].
CDD:224998	175	PRK	Bacteria:18,nodiv:1	COG2087, CobU, Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase [Coenzyme metabolism].
CDD:225000	347	PRK	Bacteria:11	COG2089, SpsE, Sialic acid synthase [Cell envelope biogenesis, outer membrane].
CDD:225001	141	PRK	Bacteria:10	COG2090, COG2090, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225002	223	EUKprk	Bacteria:16,Plants:2	COG2091, Sfp, Phosphopantetheinyl transferase [Coenzyme metabolism].
CDD:225003	88	EUKprk	Bacteria:13,Plants:2	COG2092, EFB1, Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis].
CDD:225004	64	PRK	Bacteria:13	COG2093, COG2093, DNA-directed RNA polymerase, subunit E'' [Transcription].
CDD:225005	200	EUKprk	Bacteria:15,Plants:1,nodiv:1	COG2094, Mpg, 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair].
CDD:225006	203	PRK	Bacteria:38,nodiv:2	COG2095, MarC, Multiple antibiotic transporter [Intracellular trafficking and secretion].
CDD:225007	184	PRK	Bacteria:24,nodiv:1	COG2096, COG2096, cob(I)alamin adenosyltransferase [Coenzyme transport and    metabolism].
CDD:225008	89	EUKprk	Bacteria:13,Plants:4	COG2097, RPL31A, Ribosomal protein L31E [Translation, ribosomal structure and biogenesis].
CDD:225010	257	PRK	Bacteria:13,nodiv:1	COG2099, CobK, Precorrin-6x reductase [Coenzyme metabolism].
CDD:225012	185	EUKprk	Bacteria:13,Plants:3	COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription].
CDD:225013	223	EUKprk	Bacteria:13,Plants:2	COG2102, COG2102, Predicted ATPases of PP-loop superfamily [General function prediction only].
CDD:225014	298	PRK	Bacteria:18	COG2103, COG2103, Predicted sugar phosphate isomerase [General function prediction only].
CDD:225015	68	PRK	Bacteria:33,nodiv:1	COG2104, ThiS, Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism].
CDD:225016	120	PRK	Bacteria:16	COG2105, COG2105, Uncharacterized conserved protein [Function unknown].
CDD:225017	272	EUKprk	Bacteria:9,Plants:2	COG2106, COG2106, Uncharacterized conserved protein [Function unknown].
CDD:225018	272	PRK	Bacteria:14	COG2107, COG2107, Predicted periplasmic solute-binding protein [General function prediction only].
CDD:225019	353	PRK	Bacteria:11	COG2108, COG2108, Uncharacterized conserved protein related to pyruvate formate-lyase activating enzyme [General function prediction only].
CDD:225020	198	PRK	Bacteria:25,nodiv:1	COG2109, BtuR, ATP:corrinoid adenosyltransferase [Coenzyme metabolism].
CDD:225021	179	EUKprk	Bacteria:25,Plants:1,nodiv:1	COG2110, COG2110, Predicted phosphatase homologous to the C-terminal domain of histone macroH2A1 [General function prediction only].
CDD:225022	162	PRK	Bacteria:18	COG2111, MnhB, Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism].
CDD:225023	201	PRK	Bacteria:8	COG2112, COG2112, Predicted Ser/Thr protein kinase [Signal transduction mechanisms].
CDD:225024	302	PRK	Bacteria:15,nodiv:1	COG2113, ProX, ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism].
CDD:225025	227	EUKprk	Bacteria:13,Plants:1,nodiv:1	COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms].
CDD:225027	265	EUKprk	Bacteria:19,Plants:1	COG2116, FocA, Formate/nitrite family of transporters [Inorganic ion transport and metabolism].
CDD:225029	116	EUKprk	Bacteria:13,Plants:2	COG2118, COG2118, DNA-binding protein [General function prediction only].
CDD:225030	190	EUKprk	Bacteria:10,Plants:2	COG2119, COG2119, Predicted membrane protein [Function unknown].
CDD:225031	237	EUKprk	Bacteria:19,Plants:3,nodiv:1	COG2120, COG2120, Uncharacterized proteins, LmbE homologs [Function unknown].
CDD:225032	214	PRK	Bacteria:10	COG2121, COG2121, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225034	272	EUKprk	Bacteria:11,Plants:3	COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis].
CDD:225035	411	EUKprk	Bacteria:19,Plants:2,nodiv:1	COG2124, CypX, Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225036	120	EUKprk	Bacteria:13,Plants:3	COG2125, RPS6A, Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis].
CDD:225038	107	PRK	Bacteria:23,nodiv:2	COG2127, COG2127, Uncharacterized conserved protein [Function unknown].
CDD:225039	177	PRK	Bacteria:27,nodiv:1	COG2128, COG2128, Uncharacterized conserved protein [Function unknown].
CDD:225040	226	PRK	Bacteria:12	COG2129, COG2129, Predicted phosphoesterases, related to the Icc protein [General function prediction only].
CDD:225041	340	EUKprk	Bacteria:12,Plants:2	COG2130, COG2130, Putative NADP-dependent oxidoreductases [General function prediction only].
CDD:225042	164	EUKprk	Bacteria:20,Plants:2	COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and metabolism].
CDD:225043	451	EUKprk	Bacteria:28,Plants:2,nodiv:2	COG2132, SufI, Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225044	399	PRK	Bacteria:19,nodiv:1	COG2133, COG2133, Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism].
CDD:225046	226	EUKprk	Bacteria:15,Plants:1,nodiv:1	COG2135, COG2135, Uncharacterized conserved protein [Function unknown].
CDD:225047	191	EUKprk	Bacteria:10,Plants:3	COG2136, IMP4, Predicted exosome subunit/U3 small nucleolar ribonucleoprotein (snoRNP) component, contains IMP4 domain [Translation, ribosomal structure and biogenesis / RNA processing and modification].
CDD:225048	174	PRK	Bacteria:28,nodiv:1	COG2137, OraA, Uncharacterized protein conserved in bacteria [General function prediction only].
CDD:225049	245	PRK	Bacteria:17	COG2138, COG2138, Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism].
CDD:225050	98	EUKprk	Bacteria:13,Plants:3	COG2139, RPL21A, Ribosomal protein L21E [Translation, ribosomal structure and biogenesis].
CDD:225051	209	PRK	Bacteria:11,nodiv:1	COG2140, COG2140, Thermophilic glucose-6-phosphate isomerase and related metalloenzymes [Carbohydrate transport and metabolism / General function prediction only].
CDD:225052	336	PRK	Bacteria:36,nodiv:2	COG2141, COG2141, Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion].
CDD:225053	117	PRK	Bacteria:25,nodiv:1	COG2142, SdhD, Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion].
CDD:225056	265	PRK	Bacteria:20,nodiv:1	COG2145, ThiM, Hydroxyethylthiazole kinase, sugar kinase family [Coenzyme metabolism].
CDD:225057	106	PRK	Bacteria:22,nodiv:2	COG2146, {NirD}, Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only].
CDD:225058	150	EUKprk	Bacteria:13,Plants:3	COG2147, RPL19A, Ribosomal protein L19E [Translation, ribosomal structure and biogenesis].
CDD:225059	226	PRK	Bacteria:27,nodiv:1	COG2148, WcaJ, Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane].
CDD:225061	167	PRK	Bacteria:8	COG2150, COG2150, Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only].
CDD:225062	111	PRK	Bacteria:31,nodiv:1	COG2151, PaaD, Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only].
CDD:225063	314	PRK	Bacteria:8	COG2152, COG2152, Predicted glycosylase [Carbohydrate transport and metabolism].
CDD:225064	155	EUKprk	Bacteria:12,Plants:1	COG2153, ElaA, Predicted acyltransferase [General function prediction only].
CDD:225065	101	EUKprk	Bacteria:18,Plants:2	COG2154, COG2154, Pterin-4a-carbinolamine dehydratase [Coenzyme metabolism].
CDD:225066	79	PRK	Bacteria:9	COG2155, COG2155, Uncharacterized conserved protein [Function unknown].
CDD:225067	190	PRK	Bacteria:20,nodiv:1	COG2156, KdpC, K+-transporting ATPase, c chain [Inorganic ion transport and metabolism].
CDD:225068	85	EUKprk	Bacteria:10,Plants:3	COG2157, RPL20A, Ribosomal protein L20A (L18A) [Translation, ribosomal structure and biogenesis].
CDD:225070	293	PRK	Bacteria:16,nodiv:1	COG2159, COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only].
CDD:225072	86	PRK	Bacteria:16,nodiv:1	COG2161, StbD, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning].
CDD:225073	275	PRK	Bacteria:12	COG2162, NhoA, Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225074	125	EUKprk	Bacteria:10,Plants:4	COG2163, RPL14A, Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis].
CDD:225076	149	PRK	Bacteria:31	COG2165, PulG, Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225077	144	PRK	Bacteria:21,nodiv:1	COG2166, sufE, Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones].
CDD:225078	51	EUKprk	Bacteria:12,Plants:3	COG2167, RPL39, Ribosomal protein L39E [Translation, ribosomal structure and biogenesis].
CDD:225079	96	PRK	Bacteria:12	COG2168, DsrH, Uncharacterized conserved protein involved in oxidation of intracellular sulfur [Inorganic ion transport and metabolism].
CDD:225080	187	PRK	Bacteria:5	COG2169, Ada, Adenosine deaminase [Nucleotide transport and metabolism].
CDD:225081	369	PRK	Bacteria:12	COG2170, COG2170, Uncharacterized conserved protein [Function unknown].
CDD:225082	271	PRK	Bacteria:36,nodiv:1	COG2171, DapD, Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism].
CDD:225083	146	PRK	Bacteria:13	COG2172, RsbW, Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms].
CDD:225084	211	PRK	Bacteria:10	COG2173, DdpX, D-alanyl-D-alanine dipeptidase [Cell envelope biogenesis, outer membrane].
CDD:225085	93	EUKprk	Bacteria:8,Plants:3	COG2174, RPL34A, Ribosomal protein L34E [Translation, ribosomal structure and biogenesis].
CDD:225086	286	EUKprk	Bacteria:9,Plants:2	COG2175, TauD, Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225087	1444	PRK	Bacteria:14	COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].
CDD:225088	297	PRK	Bacteria:29,nodiv:1	COG2177, FtsX, Cell division protein [Cell division and chromosome partitioning].
CDD:225089	204	EUKprk	Bacteria:9,Plants:1	COG2178, COG2178, Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis].
CDD:225090	175	PRK	Bacteria:11	COG2179, COG2179, Predicted hydrolase of the HAD superfamily [General function prediction only].
CDD:225091	179	PRK	Bacteria:16	COG2180, NarJ, Nitrate reductase delta subunit [Energy production and conversion].
CDD:225092	228	PRK	Bacteria:15	COG2181, NarI, Nitrate reductase gamma subunit [Energy production and conversion].
CDD:225093	420	PRK	Bacteria:19,nodiv:1	COG2182, MalE, Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism].
CDD:225094	780	EUKprk	Bacteria:29,Plants:3,nodiv:1	COG2183, Tex, Transcriptional accessory protein [Transcription].
CDD:225095	201	PRK	Bacteria:16,nodiv:1	COG2184, Fic, Protein involved in cell division [Cell division and chromosome partitioning].
CDD:225096	143	PRK	Bacteria:12	COG2185, Sbm, Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism].
CDD:225097	241	PRK	Bacteria:29,nodiv:3	COG2186, FadR, Transcriptional regulators [Transcription].
CDD:225099	236	PRK	Bacteria:29,nodiv:1	COG2188, PhnF, Transcriptional regulators [Transcription].
CDD:225100	590	PRK	Bacteria:16,nodiv:1	COG2189, COG2189, Adenine specific DNA methylase Mod [DNA replication, recombination, and repair].
CDD:225101	156	PRK	Bacteria:19,nodiv:1	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism].
CDD:225102	206	PRK	Bacteria:8	COG2191, COG2191, Formylmethanofuran dehydrogenase subunit E [Energy production and conversion].
CDD:225103	555	PRK	Bacteria:10	COG2192, COG2192, Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones].
CDD:225104	157	PRK	Bacteria:21,nodiv:1	COG2193, Bfr, Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism].
CDD:225105	555	PRK	Bacteria:20,nodiv:1	COG2194, COG2194, Predicted membrane-associated, metal-dependent hydrolase [General function prediction only].
CDD:225106	414	PRK	Bacteria:27	COG2195, PepD, Di- and tripeptidases [Amino acid transport and metabolism].
CDD:225107	211	PRK	Bacteria:33,nodiv:1	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription].
CDD:225108	122	EUKprk	Bacteria:8,Plants:2	COG2198, ArcB, FOG: HPt domain [Signal transduction mechanisms].
CDD:225109	181	PRK	Bacteria:29,nodiv:1	COG2199, COG2199, c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal    transduction mechanisms].
CDD:225110	256	PRK	Bacteria:25,nodiv:1	COG2200, Rtn, c-di-GMP phosphodiesterase class I (EAL domain) [Signal    transduction mechanisms].
CDD:225111	350	PRK	Bacteria:23,nodiv:1	COG2201, CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms].
CDD:225112	232	PRK	Bacteria:26,nodiv:1	COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms].
CDD:225113	175	PRK	Bacteria:11	COG2203, FhlA, FOG: GAF domain [Signal transduction mechanisms].
CDD:225114	464	PRK	Bacteria:29,nodiv:1	COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms].
CDD:225115	890	PRK	Bacteria:20,nodiv:1	COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms].
CDD:225116	344	PRK	Bacteria:11,nodiv:1	COG2206, COG2206, c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms].
CDD:225117	127	PRK	Bacteria:40,nodiv:2	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription].
CDD:225118	367	PRK	Bacteria:16	COG2208, RsbU, Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription].
CDD:225120	137	PRK	Bacteria:9	COG2210, COG2210, Peroxiredoxin family protein [General function prediction only].
CDD:225121	467	PRK	Bacteria:15	COG2211, MelB, Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism].
CDD:225122	89	PRK	Bacteria:18,nodiv:1	COG2212, MnhF, Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism].
CDD:225123	472	PRK	Bacteria:16	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism].
CDD:225124	237	EUKprk	Bacteria:25,Plants:5,nodiv:2	COG2214, CbpA, DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones].
CDD:225125	303	PRK	Bacteria:14,nodiv:1	COG2215, COG2215, ABC-type uncharacterized transport system, permease component [General function prediction only].
CDD:225126	681	PRK	Bacteria:22,nodiv:1	COG2216, KdpB, High-affinity K+ transport system, ATPase chain B [Inorganic ion transport and metabolism].
CDD:225127	713	EUKprk	Bacteria:56,Plants:2,nodiv:1	COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and metabolism].
CDD:225128	264	PRK	Bacteria:5	COG2218, FwdC, Formylmethanofuran dehydrogenase subunit C [Energy production and conversion].
CDD:225129	363	EUKprk	Bacteria:13,Plants:3	COG2219, PRI2, Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair].
CDD:225130	258	EUKprk	Bacteria:45,Plants:1,nodiv:1	COG2220, COG2220, Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only].
CDD:225131	317	PRK	Bacteria:6,nodiv:1	COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion].
CDD:225132	340	PRK	Bacteria:23,nodiv:1	COG2222, AgaS, Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane].
CDD:225133	417	PRK	Bacteria:17	COG2223, NarK, Nitrate/nitrite transporter [Inorganic ion transport and metabolism].
CDD:225134	433	EUKprk	Bacteria:19,Plants:2,nodiv:1	COG2224, AceA, Isocitrate lyase [Energy production and conversion].
CDD:225135	545	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG2225, AceB, Malate synthase [Energy production and conversion].
CDD:225136	238	EUKprk	Bacteria:40,Plants:2,nodiv:2	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].
CDD:225137	243	EUKprk	Bacteria:21,Plants:2,nodiv:1	COG2227, UbiG, 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism].
CDD:225138	187	EUKprk	Bacteria:9,Plants:2	COG2229, COG2229, Predicted GTPase [General function prediction only].
CDD:225139	283	PRK	Bacteria:24,nodiv:1	COG2230, Cfa, Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane].
CDD:225140	215	PRK	Bacteria:13	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair].
CDD:225142	451	EUKprk	Bacteria:30,Plants:1,nodiv:1	COG2233, UraA, Xanthine/uracil permeases [Nucleotide transport and metabolism].
CDD:225143	435	EUKprk	Bacteria:22,Plants:3	COG2234, Iap, Predicted aminopeptidases [General function prediction only].
CDD:225144	409	PRK	Bacteria:17	COG2235, ArcA, Arginine deiminase [Amino acid transport and metabolism].
CDD:225145	192	EUKprk	Bacteria:19,Plants:2	COG2236, COG2236, Predicted phosphoribosyltransferases [General function prediction only].
CDD:225146	364	PRK	Bacteria:11	COG2237, COG2237, Predicted membrane protein [Function unknown].
CDD:225147	147	EUKprk	Bacteria:13,Plants:3	COG2238, RPS19A, Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis].
CDD:225148	451	PRK	Bacteria:30,nodiv:1	COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism].
CDD:225149	281	EUKprk	Bacteria:18,Plants:2,nodiv:1	COG2240, PdxK, Pyridoxal/pyridoxine/pyridoxamine kinase [Coenzyme metabolism].
CDD:225150	210	PRK	Bacteria:20,nodiv:2	COG2241, CobL, Precorrin-6B methylase 1 [Coenzyme metabolism].
CDD:225151	187	PRK	Bacteria:16	COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
CDD:225152	234	PRK	Bacteria:21,nodiv:1	COG2243, CobF, Precorrin-2 methylase [Coenzyme metabolism].
CDD:225153	480	PRK	Bacteria:42,nodiv:1	COG2244, RfbX, Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only].
CDD:225155	139	PRK	Bacteria:23	COG2246, COG2246, Predicted membrane protein [Function unknown].
CDD:225156	337	PRK	Bacteria:4	COG2247, LytB, Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane].
CDD:225158	189	EUKprk	Bacteria:27,Plants:1	COG2249, MdaB, Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only].
CDD:225159	132	PRK	Bacteria:9	COG2250, COG2250, Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown].
CDD:225160	474	PRK	Bacteria:5	COG2251, COG2251, Predicted nuclease (RecB family) [General function prediction only].
CDD:225161	436	EUKprk	Bacteria:40,Plants:1	COG2252, COG2252, Xanthine/uracil/vitamin C permease [Nucleotide transport and    metabolism].
CDD:225163	230	PRK	Bacteria:7	COG2254, COG2254, Predicted HD superfamily hydrolase, possibly a nuclease [DNA replication, recombination, and repair].
CDD:225164	332	PRK	Bacteria:43,nodiv:2	COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair].
CDD:225165	436	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair].
CDD:225166	92	PRK	Bacteria:10	COG2257, COG2257, Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown].
CDD:225167	210	PRK	Bacteria:18,nodiv:1	COG2258, COG2258, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225168	142	EUKprk	Bacteria:28,Plants:2,nodiv:1	COG2259, COG2259, Predicted membrane protein [Function unknown].
CDD:225169	59	EUKprk	Bacteria:13,Plants:2	COG2260, COG2260, Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis].
CDD:225170	82	PRK	Bacteria:23,nodiv:1	COG2261, COG2261, Predicted membrane protein [Function unknown].
CDD:225171	411	PRK	Bacteria:45,nodiv:1	COG2262, HflX, GTPases [General function prediction only].
CDD:225172	198	EUKprk	Bacteria:13,Plants:1	COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal structure and biogenesis].
CDD:225173	300	PRK	Bacteria:33,nodiv:1	COG2264, PrmA, Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis].
CDD:225174	432	EUKprk	Bacteria:39,Plants:2,nodiv:1	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis].
CDD:225175	177	PRK	Bacteria:12	COG2266, COG2266, GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism].
CDD:225176	298	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG2267, PldB, Lysophospholipase [Lipid metabolism].
CDD:225177	548	PRK	Bacteria:12	COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225178	322	PRK	Bacteria:15,nodiv:1	COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis].
CDD:225179	438	EUKprk	Bacteria:13,Plants:2,nodiv:1	COG2270, COG2270, Permeases of the major facilitator superfamily [General function prediction only].
CDD:225180	448	PRK	Bacteria:19	COG2271, UhpC, Sugar phosphate permease [Carbohydrate transport and metabolism].
CDD:225181	491	EUKprk	Bacteria:10,Plants:1	COG2272, PnbA, Carboxylesterase type B [Lipid metabolism].
CDD:225182	355	EUKprk	Bacteria:9,Plants:2,nodiv:1	COG2273, SKN1, Beta-glucanase/Beta-glucan synthetase [Carbohydrate transport and metabolism].
CDD:225183	709	PRK	Bacteria:24	COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms].
CDD:225184	283	PRK	Bacteria:24,nodiv:1	COG2301, CitE, Citrate lyase beta subunit [Carbohydrate transport and metabolism].
CDD:225185	257	PRK	Bacteria:11	COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown].
CDD:225186	542	PRK	Bacteria:22,nodiv:1	COG2303, BetA, Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism].
CDD:225187	399	PRK	Bacteria:21	COG2304, COG2304, Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only].
CDD:225189	313	PRK	Bacteria:11,nodiv:1	COG2307, COG2307, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225190	488	PRK	Bacteria:10,nodiv:1	COG2308, COG2308, Uncharacterized conserved protein [Function unknown].
CDD:225191	385	PRK	Bacteria:15,nodiv:1	COG2309, AmpS, Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism].
CDD:225192	182	PRK	Bacteria:8	COG2310, TerZ, Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms].
CDD:225193	394	PRK	Bacteria:13	COG2311, COG2311, Predicted membrane protein [Function unknown].
CDD:225194	405	PRK	Bacteria:6	COG2312, COG2312, Erythromycin esterase homolog [General function prediction only].
CDD:225196	95	PRK	Bacteria:14	COG2314, XynA, Predicted membrane protein [Function unknown].
CDD:225197	118	PRK	Bacteria:15,nodiv:1	COG2315, MmcQ, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225199	497	PRK	Bacteria:15	COG2317, COG2317, Zn-dependent carboxypeptidase [Amino acid transport and metabolism].
CDD:225200	172	PRK	Bacteria:8,nodiv:1	COG2318, DinB, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225201	466	EUKprk	Bacteria:12,Plants:5,nodiv:1	COG2319, COG2319, FOG: WD40 repeat [General function prediction only].
CDD:225202	185	PRK	Bacteria:6	COG2320, GrpB, Uncharacterized conserved protein [Function unknown].
CDD:225203	295	PRK	Bacteria:15,nodiv:1	COG2321, COG2321, Predicted metalloprotease [General function prediction only].
CDD:225205	224	PRK	Bacteria:13	COG2323, COG2323, Predicted membrane protein [Function unknown].
CDD:225207	270	PRK	Bacteria:15,nodiv:1	COG2326, COG2326, Uncharacterized conserved protein [Function unknown].
CDD:225208	385	PRK	Bacteria:11,nodiv:1	COG2327, WcaK, Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis].
CDD:225209	105	PRK	Bacteria:18,nodiv:1	COG2329, COG2329, Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only].
CDD:225211	153	PRK	Bacteria:16,nodiv:1	COG2332, CcmE, Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones].
CDD:225212	293	PRK	Bacteria:8	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only].
CDD:225213	331	PRK	Bacteria:20,nodiv:1	COG2334, COG2334, Putative homoserine kinase type II (protein kinase fold) [General function prediction only].
CDD:225214	187	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG2335, COG2335, Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane].
CDD:225215	82	PRK	Bacteria:10,nodiv:1	COG2336, MazE, Growth regulator [Signal transduction mechanisms].
CDD:225216	112	PRK	Bacteria:20,nodiv:1	COG2337, MazF, Growth inhibitor [Signal transduction mechanisms].
CDD:225217	274	PRK	Bacteria:12	COG2339, prsW, Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones].
CDD:225218	207	EUKprk	Bacteria:16,Plants:2,nodiv:1	COG2340, COG2340, Uncharacterized protein with SCP/PR1 domains [Function unknown].
CDD:225219	300	PRK	Bacteria:6	COG2342, COG2342, Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism].
CDD:225220	132	PRK	Bacteria:8	COG2343, COG2343, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225221	211	PRK	Bacteria:10	COG2344, COG2344, AT-rich DNA-binding protein [General function prediction only].
CDD:225222	218	PRK	Bacteria:12	COG2345, COG2345, Predicted transcriptional regulator [Transcription].
CDD:225223	133	PRK	Bacteria:15,nodiv:1	COG2346, COG2346, Truncated hemoglobins [General function prediction only].
CDD:225224	418	PRK	Bacteria:9	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis].
CDD:225225	92	PRK	Bacteria:23,nodiv:1	COG2350, COG2350, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225226	124	EUKprk	Bacteria:13,Plants:1,nodiv:1	COG2351, COG2351, Transthyretin-like protein [General function prediction only].
CDD:225227	910	PRK	Bacteria:19	COG2352, Ppc, Phosphoenolpyruvate carboxylase [Energy production and conversion].
CDD:225228	192	PRK	Bacteria:23,nodiv:1	COG2353, COG2353, Uncharacterized conserved protein [Function unknown].
CDD:225230	313	EUKprk	Bacteria:16,Plants:1,nodiv:1	COG2355, COG2355, Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism].
CDD:225232	231	PRK	Bacteria:13	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only].
CDD:225233	321	PRK	Bacteria:13	COG2358, Imp, TRAP-type uncharacterized transport system, periplasmic component [General function prediction only].
CDD:225235	221	PRK	Bacteria:19,nodiv:1	COG2360, Aat, Leu/Phe-tRNA-protein transferase [Posttranslational modification, protein turnover, chaperones].
CDD:225236	117	PRK	Bacteria:6,nodiv:1	COG2361, COG2361, Uncharacterized conserved protein [Function unknown].
CDD:225238	124	EUKprk	Bacteria:17,Plants:1,nodiv:1	COG2363, COG2363, Uncharacterized small membrane protein [Function unknown].
CDD:225239	210	PRK	Bacteria:7	COG2364, COG2364, Predicted membrane protein [Function unknown].
CDD:225240	249	EUKprk	Bacteria:9,Plants:2,nodiv:1	COG2365, COG2365, Protein tyrosine/serine phosphatase [Signal transduction mechanisms].
CDD:225241	768	PRK	Bacteria:13	COG2366, COG2366, Protein related to penicillin acylase [General function prediction only].
CDD:225242	329	PRK	Bacteria:16,nodiv:1	COG2367, PenP, Beta-lactamase class A [Defense mechanisms].
CDD:225243	493	PRK	Bacteria:10	COG2368, COG2368, Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225244	432	PRK	Bacteria:8	COG2369, COG2369, Uncharacterized protein, homolog of phage Mu protein gp30 [Function unknown].
CDD:225246	155	PRK	Bacteria:18,nodiv:1	COG2371, UreE, Urease accessory protein UreE [Posttranslational modification, protein turnover, chaperones].
CDD:225247	127	PRK	Bacteria:9	COG2372, CopC, Uncharacterized protein, homolog of Cu resistance protein CopC [General function prediction only].
CDD:225248	1621	PRK	Bacteria:19,nodiv:1	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only].
CDD:225249	798	PRK	Bacteria:8	COG2374, COG2374, Predicted extracellular nuclease [General function prediction only].
CDD:225250	265	PRK	Bacteria:12,nodiv:1	COG2375, ViuB, Siderophore-interacting protein [Inorganic ion transport and metabolism].
CDD:225251	323	EUKprk	Bacteria:16,Plants:2,nodiv:1	COG2376, DAK1, Dihydroxyacetone kinase [Carbohydrate transport and metabolism].
CDD:225252	371	PRK	Bacteria:21,nodiv:1	COG2377, COG2377, Predicted molecular chaperone distantly related to HSP70-fold metalloproteases [Posttranslational modification, protein turnover, chaperones].
CDD:225253	311	PRK	Bacteria:23,nodiv:1	COG2378, COG2378, Predicted transcriptional regulator [Transcription].
CDD:225254	422	PRK	Bacteria:14,nodiv:1	COG2379, GckA, Putative glycerate kinase [Carbohydrate transport and metabolism].
CDD:225256	299	PRK	Bacteria:14	COG2382, Fes, Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism].
CDD:225258	226	PRK	Bacteria:13	COG2384, COG2384, Predicted SAM-dependent methyltransferase [General function prediction only].
CDD:225259	397	PRK	Bacteria:7	COG2385, SpoIID, Sporulation protein and related proteins [Cell division and chromosome partitioning].
CDD:225260	221	PRK	Bacteria:16,nodiv:1	COG2386, CcmB, ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones].
CDD:225261	99	PRK	Bacteria:18,nodiv:1	COG2388, COG2388, Predicted acetyltransferase [General function prediction only].
CDD:225263	321	PRK	Bacteria:22,nodiv:1	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription].
CDD:225264	198	PRK	Bacteria:22,nodiv:1	COG2391, COG2391, Predicted transporter component [General function prediction only].
CDD:225266	135	PRK	Bacteria:8	COG2402, COG2402, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only].
CDD:225268	339	PRK	Bacteria:9	COG2404, COG2404, Predicted phosphohydrolase (DHH superfamily) [General function prediction only].
CDD:225271	470	PRK	Bacteria:12	COG2407, FucI, L-fucose isomerase and related proteins [Carbohydrate transport and metabolism].
CDD:225272	937	PRK	Bacteria:15	COG2409, COG2409, Predicted drug exporters of the RND superfamily [General function prediction only].
CDD:225275	101	PRK	Bacteria:10	COG2412, COG2412, Uncharacterized conserved protein [Function unknown].
CDD:225277	614	PRK	Bacteria:13	COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy production and conversion].
CDD:225279	305	EUKprk	Bacteria:10,Plants:1	COG2421, COG2421, Predicted acetamidase/formamidase [Energy production and conversion].
CDD:225280	330	EUKprk	Bacteria:19,Plants:2,nodiv:2	COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism].
CDD:225281	437	PRK	Bacteria:12	COG2425, COG2425, Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only].
CDD:225283	148	PRK	Bacteria:9	COG2427, COG2427, Uncharacterized conserved protein [Function unknown].
CDD:225287	297	PRK	Bacteria:16	COG2431, COG2431, Predicted membrane protein [Function unknown].
CDD:225288	652	PRK	Bacteria:10	COG2433, COG2433, Uncharacterized conserved protein [Function unknown].
CDD:225289	99	PRK	Bacteria:14	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion].
CDD:225291	79	PRK	Bacteria:9	COG2442, COG2442, Uncharacterized conserved protein [Function unknown].
CDD:225292	65	EUKprk	Bacteria:11,Plants:3	COG2443, Sss1, Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion].
CDD:225293	138	PRK	Bacteria:10	COG2445, COG2445, Uncharacterized conserved protein [Function unknown].
CDD:225294	124	PRK	Bacteria:10	COG2450, COG2450, Uncharacterized conserved protein [Function unknown].
CDD:225296	193	PRK	Bacteria:10	COG2452, COG2452, Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair].
CDD:225297	180	EUKprk	Bacteria:11,Plants:2	COG2453, CDC14, Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].
CDD:225298	211	PRK	Bacteria:8	COG2454, COG2454, Uncharacterized conserved protein [Function unknown].
CDD:225300	199	PRK	Bacteria:8	COG2457, COG2457, Uncharacterized conserved protein [Function unknown].
CDD:225301	409	PRK	Bacteria:8	COG2461, COG2461, Uncharacterized conserved protein [Function unknown].
CDD:225303	73	PRK	Bacteria:23	COG2501, COG2501, S4-like RNA binding protein [Replication, recombination, and repair].
CDD:225306	421	PRK	Bacteria:15,nodiv:1	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225307	486	PRK	Bacteria:15	COG2509, COG2509, Uncharacterized FAD-dependent dehydrogenases [General function prediction only].
CDD:225308	140	PRK	Bacteria:11,nodiv:1	COG2510, COG2510, Predicted membrane protein [Function unknown].
CDD:225309	631	PRK	Bacteria:13	COG2511, GatE, Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis].
CDD:225310	258	PRK	Bacteria:9	COG2512, COG2512, Predicted membrane-associated trancriptional regulator    [Transcription].
CDD:225311	289	PRK	Bacteria:24	COG2513, PrpB, PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism].
CDD:225312	265	PRK	Bacteria:13,nodiv:1	COG2514, COG2514, Predicted ring-cleavage extradiol dioxygenase [General function prediction only].
CDD:225313	323	EUKprk	Bacteria:14,Plants:1	COG2515, Acd, 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism].
CDD:225316	209	EUKprk	Bacteria:28,Plants:1,nodiv:1	COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones].
CDD:225317	256	EUKprk	Bacteria:18,Plants:2	COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis].
CDD:225318	341	EUKprk	Bacteria:13,Plants:3	COG2520, COG2520, Predicted methyltransferase [General function prediction only].
CDD:225320	119	PRK	Bacteria:6	COG2522, COG2522, Predicted transcriptional regulator [General function prediction only].
CDD:225321	294	PRK	Bacteria:8	COG2524, COG2524, Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription].
CDD:225322	254	PRK	Bacteria:10,nodiv:1	COG2602, COG2602, Beta-lactamase class D [Defense mechanisms].
CDD:225324	594	PRK	Bacteria:5	COG2604, COG2604, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225325	333	PRK	Bacteria:7	COG2605, COG2605, Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only].
CDD:225326	155	PRK	Bacteria:29,nodiv:1	COG2606, EbsC, Uncharacterized conserved protein [Function unknown].
CDD:225327	287	PRK	Bacteria:13,nodiv:1	COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General function prediction only].
CDD:225328	71	EUKprk	Bacteria:33,Plants:2,nodiv:1	COG2608, CopZ, Copper chaperone [Inorganic ion transport and metabolism].
CDD:225329	887	PRK	Bacteria:18	COG2609, AceE, Pyruvate dehydrogenase complex, dehydrogenase (E1) component [Energy production and conversion].
CDD:225330	442	PRK	Bacteria:22	COG2610, GntT, H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism].
CDD:225331	144	PRK	Bacteria:6	COG2703, COG2703, Hemerythrin [Inorganic ion transport and metabolism].
CDD:225332	436	PRK	Bacteria:11	COG2704, DcuB, Anaerobic C4-dicarboxylate transporter [General function prediction only].
CDD:225333	346	EUKprk	Bacteria:14,Plants:1	COG2706, COG2706, 3-carboxymuconate cyclase [Carbohydrate transport and metabolism].
CDD:225335	456	PRK	Bacteria:10	COG2710, NifD, Nitrogenase molybdenum-iron protein, alpha and beta chains [Energy production and conversion].
CDD:225337	176	PRK	Bacteria:9	COG2716, GcvR, Glycine cleavage system regulatory protein [Amino acid transport and metabolism].
CDD:225338	209	PRK	Bacteria:15,nodiv:1	COG2717, COG2717, Predicted membrane protein [Function unknown].
CDD:225341	376	PRK	Bacteria:6	COG2720, COG2720, Uncharacterized vancomycin resistance protein [Defense mechanisms].
CDD:225342	381	PRK	Bacteria:16,nodiv:1	COG2721, UxaA, Altronate dehydratase [Carbohydrate transport and metabolism].
CDD:225343	460	PRK	Bacteria:23,nodiv:1	COG2723, BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism].
CDD:225344	407	EUKprk	Bacteria:9,Plants:2	COG2730, BglC, Endoglucanase [Carbohydrate transport and metabolism].
CDD:225345	154	PRK	Bacteria:16	COG2731, EbgC, Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism].
CDD:225347	415	PRK	Bacteria:10	COG2733, COG2733, Predicted membrane protein [Function unknown].
CDD:225349	105	PRK	Bacteria:12	COG2739, COG2739, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225350	95	PRK	Bacteria:23,nodiv:1	COG2740, COG2740, Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription].
CDD:225351	251	PRK	Bacteria:7	COG2746, COG2746, Aminoglycoside N3'-acetyltransferase [Defense mechanisms].
CDD:225352	93	PRK	Bacteria:13	COG2747, FlgM, Negative regulator of flagellin synthesis (anti-sigma28 factor) [Transcription / Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225353	216	EUKprk	Bacteria:31,Plants:2,nodiv:1	COG2755, TesA, Lysophospholipase L1 and related esterases [Amino acid transport and metabolism].
CDD:225354	554	PRK	Bacteria:16	COG2759, MIS1, Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism].
CDD:225355	225	PRK	Bacteria:16,nodiv:1	COG2761, FrnE, Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225356	136	PRK	Bacteria:18	COG2764, PhnB, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225359	83	PRK	Bacteria:4	COG2770, ResE, FOG: HAMP domain [Signal transduction mechanisms].
CDD:225360	65	PRK	Bacteria:24,nodiv:1	COG2771, CsgD, DNA-binding HTH domain-containing proteins [Transcription].
CDD:225361	232	EUKprk	Bacteria:37,Plants:4,nodiv:1	COG2801, Tra5, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225362	221	EUKprk	Bacteria:12,Plants:1,nodiv:1	COG2802, COG2802, Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only].
CDD:225363	500	PRK	Bacteria:32	COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225364	353	PRK	Bacteria:18	COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225365	395	PRK	Bacteria:14	COG2807, CynX, Cyanate permease [Inorganic ion transport and metabolism].
CDD:225366	209	EUKprk	Bacteria:8,Plants:1	COG2808, PaiB, Transcriptional regulator [Transcription].
CDD:225368	108	PRK	Bacteria:10	COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion].
CDD:225369	515	PRK	Bacteria:46,nodiv:1	COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair].
CDD:225370	300	PRK	Bacteria:29,nodiv:1	COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis].
CDD:225371	394	PRK	Bacteria:24,nodiv:1	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism].
CDD:225372	303	PRK	Bacteria:7	COG2815, COG2815, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225373	279	EUKprk	Bacteria:18,Plants:2,nodiv:1	COG2816, NPY1, NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair].
CDD:225374	188	PRK	Bacteria:24,nodiv:1	COG2818, Tag, 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair].
CDD:225375	264	PRK	Bacteria:12,nodiv:1	COG2819, COG2819, Predicted hydrolase of the alpha/beta superfamily [General function prediction only].
CDD:225376	248	PRK	Bacteria:14,nodiv:1	COG2820, Udp, Uridine phosphorylase [Nucleotide transport and metabolism].
CDD:225377	373	PRK	Bacteria:17,nodiv:1	COG2821, MltA, Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane].
CDD:225379	196	PRK	Bacteria:17	COG2823, OsmY, Predicted periplasmic or secreted lipoprotein [General function prediction only].
CDD:225380	112	PRK	Bacteria:22,nodiv:1	COG2824, PhnA, Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism].
CDD:225381	170	PRK	Bacteria:19,nodiv:1	COG2825, HlpA, Outer membrane protein [Cell envelope biogenesis, outer membrane].
CDD:225382	318	PRK	Bacteria:16,nodiv:1	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair].
CDD:225383	95	PRK	Bacteria:22	COG2827, COG2827, Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair].
CDD:225387	554	PRK	Bacteria:15	COG2831, FhaC, Hemolysin activation/secretion protein [Intracellular trafficking and secretion].
CDD:225388	119	PRK	Bacteria:14,nodiv:1	COG2832, COG2832, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225390	211	PRK	Bacteria:33,nodiv:1	COG2834, LolA, Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane].
CDD:225391	60	PRK	Bacteria:23	COG2835, COG2835, Uncharacterized conserved protein [Function unknown].
CDD:225392	232	PRK	Bacteria:9	COG2836, COG2836, Uncharacterized conserved protein [Function unknown].
CDD:225393	352	PRK	Bacteria:20	COG2837, COG2837, Predicted iron-dependent peroxidase [Inorganic ion transport and metabolism].
CDD:225396	184	PRK	Bacteria:20,nodiv:1	COG2840, COG2840, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225398	297	PRK	Bacteria:8	COG2842, COG2842, Uncharacterized ATPase, putative transposase [General function prediction only].
CDD:225399	372	PRK	Bacteria:13	COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane].
CDD:225400	867	PRK	Bacteria:17,nodiv:1	COG2844, GlnD, UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones].
CDD:225403	151	PRK	Bacteria:17,nodiv:1	COG2847, COG2847, Copper(I)-binding protein [Inorganic ion transport and    metabolism].
CDD:225404	445	PRK	Bacteria:13	COG2848, COG2848, Uncharacterized conserved protein [Function unknown].
CDD:225405	230	PRK	Bacteria:8	COG2849, COG2849, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225406	383	PRK	Bacteria:13	COG2850, COG2850, Uncharacterized conserved protein [Function unknown].
CDD:225407	433	PRK	Bacteria:11	COG2851, CitM, H+/citrate symporter [Energy production and conversion].
CDD:225408	129	PRK	Bacteria:9	COG2852, COG2852, Very-short-patch-repair endonuclease [Replication, recombination,    and repair].
CDD:225409	250	PRK	Bacteria:18	COG2853, VacJ, Surface lipoprotein [Cell envelope biogenesis, outer membrane].
CDD:225410	202	PRK	Bacteria:17	COG2854, Ttg2D, ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225411	334	PRK	Bacteria:23,nodiv:1	COG2855, COG2855, Predicted membrane protein [Function unknown].
CDD:225412	213	PRK	Bacteria:11	COG2856, COG2856, Predicted Zn peptidase [Amino acid transport and metabolism].
CDD:225413	250	EUKprk	Bacteria:16,Plants:2,nodiv:1	COG2857, CYT1, Cytochrome c1 [Energy production and conversion].
CDD:225415	209	PRK	Bacteria:26,nodiv:1	COG2860, COG2860, Predicted membrane protein [Function unknown].
CDD:225416	250	PRK	Bacteria:13,nodiv:1	COG2861, COG2861, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225417	169	PRK	Bacteria:15,nodiv:1	COG2862, COG2862, Predicted membrane protein [Function unknown].
CDD:225418	121	PRK	Bacteria:12	COG2863, COG2863, Cytochrome c553 [Energy production and conversion].
CDD:225419	218	PRK	Bacteria:13	COG2864, FdnI, Cytochrome b subunit of formate dehydrogenase [Energy production and conversion].
CDD:225420	467	PRK	Bacteria:7	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription].
CDD:225421	374	EUKprk	Bacteria:12,Plants:2	COG2866, COG2866, Predicted carboxypeptidase [Amino acid transport and metabolism].
CDD:225422	146	EUKprk	Bacteria:18,Plants:2,nodiv:1	COG2867, COG2867, Oligoketide cyclase/lipid transport protein [Lipid metabolism].
CDD:225423	109	PRK	Bacteria:14	COG2868, COG2868, Predicted ribosomal protein [Translation, ribosomal structure and biogenesis].
CDD:225425	467	PRK	Bacteria:20	COG2870, RfaE, ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane].
CDD:225427	241	EUKprk	Bacteria:19,Plants:1,nodiv:1	COG2872, COG2872, Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only].
CDD:225428	426	EUKprk	Bacteria:18,Plants:2,nodiv:1	COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism].
CDD:225429	235	PRK	Bacteria:10	COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225430	254	PRK	Bacteria:22,nodiv:2	COG2875, CobM, Precorrin-4 methylase [Coenzyme metabolism].
CDD:225431	286	PRK	Bacteria:15	COG2876, AroA, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism].
CDD:225432	279	PRK	Bacteria:24,nodiv:2	COG2877, KdsA, 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane].
CDD:225433	198	PRK	Bacteria:17	COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion].
CDD:225435	67	PRK	Bacteria:4	COG2880, COG2880, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225436	181	PRK	Bacteria:5	COG2881, COG2881, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225437	148	PRK	Bacteria:13,nodiv:1	COG2882, FliJ, Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones].
CDD:225438	223	PRK	Bacteria:26,nodiv:1	COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning].
CDD:225439	190	PRK	Bacteria:33,nodiv:1	COG2885, OmpA, Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane].
CDD:225440	88	PRK	Bacteria:8	COG2886, COG2886, Uncharacterized small protein [Function unknown].
CDD:225441	269	PRK	Bacteria:16,nodiv:1	COG2887, COG2887, RecB family exonuclease [DNA replication, recombination, and repair].
CDD:225442	61	PRK	Bacteria:13	COG2888, COG2888, Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis].
CDD:225443	280	EUKprk	Bacteria:60,Plants:3,nodiv:2	COG2890, HemK, Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis].
CDD:225444	167	PRK	Bacteria:17	COG2891, MreD, Cell shape-determining protein [Cell envelope biogenesis, outer membrane].
CDD:225445	82	PRK	Bacteria:8	COG2892, COG2892, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225446	143	PRK	Bacteria:23,nodiv:1	COG2893, ManX, Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism].
CDD:225447	272	PRK	Bacteria:25,nodiv:1	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning].
CDD:225448	431	PRK	Bacteria:14,nodiv:1	COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism].
CDD:225449	322	PRK	Bacteria:42,nodiv:1	COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism].
CDD:225450	285	EUKprk	Bacteria:25,Plants:2	COG2897, SseA, Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism].
CDD:225451	538	PRK	Bacteria:6	COG2898, COG2898, Uncharacterized conserved protein [Function unknown].
CDD:225453	72	PRK	Bacteria:13,nodiv:1	COG2900, SlyX, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225455	1592	EUKprk	Bacteria:12,Plants:2,nodiv:1	COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism].
CDD:225457	610	PRK	Bacteria:6	COG2905, COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms].
CDD:225458	63	PRK	Bacteria:12,nodiv:1	COG2906, Bfd, Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism].
CDD:225460	237	PRK	Bacteria:19,nodiv:1	COG2908, COG2908, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225461	894	PRK	Bacteria:8	COG2909, MalT, ATP-dependent transcriptional regulator [Transcription].
CDD:225462	211	PRK	Bacteria:10,nodiv:1	COG2910, COG2910, Putative NADH-flavin reductase [General function prediction only].
CDD:225463	1278	PRK	Bacteria:18,nodiv:1	COG2911, COG2911, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225464	269	PRK	Bacteria:11,nodiv:1	COG2912, COG2912, Uncharacterized conserved protein [Function unknown].
CDD:225465	147	PRK	Bacteria:20,nodiv:1	COG2913, OlmA, Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane].
CDD:225466	99	PRK	Bacteria:13	COG2914, COG2914, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225468	128	PRK	Bacteria:10,nodiv:1	COG2916, Hns, DNA-binding protein H-NS [General function prediction only].
CDD:225469	180	PRK	Bacteria:16,nodiv:1	COG2917, COG2917, Intracellular septation protein A [Cell division and chromosome partitioning].
CDD:225471	117	PRK	Bacteria:31,nodiv:1	COG2919, COG2919, Septum formation initiator [Cell division and chromosome partitioning].
CDD:225473	90	PRK	Bacteria:12	COG2921, COG2921, Uncharacterized conserved protein [Function unknown].
CDD:225475	118	PRK	Bacteria:13	COG2923, DsrF, Uncharacterized protein involved in the oxidation of intracellular sulfur [Inorganic ion transport and metabolism].
CDD:225479	144	PRK	Bacteria:19,nodiv:1	COG2927, HolC, DNA polymerase III, chi subunit [DNA replication, recombination, and repair].
CDD:225480	222	PRK	Bacteria:13,nodiv:1	COG2928, COG2928, Uncharacterized conserved protein [Function unknown].
CDD:225481	93	PRK	Bacteria:10	COG2929, COG2929, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225483	510	PRK	Bacteria:13,nodiv:1	COG2931, COG2931, RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225484	214	PRK	Bacteria:13,Phages:1,nodiv:1	COG2932, COG2932, Predicted transcriptional regulator [Transcription].
CDD:225486	253	EUKprk	Bacteria:9,Plants:2,nodiv:1	COG2935, COG2935, Putative arginyl-tRNA:protein arginylyltransferase [Posttranslational modification, protein turnover, chaperones].
CDD:225487	563	PRK	Bacteria:11	COG2936, COG2936, Predicted acyl esterases [General function prediction only].
CDD:225488	810	PRK	Bacteria:13	COG2937, PlsB, Glycerol-3-phosphate O-acyltransferase [Lipid metabolism].
CDD:225489	94	EUKprk	Bacteria:17,Plants:2,nodiv:1	COG2938, COG2938, Uncharacterized conserved protein [Function unknown].
CDD:225490	498	EUKprk	Bacteria:4,Plants:2	COG2939, COG2939, Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism].
CDD:225491	480	EUKprk	Bacteria:6,Plants:3	COG2940, COG2940, Proteins containing SET domain [General function prediction only].
CDD:225493	388	PRK	Bacteria:11,nodiv:1	COG2942, COG2942, N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism].
CDD:225495	104	PRK	Bacteria:12,nodiv:1	COG2944, COG2944, Predicted transcriptional regulator [Transcription].
CDD:225496	210	PRK	Bacteria:13,nodiv:1	COG2945, COG2945, Predicted hydrolase of the alpha/beta superfamily [General function prediction only].
CDD:225498	156	EUKprk	Bacteria:9,Plants:1,nodiv:1	COG2947, COG2947, Uncharacterized conserved protein [Function unknown].
CDD:225499	360	PRK	Bacteria:11,nodiv:1	COG2948, VirB10, Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion].
CDD:225500	235	PRK	Bacteria:11	COG2949, SanA, Uncharacterized membrane protein [Function unknown].
CDD:225501	343	PRK	Bacteria:19,nodiv:1	COG2951, MltB, Membrane-bound lytic murein transglycosylase B [Cell envelope biogenesis, outer membrane].
CDD:225503	156	PRK	Bacteria:7,nodiv:1	COG2954, COG2954, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225505	346	PRK	Bacteria:10	COG2957, COG2957, Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism].
CDD:225507	391	PRK	Bacteria:11	COG2959, HemX, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism].
CDD:225509	279	PRK	Bacteria:18,nodiv:1	COG2961, ComJ, Protein involved in catabolism of external DNA [General function prediction only].
CDD:225510	293	PRK	Bacteria:19,nodiv:1	COG2962, RarD, Predicted permeases [General function prediction only].
CDD:225511	116	PRK	Bacteria:26,nodiv:2	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225512	220	PRK	Bacteria:14	COG2964, COG2964, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225514	250	EUKprk	Bacteria:20,Plants:2	COG2966, COG2966, Uncharacterized conserved protein [Function unknown].
CDD:225515	126	PRK	Bacteria:12,nodiv:1	COG2967, ApaG, Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism].
CDD:225516	243	PRK	Bacteria:16,nodiv:1	COG2968, COG2968, Uncharacterized conserved protein [Function unknown].
CDD:225518	301	PRK	Bacteria:11	COG2971, COG2971, Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism].
CDD:225519	456	PRK	Bacteria:12	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms].
CDD:225523	207	PRK	Bacteria:14	COG2976, COG2976, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225524	228	PRK	Bacteria:12,nodiv:1	COG2977, EntD, Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225525	516	PRK	Bacteria:13	COG2978, AbgT, Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism].
CDD:225527	178	PRK	Bacteria:13	COG2980, RlpB, Rare lipoprotein B [Cell envelope biogenesis, outer membrane].
CDD:225528	250	PRK	Bacteria:11,nodiv:1	COG2981, CysZ, Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism].
CDD:225529	648	PRK	Bacteria:15	COG2982, AsmA, Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane].
CDD:225530	153	PRK	Bacteria:14,nodiv:1	COG2983, COG2983, Uncharacterized conserved protein [Function unknown].
CDD:225531	322	PRK	Bacteria:15,nodiv:1	COG2984, COG2984, ABC-type uncharacterized transport system, periplasmic component [General function prediction only].
CDD:225532	544	PRK	Bacteria:12	COG2985, COG2985, Predicted permease [General function prediction only].
CDD:225533	498	PRK	Bacteria:18,nodiv:1	COG2986, HutH, Histidine ammonia-lyase [Amino acid transport and metabolism].
CDD:225534	561	PRK	Bacteria:17,nodiv:1	COG2987, HutU, Urocanate hydratase [Amino acid transport and metabolism].
CDD:225536	561	PRK	Bacteria:12,nodiv:1	COG2989, COG2989, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225537	300	PRK	Bacteria:12	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225542	418	PRK	Bacteria:11	COG2995, PqiA, Uncharacterized paraquat-inducible protein A [Function unknown].
CDD:225543	287	PRK	Bacteria:11	COG2996, COG2996, Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only].
CDD:225546	271	EUKprk	Bacteria:10,Plants:2,nodiv:1	COG3000, ERG3, Sterol desaturase [Lipid metabolism].
CDD:225549	390	PRK	Bacteria:15	COG3004, NhaA, Na+/H+ antiporter [Inorganic ion transport and metabolism].
CDD:225550	190	PRK	Bacteria:11,nodiv:1	COG3005, TorC, Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit [Energy production and conversion].
CDD:225553	553	PRK	Bacteria:12	COG3008, PqiB, Paraquat-inducible protein B [General function prediction only].
CDD:225555	229	PRK	Bacteria:17	COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism].
CDD:225556	137	PRK	Bacteria:12	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only].
CDD:225557	151	PRK	Bacteria:13	COG3012, COG3012, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225562	206	PRK	Bacteria:11	COG3017, LolB, Outer membrane lipoprotein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane].
CDD:225564	149	PRK	Bacteria:7	COG3019, COG3019, Predicted metal-binding protein [General function prediction only].
CDD:225565	309	PRK	Bacteria:10,nodiv:1	COG3021, COG3021, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225566	253	PRK	Bacteria:20	COG3022, COG3022, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225567	257	PRK	Bacteria:20,nodiv:1	COG3023, ampD, N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane].
CDD:225568	65	PRK	Bacteria:14	COG3024, COG3024, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225569	432	PRK	Bacteria:13	COG3025, COG3025, Uncharacterized conserved protein [Function unknown].
CDD:225571	105	PRK	Bacteria:22,nodiv:1	COG3027, zapA, Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division,    chromosome partitioning].
CDD:225574	158	PRK	Bacteria:20,nodiv:1	COG3030, FxsA, Protein affecting phage T7 exclusion by the F plasmid [General function prediction only].
CDD:225577	298	PRK	Bacteria:12,nodiv:1	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225579	481	PRK	Bacteria:16	COG3037, SgaT, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225580	181	PRK	Bacteria:17,nodiv:1	COG3038, CybB, Cytochrome B561 [Energy production and conversion].
CDD:225581	230	PRK	Bacteria:14,nodiv:1	COG3039, COG3039, Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair].
CDD:225582	174	PRK	Bacteria:8,nodiv:1	COG3040, Blc, Bacterial lipocalin [Cell envelope biogenesis, outer membrane].
CDD:225583	91	PRK	Bacteria:11,nodiv:1	COG3041, COG3041, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225584	85	PRK	Bacteria:11	COG3042, Hlx, Putative hemolysin [General function prediction only].
CDD:225585	155	PRK	Bacteria:11,nodiv:1	COG3043, NapB, Nitrate reductase cytochrome c-type subunit [Energy production and conversion].
CDD:225589	213	PRK	Bacteria:15,nodiv:1	COG3047, OmpW, Outer membrane protein W [Cell envelope biogenesis, outer membrane].
CDD:225591	353	PRK	Bacteria:9,nodiv:1	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane].
CDD:225597	381	PRK	Bacteria:10	COG3055, COG3055, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225604	94	PRK	Bacteria:9,nodiv:1	COG3062, NapD, Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism].
CDD:225605	250	PRK	Bacteria:9	COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225612	121	PRK	Bacteria:18	COG3070, TfoX, Regulator of competence-specific genes [Transcription].
CDD:225613	400	PRK	Bacteria:11	COG3071, HemY, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism].
CDD:225615	213	PRK	Bacteria:11	COG3073, RseA, Negative regulator of sigma E activity [Signal transduction mechanisms].
CDD:225619	88	PRK	Bacteria:14,nodiv:1	COG3077, RelB, DNA-damage-inducible protein J [DNA replication, recombination, and repair].
CDD:225628	150	PRK	Bacteria:11	COG3086, RseC, Positive regulator of sigma E activity [Signal transduction mechanisms].
CDD:225629	264	PRK	Bacteria:13	COG3087, FtsN, Cell division protein [Cell division and chromosome partitioning].
CDD:225630	153	PRK	Bacteria:14,nodiv:1	COG3088, CcmH, Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones].
CDD:225632	177	PRK	Bacteria:12,nodiv:1	COG3090, DctM, TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism].
CDD:225633	156	PRK	Bacteria:16	COG3091, SprT, Zn-dependent metalloprotease, SprT family [General function prediction only].
CDD:225635	104	PRK	Bacteria:14	COG3093, VapI, Plasmid maintenance system antidote protein [General function prediction only].
CDD:225645	205	PRK	Bacteria:9	COG3103, COG3103, SH3 domain protein [Signal transduction mechanisms].
CDD:225646	498	EUKprk	Bacteria:16,Plants:3	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism].
CDD:225650	185	PRK	Bacteria:11,nodiv:1	COG3108, COG3108, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225653	128	PRK	Bacteria:10	COG3111, COG3111, Periplasmic protein with OB-fold [Function unknown].
CDD:225655	99	PRK	Bacteria:12	COG3113, COG3113, Predicted NTP binding protein (contains STAS domain) [General function prediction only].
CDD:225659	188	PRK	Bacteria:11	COG3117, COG3117, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225660	304	PRK	Bacteria:18,nodiv:1	COG3118, COG3118, Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones].
CDD:225661	475	EUKprk	Bacteria:18,Plants:1,nodiv:1	COG3119, AslA, Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism].
CDD:225663	235	PRK	Bacteria:15,nodiv:1	COG3121, FimC, P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225667	111	PRK	Bacteria:14,nodiv:1	COG3125, CyoD, Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion].
CDD:225668	158	PRK	Bacteria:9,nodiv:1	COG3126, COG3126, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225669	829	PRK	Bacteria:12,nodiv:1	COG3127, COG3127, Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225677	402	PRK	Bacteria:11	COG3135, BenE, Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225684	241	PRK	Bacteria:16,nodiv:1	COG3142, CutC, Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism].
CDD:225686	417	PRK	Bacteria:13	COG3144, FliK, Flagellar hook-length control protein [Cell motility and secretion].
CDD:225687	194	EUKprk	Bacteria:17,Plants:2,nodiv:1	COG3145, AlkB, Alkylated DNA repair protein [DNA replication, recombination, and repair].
CDD:225688	387	PRK	Bacteria:9,nodiv:1	COG3146, COG3146, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225694	125	PRK	Bacteria:11	COG3152, COG3152, Predicted membrane protein [Function unknown].
CDD:225695	171	PRK	Bacteria:16,nodiv:1	COG3153, COG3153, Predicted acetyltransferase [General function prediction only].
CDD:225696	168	PRK	Bacteria:8,nodiv:1	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism].
CDD:225698	323	PRK	Bacteria:8	COG3156, PulK, Type II secretory pathway, component PulK [Intracellular trafficking and secretion].
CDD:225699	162	PRK	Bacteria:9,nodiv:1	COG3157, Hcp, Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion,    and vesicular transport].
CDD:225700	627	PRK	Bacteria:17,nodiv:1	COG3158, Kup, K+ transporter [Inorganic ion transport and metabolism].
CDD:225701	218	PRK	Bacteria:11	COG3159, COG3159, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225703	174	PRK	Bacteria:19	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism].
CDD:225706	204	PRK	Bacteria:12	COG3165, COG3165, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225707	206	PRK	Bacteria:14	COG3166, PilN, Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225714	321	PRK	Bacteria:15,nodiv:1	COG3173, COG3173, Predicted aminoglycoside phosphotransferase [General function prediction only].
CDD:225715	371	PRK	Bacteria:10	COG3174, COG3174, Predicted membrane protein [Function unknown].
CDD:225716	195	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG3175, COX11, Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones].
CDD:225717	292	PRK	Bacteria:10,nodiv:1	COG3176, COG3176, Putative hemolysin [General function prediction only].
CDD:225718	348	PRK	Bacteria:22,nodiv:1	COG3177, COG3177, Fic family protein [Function unknown].
CDD:225719	351	PRK	Bacteria:6	COG3178, COG3178, Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only].
CDD:225721	352	PRK	Bacteria:14,nodiv:1	COG3180, AbrB, Putative ammonia monooxygenase [General function prediction only].
CDD:225722	319	PRK	Bacteria:10,nodiv:1	COG3181, COG3181, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225723	442	PRK	Bacteria:9,nodiv:1	COG3182, PiuB, Uncharacterized iron-regulated membrane protein [Function unknown].
CDD:225726	363	PRK	Bacteria:8,nodiv:1	COG3185, COG3185, 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only].
CDD:225728	142	PRK	Bacteria:17	COG3187, HslJ, Heat shock protein [Posttranslational modification, protein turnover, chaperones].
CDD:225729	835	PRK	Bacteria:14,nodiv:1	COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225730	117	PRK	Bacteria:15,nodiv:1	COG3189, COG3189, Uncharacterized conserved protein [Function unknown].
CDD:225731	137	PRK	Bacteria:11,nodiv:1	COG3190, FliO, Flagellar biogenesis protein [Cell motility and secretion].
CDD:225732	348	PRK	Bacteria:13,nodiv:1	COG3191, DmpA, L-aminopeptidase/D-esterase [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225734	141	PRK	Bacteria:9,nodiv:1	COG3193, GlcG, Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only].
CDD:225735	168	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG3194, DAL3, Ureidoglycolate hydrolase [Nucleotide transport and metabolism].
CDD:225736	176	PRK	Bacteria:7,nodiv:1	COG3195, COG3195, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225738	58	PRK	Bacteria:11	COG3197, FixS, Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism].
CDD:225740	355	PRK	Bacteria:9	COG3199, COG3199, Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only].
CDD:225742	222	PRK	Bacteria:14	COG3201, PnuC, Nicotinamide mononucleotide transporter [Coenzyme metabolism].
CDD:225743	509	EUKprk	Bacteria:5,Plants:1	COG3202, COG3202, ATP/ADP translocase [Energy production and conversion].
CDD:225744	354	PRK	Bacteria:14,nodiv:1	COG3203, OmpC, Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane].
CDD:225745	316	PRK	Bacteria:5	COG3204, COG3204, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225747	458	PRK	Bacteria:10,nodiv:1	COG3206, GumC, Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane].
CDD:225749	244	PRK	Bacteria:10,nodiv:1	COG3208, GrsT, Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225750	796	PRK	Bacteria:13	COG3209, RhsA, Rhs family protein [Cell envelope biogenesis, outer membrane].
CDD:225751	1013	PRK	Bacteria:15	COG3210, FhaB, Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion].
CDD:225752	616	PRK	Bacteria:8,nodiv:1	COG3211, PhoX, Predicted phosphatase [General function prediction only].
CDD:225753	144	PRK	Bacteria:13	COG3212, COG3212, Predicted membrane protein [Function unknown].
CDD:225754	396	PRK	Bacteria:7,nodiv:1	COG3213, NnrS, Uncharacterized protein involved in response to NO [Inorganic ion transport and metabolism].
CDD:225755	400	PRK	Bacteria:11,nodiv:1	COG3214, COG3214, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225758	270	PRK	Bacteria:6,nodiv:1	COG3217, COG3217, Uncharacterized Fe-S protein [General function prediction only].
CDD:225759	205	PRK	Bacteria:7,nodiv:1	COG3218, COG3218, ABC-type uncharacterized transport system, auxiliary component [General function prediction only].
CDD:225761	282	PRK	Bacteria:9	COG3220, COG3220, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225762	299	PRK	Bacteria:19,nodiv:1	COG3221, PhnD, ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:225768	507	PRK	Bacteria:8	COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid transport and metabolism].
CDD:225777	67	PRK	Bacteria:14,nodiv:1	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225778	150	PRK	Bacteria:14,nodiv:1	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225779	343	PRK	Bacteria:11	COG3239, DesA, Fatty acid desaturase [Lipid metabolism].
CDD:225780	370	PRK	Bacteria:7	COG3240, COG3240, Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only].
CDD:225783	445	PRK	Bacteria:12,nodiv:1	COG3243, PhaC, Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism].
CDD:225785	298	PRK	Bacteria:8,nodiv:1	COG3246, COG3246, Uncharacterized conserved protein [Function unknown].
CDD:225786	185	PRK	Bacteria:14	COG3247, HdeD, Uncharacterized conserved protein [Function unknown].
CDD:225789	808	PRK	Bacteria:13,nodiv:1	COG3250, LacZ, Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism].
CDD:225792	230	PRK	Bacteria:13	COG3253, ywfI, Predicted heme peroxidase involved in anaerobic stress response [General function prediction only].
CDD:225793	105	PRK	Bacteria:14,nodiv:1	COG3254, COG3254, Uncharacterized conserved protein [Function unknown].
CDD:225794	134	PRK	Bacteria:11	COG3255, COG3255, Putative sterol carrier protein [Lipid metabolism].
CDD:225798	441	PRK	Bacteria:9	COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion].
CDD:225799	148	PRK	Bacteria:14	COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy production and conversion].
CDD:225800	382	PRK	Bacteria:11	COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy production and conversion].
CDD:225803	835	PRK	Bacteria:13,nodiv:1	COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].
CDD:225804	161	EUKprk	Bacteria:15,Plants:2,nodiv:1	COG3265, GntK, Gluconate kinase [Carbohydrate transport and metabolism].
CDD:225806	269	PRK	Bacteria:5	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion].
CDD:225808	73	PRK	Bacteria:7	COG3269, COG3269, Predicted RNA-binding protein, contains TRAM domain [General function prediction only].
CDD:225810	201	PRK	Bacteria:7	COG3271, COG3271, Predicted double-glycine peptidase [General function prediction only].
CDD:225813	332	PRK	Bacteria:9	COG3274, COG3274, Predicted O-acyltransferase [General function prediction only].
CDD:225814	557	PRK	Bacteria:10	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms].
CDD:225815	447	PRK	Bacteria:16	COG3276, SelB, Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis].
CDD:225816	98	EUKprk	Bacteria:12,Plants:3	COG3277, GAR1, RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis].
CDD:225818	244	PRK	Bacteria:22,nodiv:1	COG3279, LytT, Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms].
CDD:225819	889	PRK	Bacteria:9	COG3280, TreY, Maltooligosyl trehalose synthase [Carbohydrate transport and metabolism].
CDD:225822	606	PRK	Bacteria:11,nodiv:1	COG3284, AcoR, Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription].
CDD:225823	299	PRK	Bacteria:2,nodiv:1	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair].
CDD:225825	379	PRK	Bacteria:6	COG3287, COG3287, Uncharacterized conserved protein [Function unknown].
CDD:225826	356	PRK	Bacteria:22,nodiv:1	COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy production and conversion].
CDD:225827	537	PRK	Bacteria:10	COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms].
CDD:225828	297	PRK	Bacteria:7	COG3291, COG3291, FOG: PKD repeat [General function prediction only].
CDD:225830	124	PRK	Bacteria:12,nodiv:1	COG3293, COG3293, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225836	353	PRK	Bacteria:8	COG3299, XkdT, Uncharacterized homolog of phage Mu protein gp47 [Function unknown].
CDD:225837	236	miss	miss	COG3300, COG3300, MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms].
CDD:225839	281	PRK	Bacteria:9	COG3302, DmsC, DMSO reductase anchor subunit [General function prediction only].
CDD:225843	255	PRK	Bacteria:10,nodiv:1	COG3306, COG3306, Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane].
CDD:225844	424	PRK	Bacteria:28,nodiv:1	COG3307, RfaL, Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane].
CDD:225848	70	PRK	Bacteria:11	COG3311, AlpA, Predicted transcriptional regulator [Transcription].
CDD:225850	74	PRK	Bacteria:12	COG3313, COG3313, Predicted Fe-S protein [General function prediction only].
CDD:225851	427	PRK	Bacteria:11	COG3314, COG3314, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225852	297	PRK	Bacteria:13	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225853	215	PRK	Bacteria:12	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225854	342	PRK	Bacteria:12	COG3317, NlpB, Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane].
CDD:225855	216	PRK	Bacteria:11	COG3318, COG3318, Predicted metal-binding protein related to the C-terminal domain of SecA [General function prediction only].
CDD:225856	257	PRK	Bacteria:6	COG3319, COG3319, Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225857	382	PRK	Bacteria:2	COG3320, COG3320, Putative dehydrogenase domain of multifunctional non-ribosomal peptide synthetases and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225858	1061	PRK	Bacteria:9,nodiv:1	COG3321, COG3321, Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:225859	295	miss	miss	COG3322, COG3322, Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms].
CDD:225860	109	PRK	Bacteria:3	COG3323, COG3323, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225861	127	PRK	Bacteria:15,nodiv:1	COG3324, COG3324, Predicted enzyme related to lactoylglutathione lyase [General function prediction only].
CDD:225862	441	EUKprk	Bacteria:5,Plants:1	COG3325, ChiA, Chitinase [Carbohydrate transport and metabolism].
CDD:225863	94	PRK	Bacteria:11,nodiv:1	COG3326, COG3326, Predicted membrane protein [Function unknown].
CDD:225865	379	PRK	Bacteria:20	COG3328, COG3328, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225868	177	PRK	Bacteria:11	COG3331, PrfA, Penicillin-binding protein-related factor A, putative recombinase [General function prediction only].
CDD:225870	504	PRK	Bacteria:9,nodiv:1	COG3333, COG3333, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225871	192	PRK	Bacteria:10,nodiv:1	COG3334, COG3334, Uncharacterized conserved protein [Function unknown].
CDD:225872	132	PRK	Bacteria:18	COG3335, COG3335, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225873	299	PRK	Bacteria:8	COG3336, COG3336, Predicted membrane protein [Function unknown].
CDD:225875	250	PRK	Bacteria:9	COG3338, Cah, Carbonic anhydrase [Inorganic ion transport and metabolism].
CDD:225876	116	PRK	Bacteria:12,nodiv:1	COG3339, COG3339, Uncharacterized conserved protein [Function unknown].
CDD:225877	224	PRK	Bacteria:11	COG3340, PepE, Peptidase E [Amino acid transport and metabolism].
CDD:225879	265	PRK	Bacteria:6	COG3342, COG3342, Uncharacterized conserved protein [Function unknown].
CDD:225880	175	PRK	Bacteria:10	COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription].
CDD:225881	328	EUKprk	Bacteria:15,Plants:1	COG3344, COG3344, Retron-type reverse transcriptase [DNA replication, recombination, and repair].
CDD:225883	252	EUKprk	Bacteria:11,Plants:2,nodiv:1	COG3346, COG3346, Uncharacterized conserved protein [Function unknown].
CDD:225884	404	PRK	Bacteria:2	COG3347, COG3347, Uncharacterized conserved protein [Function unknown].
CDD:225885	485	PRK	Bacteria:5	COG3349, COG3349, Uncharacterized conserved protein [Function unknown].
CDD:225886	53	PRK	Bacteria:9	COG3350, COG3350, Uncharacterized conserved protein [Function unknown].
CDD:225891	126	PRK	Bacteria:6	COG3355, COG3355, Predicted transcriptional regulator [Transcription].
CDD:225892	578	PRK	Bacteria:8	COG3356, COG3356, Predicted membrane protein [Function unknown].
CDD:225901	311	PRK	Bacteria:5	COG3366, COG3366, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225902	339	PRK	Bacteria:8	COG3367, COG3367, Uncharacterized conserved protein [Function unknown].
CDD:225906	181	PRK	Bacteria:8	COG3371, COG3371, Predicted membrane protein [Function unknown].
CDD:225907	396	PRK	Bacteria:10	COG3372, COG3372, Predicted nuclease of restriction endonuclease-like fold [General function prediction only].
CDD:225909	197	PRK	Bacteria:6	COG3374, COG3374, Predicted membrane protein [Function unknown].
CDD:225911	342	EUKprk	Bacteria:10,Plants:1	COG3376, HoxN, High-affinity nickel permease [Inorganic ion transport and metabolism].
CDD:225913	517	PRK	Bacteria:12	COG3378, COG3378, Phage associated DNA primase [General function prediction only].
CDD:225916	204	PRK	Bacteria:13	COG3381, TorD, Uncharacterized component of anaerobic dehydrogenases [General function prediction only].
CDD:225917	229	PRK	Bacteria:13	COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only].
CDD:225919	268	EUKprk	Bacteria:13,Plants:1	COG3384, COG3384, Aromatic ring-opening dioxygenase, catalytic LigB subunit related    enzyme [Amino acid transport and metabolism].
CDD:225920	292	PRK	Bacteria:12	COG3385, COG3385, FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225921	307	EUKprk	Bacteria:15,Plants:1,nodiv:1	COG3386, COG3386, Gluconolactonase [Carbohydrate transport and metabolism].
CDD:225922	612	EUKprk	Bacteria:13,Plants:2,nodiv:1	COG3387, SGA1, Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism].
CDD:225926	381	PRK	Bacteria:18	COG3391, COG3391, Uncharacterized conserved protein [Function unknown].
CDD:225928	268	PRK	Bacteria:8	COG3393, COG3393, Predicted acetyltransferase [General function prediction only].
CDD:225929	257	PRK	Bacteria:10	COG3394, COG3394, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225930	413	PRK	Bacteria:12,nodiv:1	COG3395, COG3395, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225931	265	PRK	Bacteria:6	COG3396, COG3396, Uncharacterized conserved protein [Function unknown].
CDD:225936	343	PRK	Bacteria:3	COG3401, COG3401, Fibronectin type 3 domain-containing protein [General function prediction only].
CDD:225937	161	PRK	Bacteria:7	COG3402, COG3402, Uncharacterized conserved protein [Function unknown].
CDD:225939	208	PRK	Bacteria:7	COG3404, COG3404, Methenyl tetrahydrofolate cyclohydrolase [Amino acid transport and metabolism].
CDD:225941	329	EUKprk	Bacteria:10,Plants:3	COG3407, MVD1, Mevalonate pyrophosphate decarboxylase [Lipid metabolism].
CDD:225942	641	EUKprk	Bacteria:11,Plants:1	COG3408, GDB1, Glycogen debranching enzyme [Carbohydrate transport and metabolism].
CDD:225943	185	PRK	Bacteria:13,nodiv:1	COG3409, COG3409, Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane].
CDD:225945	64	PRK	Bacteria:8	COG3411, COG3411, Ferredoxin [Energy production and conversion].
CDD:225946	129	PRK	Bacteria:8	COG3412, COG3412, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225947	215	PRK	Bacteria:6	COG3413, COG3413, Predicted DNA binding protein [General function prediction only].
CDD:225948	93	PRK	Bacteria:13	COG3414, SgaB, Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism].
CDD:225949	138	PRK	Bacteria:8	COG3415, COG3415, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225953	1036	PRK	Bacteria:4	COG3419, PilY1, Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:225959	377	EUKprk	Bacteria:21,Plants:3	COG3425, PksG, 3-hydroxy-3-methylglutaryl CoA synthase [Lipid metabolism].
CDD:225961	146	PRK	Bacteria:13	COG3427, COG3427, Carbon monoxide dehydrogenase subunit G, CoxG [Energy production and conversion].
CDD:225962	494	PRK	Bacteria:8	COG3428, COG3428, Predicted membrane protein [Function unknown].
CDD:225964	161	PRK	Bacteria:5	COG3430, COG3430, Uncharacterized protein conserved in archaea [Function unknown].
CDD:225965	142	PRK	Bacteria:12	COG3431, COG3431, Predicted membrane protein [Function unknown].
CDD:225966	95	PRK	Bacteria:8	COG3432, COG3432, Predicted transcriptional regulator [Transcription].
CDD:225970	157	PRK	Bacteria:12,nodiv:1	COG3436, COG3436, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225971	360	PRK	Bacteria:7	COG3437, COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms].
CDD:225972	137	PRK	Bacteria:10	COG3439, COG3439, Uncharacterized conserved protein [Function unknown].
CDD:225976	159	PRK	Bacteria:12	COG3444, COG3444, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism].
CDD:225978	308	PRK	Bacteria:2	COG3447, COG3447, Predicted integral membrane sensor domain [Signal transduction mechanisms].
CDD:225980	154	PRK	Bacteria:6,nodiv:1	COG3449, COG3449, DNA gyrase inhibitor [DNA replication, recombination, and repair].
CDD:225981	116	PRK	Bacteria:6,nodiv:1	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only].
CDD:225982	796	PRK	Bacteria:14,nodiv:1	COG3451, VirB4, Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion].
CDD:225984	130	PRK	Bacteria:6,nodiv:1	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:225985	377	PRK	Bacteria:9,nodiv:1	COG3454, COG3454, Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism].
CDD:225986	262	PRK	Bacteria:6,nodiv:1	COG3455, COG3455, Type VI protein secretion system component VasF [Intracellular    trafficking, secretion, and vesicular transport].
CDD:225987	430	PRK	Bacteria:6,nodiv:1	COG3456, COG3456, Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular    transport; Signal transduction mechanisms].
CDD:225990	1056	PRK	Bacteria:8,nodiv:1	COG3459, COG3459, Cellobiose phosphorylase [Carbohydrate transport and metabolism].
CDD:225995	402	PRK	Bacteria:14,nodiv:1	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:225998	166	PRK	Bacteria:17	COG3467, COG3467, Predicted flavin-nucleotide-binding protein [General function prediction only].
CDD:225999	592	PRK	Bacteria:17,nodiv:1	COG3468, AidA, Type V secretory pathway, adhesin AidA [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].
CDD:226005	135	EUKprk	Bacteria:6,Plants:2,nodiv:1	COG3474, COG3474, Cytochrome c2 [Energy production and conversion].
CDD:226006	256	PRK	Bacteria:6	COG3475, COG3475, LPS biosynthesis protein [Cell envelope biogenesis, outer membrane].
CDD:226007	161	EUKprk	Bacteria:8,Plants:1,nodiv:1	COG3476, COG3476, Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog) [Signal transduction mechanisms].
CDD:226011	342	PRK	Bacteria:10	COG3480, SdrC, Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms].
CDD:226012	287	PRK	Bacteria:12	COG3481, COG3481, Predicted HD-superfamily hydrolase [General function prediction only].
CDD:226013	237	PRK	Bacteria:6,nodiv:1	COG3482, COG3482, Uncharacterized conserved protein [Function unknown].
CDD:226016	226	PRK	Bacteria:10,nodiv:1	COG3485, PcaH, Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226017	436	EUKprk	Bacteria:8,Plants:1	COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226022	322	EUKprk	Bacteria:6,Plants:2	COG3491, PcbC, Isopenicillin N synthase and related dioxygenases [General function prediction only].
CDD:226025	279	PRK	Bacteria:8,nodiv:1	COG3494, COG3494, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226028	394	PRK	Bacteria:9,nodiv:1	COG3497, COG3497, Phage tail sheath protein FI [General function prediction only].
CDD:226031	350	PRK	Bacteria:9,nodiv:1	COG3500, COG3500, Phage protein D [General function prediction only].
CDD:226032	550	PRK	Bacteria:8,nodiv:1	COG3501, VgrG, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226034	323	PRK	Bacteria:9,nodiv:1	COG3503, COG3503, Predicted membrane protein [Function unknown].
CDD:226035	265	PRK	Bacteria:10,nodiv:2	COG3504, VirB9, Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion].
CDD:226036	596	PRK	Bacteria:11,nodiv:2	COG3505, VirD4, Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion].
CDD:226038	549	PRK	Bacteria:8	COG3507, XynB, Beta-xylosidase [Carbohydrate transport and metabolism].
CDD:226040	312	PRK	Bacteria:9,nodiv:1	COG3509, LpqC, Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226042	527	PRK	Bacteria:8	COG3511, PlcC, Phospholipase C [Cell envelope biogenesis, outer membrane].
CDD:226045	93	PRK	Bacteria:7,nodiv:1	COG3514, COG3514, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226046	346	PRK	Bacteria:8,nodiv:1	COG3515, COG3515, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226047	169	PRK	Bacteria:8,nodiv:1	COG3516, COG3516, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226048	495	PRK	Bacteria:8,nodiv:1	COG3517, COG3517, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226049	157	PRK	Bacteria:8,nodiv:1	COG3518, COG3518, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226050	621	PRK	Bacteria:8,nodiv:1	COG3519, COG3519, Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226051	335	PRK	Bacteria:8,nodiv:1	COG3520, COG3520, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226052	159	PRK	Bacteria:8	COG3521, COG3521, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226053	446	PRK	Bacteria:8,nodiv:1	COG3522, COG3522, Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226054	1188	PRK	Bacteria:8,nodiv:1	COG3523, IcmF, Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and    vesicular transport].
CDD:226056	732	PRK	Bacteria:6,nodiv:1	COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism].
CDD:226058	234	PRK	Bacteria:8	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226062	212	PRK	Bacteria:5	COG3531, COG3531, Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones].
CDD:226064	501	PRK	Bacteria:7,nodiv:1	COG3534, AbfA, Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism].
CDD:226065	357	PRK	Bacteria:5,nodiv:1	COG3535, COG3535, Uncharacterized conserved protein [Function unknown].
CDD:226069	184	PRK	Bacteria:9	COG3539, FimA, P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:226070	522	PRK	Bacteria:7	COG3540, PhoD, Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism].
CDD:226071	248	PRK	Bacteria:7	COG3541, COG3541, Predicted nucleotidyltransferase [General function prediction only].
CDD:226074	190	PRK	Bacteria:6	COG3544, COG3544, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226075	181	PRK	Bacteria:10,nodiv:1	COG3545, COG3545, Predicted esterase of the alpha/beta hydrolase fold [General function prediction only].
CDD:226076	277	PRK	Bacteria:10	COG3546, COG3546, Mn-containing catalase [Inorganic ion transport and metabolism].
CDD:226077	303	PRK	Bacteria:18,nodiv:1	COG3547, COG3547, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:226078	197	PRK	Bacteria:5	COG3548, COG3548, Predicted integral membrane protein [Function unknown].
CDD:226080	392	PRK	Bacteria:12,nodiv:1	COG3550, HipA, Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only].
CDD:226082	395	PRK	Bacteria:7	COG3552, CoxE, Protein containing von Willebrand factor type A (vWA) domain [General function prediction only].
CDD:226085	291	PRK	Bacteria:7	COG3555, COG3555, Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones].
CDD:226091	110	PRK	Bacteria:7,Phages:2	COG3561, COG3561, Phage anti-repressor protein [Transcription].
CDD:226098	259	PRK	Bacteria:12,nodiv:1	COG3568, ElsH, Metal-dependent hydrolase [General function prediction only].
CDD:226104	184	PRK	Bacteria:8,nodiv:1	COG3575, COG3575, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226105	173	PRK	Bacteria:14,nodiv:1	COG3576, COG3576, Predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase [General function prediction only].
CDD:226106	215	PRK	Bacteria:7,nodiv:1	COG3577, COG3577, Predicted aspartyl protease [General function prediction only].
CDD:226110	162	EUKprk	Bacteria:1,Plants:2	COG3582, COG3582, Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only].
CDD:226112	109	PRK	Bacteria:7	COG3584, COG3584, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226117	360	PRK	Bacteria:7	COG3589, COG3589, Uncharacterized conserved protein [Function unknown].
CDD:226118	654	PRK	Bacteria:10	COG3590, PepO, Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones].
CDD:226119	251	PRK	Bacteria:10	COG3591, COG3591, V8-like Glu-specific endopeptidase [Amino acid transport and metabolism].
CDD:226121	581	PRK	Bacteria:13,nodiv:1	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair].
CDD:226122	343	PRK	Bacteria:8	COG3594, NolL, Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism].
CDD:226123	318	PRK	Bacteria:8	COG3595, COG3595, Uncharacterized conserved protein [Function unknown].
CDD:226124	296	PRK	Bacteria:8	COG3596, COG3596, Predicted GTPase [General function prediction only].
CDD:226127	212	PRK	Bacteria:17	COG3599, DivIVA, Cell division initiation protein [Cell division and chromosome partitioning].
CDD:226129	186	PRK	Bacteria:10	COG3601, COG3601, Predicted membrane protein [Function unknown].
CDD:226132	550	PRK	Bacteria:14	COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms].
CDD:226135	331	PRK	Bacteria:8,nodiv:1	COG3608, COG3608, Predicted deacylase [General function prediction only].
CDD:226136	89	PRK	Bacteria:21,nodiv:1	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription].
CDD:226137	156	PRK	Bacteria:12	COG3610, COG3610, Uncharacterized conserved protein [Function unknown].
CDD:226138	417	PRK	Bacteria:10	COG3611, DnaB, Replication initiation/membrane attachment protein [DNA replication, recombination, and repair].
CDD:226140	172	EUKprk	Bacteria:7,Plants:1,nodiv:1	COG3613, COG3613, Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism].
CDD:226143	368	EUKprk	Bacteria:11,Plants:2,nodiv:1	COG3616, COG3616, Predicted amino acid aldolase or racemase [Amino acid transport and metabolism].
CDD:226144	176	PRK	Bacteria:7,Phages:1	COG3617, COG3617, Prophage antirepressor [Transcription].
CDD:226145	279	PRK	Bacteria:7,nodiv:1	COG3618, COG3618, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only].
CDD:226146	226	PRK	Bacteria:16,nodiv:1	COG3619, COG3619, Predicted membrane protein [Function unknown].
CDD:226149	260	PRK	Bacteria:13	COG3622, Hfi, Hydroxypyruvate isomerase [Carbohydrate transport and metabolism].
CDD:226152	196	PRK	Bacteria:8,nodiv:1	COG3625, PhnH, Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism].
CDD:226155	116	PRK	Bacteria:7	COG3628, COG3628, Phage baseplate assembly protein W [General function prediction only].
CDD:226156	280	PRK	Bacteria:6,nodiv:1	COG3629, DnrI, DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms].
CDD:226157	84	PRK	Bacteria:7	COG3630, OadG, Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, gamma subunit [Energy production and conversion].
CDD:226158	133	PRK	Bacteria:10,nodiv:1	COG3631, COG3631, Ketosteroid isomerase-related protein [General function prediction only].
CDD:226161	408	PRK	Bacteria:15	COG3635, COG3635, Predicted phosphoglycerate mutase, AP superfamily [Carbohydrate transport and metabolism].
CDD:226163	199	PRK	Bacteria:15,nodiv:1	COG3637, COG3637, Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane].
CDD:226164	258	PRK	Bacteria:16,nodiv:1	COG3638, COG3638, ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:226165	283	PRK	Bacteria:19,nodiv:1	COG3639, COG3639, ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism].
CDD:226166	255	PRK	Bacteria:5	COG3640, CooC, CO dehydrogenase maturation factor [Cell division and chromosome partitioning].
CDD:226168	204	EUKprk	Bacteria:7,Plants:3	COG3642, COG3642, Mn2+-dependent serine/threonine protein kinase [Signal transduction mechanisms].
CDD:226171	135	PRK	Bacteria:4,Phages:3	COG3645, COG3645, Uncharacterized phage-encoded protein [Function unknown].
CDD:226172	167	PRK	Bacteria:4	COG3646, COG3646, Uncharacterized phage-encoded protein [Function unknown].
CDD:226180	132	PRK	Bacteria:10	COG3654, Doc, Prophage maintenance system killer protein [General function prediction only].
CDD:226181	73	PRK	Bacteria:10	COG3655, COG3655, Predicted transcriptional regulator [Transcription].
CDD:226189	169	EUKprk	Bacteria:10,Plants:1	COG3663, Mug, G:T/U mismatch-specific DNA glycosylase [DNA replication, recombination, and repair].
CDD:226191	264	EUKprk	Bacteria:3,Plants:1,nodiv:1	COG3665, COG3665, Uncharacterized conserved protein [Function unknown].
CDD:226192	161	PRK	Bacteria:11,nodiv:1	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:226194	98	PRK	Bacteria:15,nodiv:1	COG3668, ParE, Plasmid stabilization system protein [General function prediction only].
CDD:226196	490	PRK	Bacteria:6	COG3670, COG3670, Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226198	191	PRK	Bacteria:6,nodiv:1	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General    function prediction only].
CDD:226201	126	PRK	Bacteria:4	COG3676, COG3676, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:226202	129	PRK	Bacteria:12	COG3677, COG3677, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:226203	160	PRK	Bacteria:13	COG3678, CpxP, P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism].
CDD:226204	118	PRK	Bacteria:9	COG3679, COG3679, Regulatory protein involved in competence development and sporulation [Replication, recombination and repair;    Signal transduction mechanisms].
CDD:226207	123	PRK	Bacteria:14	COG3682, COG3682, Predicted transcriptional regulator [Transcription].
CDD:226208	213	PRK	Bacteria:9,nodiv:1	COG3683, COG3683, ABC-type uncharacterized transport system, periplasmic component [General function prediction only].
CDD:226210	167	PRK	Bacteria:8,nodiv:1	COG3685, COG3685, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226213	173	PRK	Bacteria:8	COG3688, COG3688, Predicted RNA-binding protein containing a PIN domain [General function prediction only].
CDD:226214	271	PRK	Bacteria:8	COG3689, COG3689, Predicted membrane protein [Function unknown].
CDD:226217	345	PRK	Bacteria:5,nodiv:1	COG3693, XynA, Beta-1,4-xylanase [Carbohydrate transport and metabolism].
CDD:226219	103	EUKprk	Bacteria:13,Plants:1	COG3695, COG3695, Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair].
CDD:226220	1027	PRK	Bacteria:13	COG3696, COG3696, Putative silver efflux pump [Inorganic ion transport and metabolism].
CDD:226225	105	PRK	Bacteria:6,nodiv:2	COG3702, VirB3, Type IV secretory pathway, VirB3 components [Intracellular trafficking and secretion].
CDD:226226	190	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG3703, ChaC, Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism].
CDD:226227	406	PRK	Bacteria:7,nodiv:2	COG3704, VirB6, Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion].
CDD:226228	390	PRK	Bacteria:17,nodiv:1	COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism].
CDD:226229	435	PRK	Bacteria:13,nodiv:1	COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms].
CDD:226230	194	PRK	Bacteria:12,nodiv:1	COG3707, AmiR, Response regulator with putative antiterminator output domain [Signal transduction mechanisms].
CDD:226231	157	PRK	Bacteria:7	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226232	192	PRK	Bacteria:8,nodiv:1	COG3709, COG3709, Uncharacterized component of phosphonate metabolism [Inorganic ion transport and metabolism].
CDD:226233	148	PRK	Bacteria:8	COG3710, CadC, DNA-binding winged-HTH domains [Transcription].
CDD:226234	491	PRK	Bacteria:16	COG3711, BglG, Transcriptional antiterminator [Transcription].
CDD:226235	322	PRK	Bacteria:5,nodiv:1	COG3712, FecR, Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms].
CDD:226236	258	PRK	Bacteria:14,nodiv:1	COG3713, OmpV, Outer membrane protein V [Cell envelope biogenesis, outer membrane].
CDD:226237	212	PRK	Bacteria:11	COG3714, COG3714, Predicted membrane protein [Function unknown].
CDD:226238	265	PRK	Bacteria:14	COG3715, ManY, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism].
CDD:226239	269	PRK	Bacteria:15	COG3716, ManZ, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism].
CDD:226241	270	PRK	Bacteria:11,nodiv:1	COG3718, IolB, Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism].
CDD:226242	249	PRK	Bacteria:10,nodiv:1	COG3719, Rna, Ribonuclease I [Translation, ribosomal structure and biogenesis].
CDD:226251	179	PRK	Bacteria:10	COG3728, XtmA, Phage terminase, small subunit [DNA replication, recombination, and repair].
CDD:226257	306	PRK	Bacteria:7,nodiv:1	COG3734, DgoK, 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism].
CDD:226258	299	PRK	Bacteria:12,nodiv:1	COG3735, COG3735, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226259	239	PRK	Bacteria:8,nodiv:2	COG3736, VirB8, Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion].
CDD:226263	194	PRK	Bacteria:9,nodiv:1	COG3740, COG3740, Phage head maturation protease [General function prediction only].
CDD:226264	272	PRK	Bacteria:7,nodiv:1	COG3741, HutG, N-formylglutamate amidohydrolase [Amino acid transport and metabolism].
CDD:226265	131	PRK	Bacteria:6	COG3742, COG3742, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226266	133	PRK	Bacteria:5	COG3743, COG3743, Uncharacterized conserved protein [Function unknown].
CDD:226267	130	PRK	Bacteria:6,nodiv:1	COG3744, COG3744, PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Signal transduction mechanisms].
CDD:226268	276	PRK	Bacteria:5,nodiv:1	COG3745, CpaB, Flp pilus assembly protein CpaB [Intracellular trafficking and secretion].
CDD:226272	167	PRK	Bacteria:6,nodiv:1	COG3749, COG3749, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226274	252	EUKprk	Bacteria:6,Plants:3	COG3751, EGL-9, Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones].
CDD:226277	595	PRK	Bacteria:4	COG3754, RgpF, Lipopolysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane].
CDD:226278	127	PRK	Bacteria:10,nodiv:1	COG3755, COG3755, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226280	269	PRK	Bacteria:10,nodiv:1	COG3757, Acm, Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell envelope biogenesis, outer membrane].
CDD:226281	193	PRK	Bacteria:11,nodiv:1	COG3758, COG3758, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226282	121	PRK	Bacteria:10,nodiv:1	COG3759, COG3759, Predicted membrane protein [Function unknown].
CDD:226287	210	PRK	Bacteria:11	COG3764, SrtA, Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane].
CDD:226288	347	PRK	Bacteria:10	COG3765, WzzB, Chain length determinant protein [Cell envelope biogenesis, outer membrane].
CDD:226295	152	PRK	Bacteria:11,Phages:1	COG3772, COG3772, Phage-related lysozyme (muraminidase) [General function prediction only].
CDD:226296	249	PRK	Bacteria:9,nodiv:1	COG3773, SleB, Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane].
CDD:226297	347	EUKprk	Bacteria:4,Plants:2,nodiv:1	COG3774, OCH1, Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane].
CDD:226298	446	PRK	Bacteria:11	COG3775, GatC, Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism].
CDD:226309	217	PRK	Bacteria:9,nodiv:1	COG3786, COG3786, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226314	133	EUKprk	Bacteria:7,Plants:1,nodiv:1	COG3791, COG3791, Uncharacterized conserved protein [Function unknown].
CDD:226315	122	PRK	Bacteria:3	COG3792, COG3792, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226316	144	PRK	Bacteria:7,nodiv:1	COG3793, TerB, Tellurite resistance protein [Inorganic ion transport and metabolism].
CDD:226317	128	PRK	Bacteria:7,nodiv:1	COG3794, PetE, Plastocyanin [Energy production and conversion].
CDD:226318	123	PRK	Bacteria:5,nodiv:1	COG3795, COG3795, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226319	178	PRK	Bacteria:7,nodiv:1	COG3797, COG3797, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226322	332	PRK	Bacteria:1,nodiv:1	COG3800, COG3800, Predicted transcriptional regulator [General function prediction only].
CDD:226325	182	PRK	Bacteria:6,nodiv:1	COG3803, COG3803, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226350	560	PRK	Bacteria:11	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
CDD:226351	90	PRK	Bacteria:12	COG3830, COG3830, ACT domain-containing protein [Signal transduction mechanisms].
CDD:226352	85	PRK	Bacteria:6,nodiv:1	COG3831, COG3831, Uncharacterized conserved protein [Function unknown].
CDD:226353	149	PRK	Bacteria:13,nodiv:1	COG3832, COG3832, Uncharacterized conserved protein [Function unknown].
CDD:226354	282	PRK	Bacteria:18	COG3833, MalG, ABC-type maltose transport systems, permease component [Carbohydrate transport and metabolism].
CDD:226355	376	PRK	Bacteria:11	COG3835, CdaR, Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms].
CDD:226356	255	PRK	Bacteria:14,nodiv:1	COG3836, HpcH, 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism].
CDD:226357	161	PRK	Bacteria:7	COG3837, COG3837, Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown].
CDD:226358	108	PRK	Bacteria:7,nodiv:1	COG3838, VirB2, Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion].
CDD:226359	338	PRK	Bacteria:51,nodiv:1	COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism].
CDD:226361	352	PRK	Bacteria:43,nodiv:1	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism].
CDD:226362	326	PRK	Bacteria:6,nodiv:1	COG3843, VirD2, Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion].
CDD:226364	501	PRK	Bacteria:26,nodiv:1	COG3845, COG3845, ABC-type uncharacterized transport systems, ATPase components [General function prediction only].
CDD:226365	452	PRK	Bacteria:5,nodiv:1	COG3846, TrbL, Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion].
CDD:226366	58	PRK	Bacteria:6,nodiv:1	COG3847, Flp, Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion].
CDD:226368	574	PRK	Bacteria:13	COG3850, NarQ, Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms].
CDD:226370	363	PRK	Bacteria:10,nodiv:2	COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms].
CDD:226371	386	PRK	Bacteria:9	COG3853, TelA, Uncharacterized protein involved in tellurite resistance [Inorganic ion transport and metabolism].
CDD:226375	1108	PRK	Bacteria:8	COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair].
CDD:226376	423	PRK	Bacteria:4	COG3858, COG3858, Predicted glycosyl hydrolase [General function prediction only].
CDD:226379	195	PRK	Bacteria:4	COG3861, COG3861, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226383	151	PRK	Bacteria:9,nodiv:1	COG3865, COG3865, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226386	306	PRK	Bacteria:5	COG3868, COG3868, Uncharacterized conserved protein [Function unknown].
CDD:226389	145	PRK	Bacteria:6,nodiv:1	COG3871, COG3871, Uncharacterized stress protein (general stress protein 26) [General function prediction only].
CDD:226396	247	PRK	Bacteria:6	COG3879, COG3879, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226400	265	PRK	Bacteria:3	COG3883, COG3883, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226403	198	PRK	Bacteria:2	COG3886, COG3886, Predicted HKD family nuclease [DNA replication, recombination, and repair].
CDD:226404	655	PRK	Bacteria:9	COG3887, COG3887, Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms].
CDD:226409	697	miss	miss	COG3893, COG3893, Inactivated superfamily I helicase [DNA replication, recombination, and repair].
CDD:226411	112	PRK	Bacteria:9,nodiv:1	COG3895, COG3895, Predicted periplasmic protein [General function prediction only].
CDD:226413	218	EUKprk	Bacteria:5,Plants:2,nodiv:1	COG3897, COG3897, Predicted methyltransferase [General function prediction only].
CDD:226415	849	miss	miss	COG3899, COG3899, Predicted ATPase [General function prediction only].
CDD:226418	414	PRK	Bacteria:2	COG3903, COG3903, Predicted ATPase [General function prediction only].
CDD:226420	83	PRK	Bacteria:5,nodiv:1	COG3905, COG3905, Predicted transcriptional regulator [Transcription].
CDD:226430	209	PRK	Bacteria:5,nodiv:1	COG3916, LasI, N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226434	221	PRK	Bacteria:12,nodiv:1	COG3920, COG3920, Signal transduction histidine kinase [Signal transduction mechanisms].
CDD:226435	300	PRK	Bacteria:5,nodiv:1	COG3921, COG3921, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226443	470	miss	miss	COG3933, COG3933, Transcriptional antiterminator [Transcription].
CDD:226445	246	PRK	Bacteria:8	COG3935, DnaD, Putative primosome component and related proteins [DNA replication, recombination, and repair].
CDD:226451	173	PRK	Bacteria:7	COG3942, COG3942, Surface antigen [General function prediction only].
CDD:226453	226	PRK	Bacteria:5	COG3944, COG3944, Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane].
CDD:226455	456	PRK	Bacteria:5,nodiv:1	COG3946, VirJ, Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion].
CDD:226458	349	PRK	Bacteria:7	COG3949, COG3949, Uncharacterized membrane protein [Function unknown].
CDD:226466	793	EUKprk	Bacteria:8,Plants:1	COG3957, COG3957, Phosphoketolase [Carbohydrate transport and metabolism].
CDD:226467	312	PRK	Bacteria:14,nodiv:1	COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate transport and metabolism].
CDD:226468	243	PRK	Bacteria:14,nodiv:1	COG3959, COG3959, Transketolase, N-terminal subunit [Carbohydrate transport and metabolism].
CDD:226470	557	EUKprk	Bacteria:8,Plants:4	COG3961, COG3961, Pyruvate decarboxylase and related thiamine pyrophosphate-requiring enzymes [Carbohydrate transport and metabolism / Coenzyme metabolism / General function prediction only].
CDD:226471	617	PRK	Bacteria:11,nodiv:1	COG3962, COG3962, Acetolactate synthase [Amino acid transport and metabolism].
CDD:226476	245	PRK	Bacteria:6,nodiv:1	COG3967, DltE, Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane].
CDD:226480	264	PRK	Bacteria:13,nodiv:1	COG3971, COG3971, 2-keto-4-pentenoate hydratase [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226483	558	PRK	Bacteria:8	COG3975, COG3975, Predicted protease with the C-terminal PDZ domain [General function prediction only].
CDD:226487	181	PRK	Bacteria:7	COG3979, COG3979, Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only].
CDD:226489	174	PRK	Bacteria:11	COG3981, COG3981, Predicted acetyltransferase [General function prediction only].
CDD:226553	162	PRK	Bacteria:3	COG4067, COG4067, Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones].
CDD:226581	875	PRK	Bacteria:8	COG4096, HsdR, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms].
CDD:226589	98	PRK	Bacteria:7,nodiv:1	COG4104, COG4104, Uncharacterized conserved protein [Function unknown].
CDD:226590	254	PRK	Bacteria:22,nodiv:1	COG4105, ComL, DNA uptake lipoprotein [General function prediction only].
CDD:226591	257	PRK	Bacteria:9,nodiv:1	COG4106, Tam, Trans-aconitate methyltransferase [General function prediction only].
CDD:226593	528	PRK	Bacteria:26,nodiv:1	COG4108, PrfC, Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis].
CDD:226598	134	PRK	Bacteria:10	COG4113, COG4113, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only].
CDD:226603	84	PRK	Bacteria:8	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning].
CDD:226605	293	PRK	Bacteria:12,nodiv:1	COG4120, COG4120, ABC-type uncharacterized transport system, permease component [General function prediction only].
CDD:226606	252	PRK	Bacteria:13,nodiv:1	COG4121, COG4121, Uncharacterized conserved protein [Function unknown].
CDD:226607	219	EUKprk	Bacteria:23,Plants:1	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only].
CDD:226608	248	PRK	Bacteria:28,nodiv:1	COG4123, COG4123, Predicted O-methyltransferase [General function prediction only].
CDD:226609	355	PRK	Bacteria:5,nodiv:1	COG4124, ManB, Beta-mannanase [Carbohydrate transport and metabolism].
CDD:226611	230	EUKprk	Bacteria:3,Plants:2,nodiv:1	COG4126, COG4126, Hydantoin racemase [Amino acid transport and metabolism].
CDD:226614	332	PRK	Bacteria:11,nodiv:1	COG4129, COG4129, Predicted membrane protein [Function unknown].
CDD:226617	209	PRK	Bacteria:16,nodiv:1	COG4133, CcmA, ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones].
CDD:226621	265	PRK	Bacteria:12	COG4137, COG4137, ABC-type uncharacterized transport system, permease component [General function prediction only].
CDD:226624	336	PRK	Bacteria:19,nodiv:1	COG4143, TbpA, ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism].
CDD:226627	529	PRK	Bacteria:16	COG4147, DhlC, Predicted symporter [General function prediction only].
CDD:226628	352	PRK	Bacteria:13,nodiv:1	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:226629	225	PRK	Bacteria:25,nodiv:1	COG4149, ModC, ABC-type molybdate transport system, permease component [Inorganic ion transport and metabolism].
CDD:226634	228	PRK	Bacteria:10,nodiv:2	COG4160, ArtM, ABC-type arginine/histidine transport system, permease component [Amino acid transport and metabolism].
CDD:226636	562	PRK	Bacteria:34,nodiv:1	COG4166, OppA, ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism].
CDD:226641	534	PRK	Bacteria:12,nodiv:1	COG4172, COG4172, ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only].
CDD:226643	386	PRK	Bacteria:16,nodiv:1	COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism].
CDD:226644	290	PRK	Bacteria:14,nodiv:1	COG4176, ProW, ABC-type proline/glycine betaine transport system, permease component [Amino acid transport and metabolism].
CDD:226645	314	PRK	Bacteria:24,nodiv:1	COG4177, LivM, ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism].
CDD:226646	604	EUKprk	Bacteria:14,Plants:1,nodiv:1	COG4178, COG4178, ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only].
CDD:226651	365	PRK	Bacteria:6,nodiv:1	COG4188, COG4188, Predicted dienelactone hydrolase [General function prediction only].
CDD:226654	603	PRK	Bacteria:5,nodiv:1	COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms].
CDD:226665	287	PRK	Bacteria:20,nodiv:1	COG4208, CysW, ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism].
CDD:226666	309	PRK	Bacteria:6,nodiv:1	COG4209, LplB, ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism].
CDD:226668	341	PRK	Bacteria:11,nodiv:1	COG4213, XylF, ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism].
CDD:226669	394	PRK	Bacteria:9,nodiv:1	COG4214, XylH, ABC-type xylose transport system, permease component [Carbohydrate transport and metabolism].
CDD:226670	230	PRK	Bacteria:12,nodiv:2	COG4215, ArtQ, ABC-type arginine transport system, permease component [Amino acid transport and metabolism].
CDD:226672	337	PRK	Bacteria:2	COG4219, MecR1, Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms].
CDD:226674	246	EUKprk	Bacteria:28,Plants:2,nodiv:2	COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only].
CDD:226675	391	PRK	Bacteria:6,nodiv:1	COG4222, COG4222, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226677	77	PRK	Bacteria:9	COG4224, COG4224, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226678	357	PRK	Bacteria:5,nodiv:1	COG4225, COG4225, Predicted unsaturated glucuronyl hydrolase involved in regulation of bacterial surface properties, and related proteins [General function prediction only].
CDD:226684	640	PRK	Bacteria:12	COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion].
CDD:226685	569	PRK	Bacteria:17	COG4232, COG4232, Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion].
CDD:226686	273	PRK	Bacteria:4,nodiv:1	COG4233, COG4233, Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion].
CDD:226687	287	PRK	Bacteria:12,nodiv:1	COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones].
CDD:226694	156	PRK	Bacteria:9	COG4243, COG4243, Predicted membrane protein [Function unknown].
CDD:226695	160	PRK	Bacteria:6	COG4244, COG4244, Predicted membrane protein [Function unknown].
CDD:226700	380	PRK	Bacteria:2	COG4249, COG4249, Uncharacterized protein containing caspase domain [General function prediction only].
CDD:226703	400	PRK	Bacteria:1	COG4252, COG4252, Predicted transmembrane sensor domain [Signal transduction mechanisms].
CDD:226704	278	PRK	Bacteria:1	COG4253, COG4253, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226715	602	PRK	Bacteria:7	COG4264, RhbC, Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:226729	266	PRK	Bacteria:7	COG4279, COG4279, Uncharacterized conserved protein [Function unknown].
CDD:226734	472	EUKprk	Bacteria:4,Plants:3	COG4284, COG4284, UDP-glucose pyrophosphorylase [Carbohydrate transport and metabolism].
CDD:226761	97	PRK	Bacteria:5,nodiv:1	COG4311, SoxD, Sarcosine oxidase delta subunit [Amino acid transport and metabolism].
CDD:226763	304	PRK	Bacteria:4	COG4313, COG4313, Protein involved in meta-pathway of phenol degradation [Energy production and conversion].
CDD:226769	137	PRK	Bacteria:6	COG4319, COG4319, Ketosteroid isomerase homolog [Function unknown].
CDD:226827	107	PRK	Bacteria:9	COG4392, COG4392, Predicted membrane protein [Function unknown].
CDD:226830	281	PRK	Bacteria:9,nodiv:1	COG4395, COG4395, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226834	376	PRK	Bacteria:7	COG4399, COG4399, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226837	963	PRK	Bacteria:5	COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms].
CDD:226838	140	PRK	Bacteria:9	COG4405, COG4405, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226840	728	PRK	Bacteria:5	COG4409, NanH, Neuraminidase (sialidase) [Carbohydrate transport and metabolism].
CDD:226844	191	PRK	Bacteria:8,nodiv:1	COG4420, COG4420, Predicted membrane protein [Function unknown].
CDD:226847	81	PRK	Bacteria:4	COG4423, COG4423, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226851	200	PRK	Bacteria:8	COG4430, COG4430, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226860	95	PRK	Bacteria:10	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226861	158	PRK	Bacteria:6,nodiv:1	COG4454, COG4454, Uncharacterized copper-binding protein [Inorganic ion transport and metabolism].
CDD:226863	74	PRK	Bacteria:7	COG4456, VagC, Virulence-associated protein and related proteins [Function unknown].
CDD:226868	185	PRK	Bacteria:5,nodiv:1	COG4461, LprI, Uncharacterized protein conserved in bacteria, putative lipoprotein [Function unknown].
CDD:226875	342	PRK	Bacteria:7	COG4469, CoiA, Competence protein CoiA-like family, contains a predicted nuclease    domain [General function prediction only].
CDD:226879	379	PRK	Bacteria:7	COG4473, EcsB, Predicted ABC-type exoprotein transport system, permease component [Intracellular trafficking and secretion].
CDD:226889	438	PRK	Bacteria:9	COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226906	474	PRK	Bacteria:9,nodiv:1	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226909	564	PRK	Bacteria:11	COG4533, COG4533, ABC-type uncharacterized transport system, periplasmic component [General function prediction only].
CDD:226911	423	PRK	Bacteria:17	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism].
CDD:226928	300	PRK	Bacteria:10,nodiv:1	COG4558, ChuT, ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:226929	259	PRK	Bacteria:9,nodiv:1	COG4559, COG4559, ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:226931	224	PRK	Bacteria:7	COG4565, CitB, Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms].
CDD:226932	202	PRK	Bacteria:8,nodiv:1	COG4566, TtrR, Response regulator [Signal transduction mechanisms].
CDD:226936	132	PRK	Bacteria:9	COG4570, Rus, Holliday junction resolvase [DNA replication, recombination, and repair].
CDD:226941	104	PRK	Bacteria:6	COG4575, ElaB, Uncharacterized conserved protein [Function unknown].
CDD:226943	150	PRK	Bacteria:9,nodiv:1	COG4577, CcmK, Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion].
CDD:226944	128	PRK	Bacteria:10	COG4578, GutM, Glucitol operon activator [Transcription].
CDD:226947	1041	EUKprk	Bacteria:5,Plants:3	COG4581, COG4581, Superfamily II RNA helicase [DNA replication, recombination, and repair].
CDD:226949	189	PRK	Bacteria:5,nodiv:1	COG4583, COG4583, Sarcosine oxidase gamma subunit [Amino acid transport and metabolism].
CDD:226950	278	PRK	Bacteria:10,nodiv:2	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:226951	365	PRK	Bacteria:19,nodiv:1	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms].
CDD:226952	325	EUKprk	Bacteria:6,Plants:2	COG4586, COG4586, ABC-type uncharacterized transport system, ATPase component [General function prediction only].
CDD:226957	408	PRK	Bacteria:31,nodiv:1	COG4591, LolE, ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane].
CDD:226962	356	PRK	Bacteria:26,nodiv:1	COG4603, COG4603, ABC-type uncharacterized transport system, permease component [General function prediction only].
CDD:226963	252	PRK	Bacteria:11,nodiv:1	COG4604, CeuD, ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism].
CDD:226964	316	PRK	Bacteria:11,nodiv:1	COG4605, CeuC, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism].
CDD:226966	320	PRK	Bacteria:11,nodiv:1	COG4607, CeuA, ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:226967	268	PRK	Bacteria:47,nodiv:1	COG4608, AppF, ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism].
CDD:226969	580	PRK	Bacteria:8,nodiv:1	COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only].
CDD:226972	411	EUKprk	Bacteria:2,Plants:3	COG4624, COG4624, Iron only hydrogenase large subunit, C-terminal domain [General function prediction only].
CDD:226973	577	PRK	Bacteria:2,nodiv:1	COG4625, COG4625, Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown].
CDD:226974	546	PRK	Bacteria:8	COG4626, COG4626, Phage terminase-like protein, large subunit [General function prediction only].
CDD:226983	200	PRK	Bacteria:6	COG4636, Uma2, Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only].
CDD:226985	367	PRK	Bacteria:14,nodiv:1	COG4638, HcaE, Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only].
CDD:226986	168	PRK	Bacteria:1	COG4639, COG4639, Predicted kinase [General function prediction only].
CDD:226988	373	PRK	Bacteria:4	COG4641, COG4641, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:226991	323	PRK	Bacteria:4,nodiv:1	COG4644, COG4644, Transposase and inactivated derivatives, TnpA family [DNA replication, recombination, and repair].
CDD:226999	657	PRK	Bacteria:4	COG4652, COG4652, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227003	529	PRK	Bacteria:16	COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion].
CDD:227005	338	PRK	Bacteria:13	COG4658, RnfD, Predicted NADH:ubiquinone oxidoreductase, subunit RnfD [Energy production and conversion].
CDD:227006	195	PRK	Bacteria:12	COG4659, RnfG, Predicted NADH:ubiquinone oxidoreductase, subunit RnfG [Energy production and conversion].
CDD:227012	642	PRK	Bacteria:10	COG4666, COG4666, TRAP-type uncharacterized transport system, fused permease components [General function prediction only].
CDD:227014	142	PRK	Bacteria:10	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism].
CDD:227015	246	PRK	Bacteria:10	COG4669, EscJ, Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion].
CDD:227016	527	PRK	Bacteria:16	COG4670, COG4670, Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism].
CDD:227017	400	PRK	Bacteria:4,nodiv:1	COG4671, COG4671, Predicted glycosyl transferase [General function prediction only].
CDD:227019	249	PRK	Bacteria:10,nodiv:1	COG4674, COG4674, Uncharacterized ABC-type transport system, ATPase component [General function prediction only].
CDD:227024	116	PRK	Bacteria:8	COG4679, COG4679, Phage-related protein [Function unknown].
CDD:227039	398	PRK	Bacteria:10,nodiv:1	COG4695, COG4695, Phage-related protein [Function unknown].
CDD:227059	587	PRK	Bacteria:6	COG4715, COG4715, Uncharacterized conserved protein [Function unknown].
CDD:227062	111	PRK	Bacteria:6	COG4718, COG4718, Phage-related protein [Function unknown].
CDD:227064	177	PRK	Bacteria:7	COG4720, COG4720, Predicted membrane protein [Function unknown].
CDD:227066	239	PRK	Bacteria:6	COG4722, COG4722, Phage-related protein [Function unknown].
CDD:227067	198	PRK	Bacteria:6	COG4723, COG4723, Phage-related protein, tail component [Function unknown].
CDD:227070	196	PRK	Bacteria:5	COG4726, PilX, Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227074	162	PRK	Bacteria:9,nodiv:1	COG4731, COG4731, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227076	952	PRK	Bacteria:7	COG4733, COG4733, Phage-related protein, tail component [Function unknown].
CDD:227079	60	PRK	Bacteria:9	COG4736, CcoQ, Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones].
CDD:227085	260	PRK	Bacteria:3	COG4742, COG4742, Predicted transcriptional regulator [Transcription].
CDD:227095	475	PRK	Bacteria:7	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms].
CDD:227100	235	PRK	Bacteria:7	COG4758, COG4758, Predicted membrane protein [Function unknown].
CDD:227101	316	PRK	Bacteria:3	COG4759, COG4759, Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones].
CDD:227108	199	PRK	Bacteria:6	COG4767, VanZ, Glycopeptide antibiotics resistance protein [Defense mechanisms].
CDD:227111	645	PRK	Bacteria:14,nodiv:1	COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism].
CDD:227112	699	PRK	Bacteria:8,nodiv:1	COG4771, FepA, Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism].
CDD:227113	753	PRK	Bacteria:6	COG4772, FecA, Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism].
CDD:227114	719	PRK	Bacteria:8	COG4773, FhuE, Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism].
CDD:227116	766	EUKprk	Bacteria:30,Plants:2,nodiv:1	COG4775, COG4775, Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane].
CDD:227121	377	PRK	Bacteria:5,nodiv:1	COG4782, COG4782, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227122	484	PRK	Bacteria:13,nodiv:1	COG4783, COG4783, Putative Zn-dependent protease, contains TPR repeats [General function prediction only].
CDD:227125	265	PRK	Bacteria:22,nodiv:2	COG4786, FlgG, Flagellar basal body rod protein [Cell motility and secretion].
CDD:227127	689	PRK	Bacteria:10,nodiv:1	COG4789, EscV, Type III secretory pathway, component EscV [Intracellular trafficking and secretion].
CDD:227129	259	PRK	Bacteria:11	COG4791, EscT, Type III secretory pathway, component EscT [Intracellular trafficking and secretion].
CDD:227132	194	PRK	Bacteria:11	COG4795, PulJ, Type II secretory pathway, component PulJ [Intracellular trafficking and secretion].
CDD:227133	709	PRK	Bacteria:16	COG4796, HofQ, Type II secretory pathway, component HofQ [Intracellular trafficking and secretion].
CDD:227136	526	PRK	Bacteria:24,nodiv:1	COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism].
CDD:227142	588	PRK	Bacteria:3	COG4805, COG4805, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227176	120	PRK	Bacteria:7	COG4839, FtsL, Protein required for the initiation of cell division [Cell division and chromosome partitioning].
CDD:227179	97	PRK	Bacteria:10	COG4842, COG4842, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227199	224	PRK	Bacteria:7	COG4862, MecA, Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion].
CDD:227207	372	PRK	Bacteria:4	COG4870, COG4870, Cysteine protease [Posttranslational modification, protein turnover, chaperones].
CDD:227223	394	EUKprk	Bacteria:11,Plants:4	COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function unknown].
CDD:227249	222	PRK	Bacteria:8	COG4912, COG4912, Predicted DNA alkylation repair enzyme [DNA replication, recombination, and repair].
CDD:227265	646	PRK	Bacteria:6,nodiv:1	COG4928, COG4928, Predicted P-loop ATPase [General function prediction only].
CDD:227268	1531	PRK	Bacteria:3	COG4932, COG4932, Predicted outer membrane protein [Cell envelope biogenesis, outer membrane].
CDD:227270	1174	PRK	Bacteria:4	COG4934, COG4934, Predicted protease [Posttranslational modification, protein turnover, chaperones].
CDD:227271	177	PRK	Bacteria:1	COG4935, COG4935, Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones].
CDD:227276	154	PRK	Bacteria:7	COG4940, ComGF, Competence protein ComGF [Intracellular trafficking and secretion].
CDD:227278	420	PRK	Bacteria:17,nodiv:1	COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning].
CDD:227284	372	PRK	Bacteria:35,nodiv:1	COG4948, COG4948, L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only].
CDD:227289	733	PRK	Bacteria:12,nodiv:1	COG4953, PbpC, Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane].
CDD:227293	148	PRK	Bacteria:4,nodiv:1	COG4957, COG4957, Predicted transcriptional regulator [Transcription].
CDD:227295	168	PRK	Bacteria:7,nodiv:1	COG4960, CpaA, Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:227296	185	PRK	Bacteria:7,nodiv:1	COG4961, TadG, Flp pilus assembly protein TadG [Intracellular trafficking and secretion].
CDD:227297	355	PRK	Bacteria:14,nodiv:1	COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion].
CDD:227298	366	PRK	Bacteria:6	COG4963, CpaE, Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion].
CDD:227299	455	PRK	Bacteria:7,nodiv:1	COG4964, CpaC, Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion].
CDD:227300	309	PRK	Bacteria:10,nodiv:1	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion].
CDD:227301	318	PRK	Bacteria:5	COG4966, PilW, Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227302	162	PRK	Bacteria:11	COG4967, PilV, Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227303	139	PRK	Bacteria:6	COG4968, PilE, Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227304	125	PRK	Bacteria:14	COG4969, PilA, Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227305	181	PRK	Bacteria:7	COG4970, FimT, Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227306	354	PRK	Bacteria:9	COG4972, PilM, Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion].
CDD:227308	300	PRK	Bacteria:30,nodiv:2	COG4974, XerD, Site-specific recombinase XerD [DNA replication, recombination, and repair].
CDD:227311	328	PRK	Bacteria:8,nodiv:1	COG4977, COG4977, Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription].
CDD:227312	153	PRK	Bacteria:6	COG4978, COG4978, Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms].
CDD:227313	115	PRK	Bacteria:8	COG4980, GvpP, Gas vesicle protein [General function prediction only].
CDD:227320	573	PRK	Bacteria:15,nodiv:1	COG4987, CydC, ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones].
CDD:227321	559	PRK	Bacteria:20,nodiv:1	COG4988, CydD, ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones].
CDD:227322	298	PRK	Bacteria:13,nodiv:1	COG4989, COG4989, Predicted oxidoreductase [General function prediction only].
CDD:227324	155	PRK	Bacteria:5,nodiv:1	COG4991, COG4991, Uncharacterized protein with a bacterial SH3 domain homologue [Function unknown].
CDD:227325	404	EUKprk	Bacteria:44,Plants:2,nodiv:1	COG4992, ArgD, Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism].
CDD:227328	420	PRK	Bacteria:3	COG4995, COG4995, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227333	712	PRK	Bacteria:10,nodiv:1	COG5000, NtrY, Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms].
CDD:227339	292	PRK	Bacteria:10	COG5006, rhtA, Threonine/homoserine efflux transporter [Amino acid transport and metabolism].
CDD:227340	80	PRK	Bacteria:14	COG5007, COG5007, Predicted transcriptional regulator, BolA superfamily [Transcription].
CDD:227342	797	PRK	Bacteria:21,nodiv:1	COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane].
CDD:227343	257	PRK	Bacteria:7,nodiv:1	COG5010, TadD, Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion].
CDD:227345	227	PRK	Bacteria:6	COG5012, COG5012, Predicted cobalamin binding protein [General function prediction only].
CDD:227346	1227	PRK	Bacteria:14	COG5013, NarG, Nitrate reductase alpha subunit [Energy production and conversion].
CDD:227349	472	PRK	Bacteria:5	COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion].
CDD:227352	373	EUK	Plants:4	COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].
CDD:227353	399	EUK	Plants:4	COG5020, KTR1, Mannosyltransferase [Carbohydrate transport and metabolism].
CDD:227354	872	EUK	Plants:4	COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
CDD:227355	1463	EUK	Plants:3	COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
CDD:227357	440	EUK	Plants:4	COG5024, COG5024, Cyclin [Cell division and chromosome partitioning].
CDD:227358	610	EUK	Plants:3	COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family [Transcription].
CDD:227359	466	EUKprk	Bacteria:1,Plants:4	COG5026, COG5026, Hexokinase [Carbohydrate transport and metabolism].
CDD:227365	2105	EUK	Plants:4	COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of the PI-3 kinase family [Signal transduction mechanisms / Cell division and chromosome partitioning / Chromatin structure and dynamics / DNA replication, recombination, and repair / Intracellular trafficking and secretion].
CDD:227371	1227	EUK	Plants:3	COG5038, COG5038, Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
CDD:227381	467	EUKprk	Bacteria:1,Plants:4	COG5048, COG5048, FOG: Zn-finger [General function prediction only].
CDD:227392	568	EUK	Plants:5	COG5059, KIP1, Kinesin-like protein [Cytoskeleton].
CDD:227400	412	EUK	Plants:4	COG5068, ARG80, Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription].
CDD:227408	371	EUK	Plants:4	COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
CDD:227410	153	EUK	Plants:4	COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
CDD:227414	190	EUK	Plants:3	COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion].
CDD:227416	285	EUK	Plants:4	COG5084, YTH1, Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only].
CDD:227427	757	EUK	Plants:3	COG5096, COG5096, Vesicle coat complex, various subunits [Intracellular trafficking and secretion].
CDD:227430	777	EUK	Plants:3	COG5099, COG5099, RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis].
CDD:227455	160	EUKprk	Bacteria:1,Plants:4	COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
CDD:227472	190	EUK	Plants:3	COG5143, SNC1, Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion].
CDD:227476	512	EUK	Plants:4	COG5147, REB1, Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning].
CDD:227487	582	EUK	Plants:3	COG5158, SEC1, Proteins involved in synaptic transmission and general secretion, Sec1 family [Intracellular trafficking and secretion].
CDD:227497	282	EUK	Plants:3	COG5169, HSF1, Heat shock transcription factor [Transcription].
CDD:227511	476	EUKprk	Bacteria:1,Plants:3	COG5184, ATS1, Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].
CDD:227517	390	EUK	Plants:3	COG5190, FCP1, TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription].
CDD:227535	496	EUK	Plants:4	COG5210, COG5210, GTPase-activating protein [General function prediction only].
CDD:227564	378	EUK	Plants:2	COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification].
CDD:227581	428	EUKprk	Bacteria:13,Plants:4	COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis].
CDD:227582	415	EUKprk	Bacteria:13,Plants:3	COG5257, GCD11, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis].
CDD:227585	482	EUK	Plants:5	COG5260, TRF4, DNA polymerase sigma [DNA replication, recombination, and repair].
CDD:227588	313	PRK	Bacteria:3	COG5263, COG5263, FOG: Glucan-binding domain (YG repeat) [General function prediction only].
CDD:227589	126	EUK	Plants:4	COG5264, VTC1, Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones].
CDD:227590	497	EUKprk	Bacteria:8,Plants:2,nodiv:1	COG5265, ATM1, ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones].
CDD:227591	264	PRK	Bacteria:6	COG5266, CbiK, ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism].
CDD:227597	57	EUK	Plants:4,Primates:1	COG5272, UBI4, Ubiquitin [Posttranslational modification, protein turnover, chaperones].
CDD:227598	309	EUK	Plants:4	COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].
CDD:227599	164	EUK	Plants:3	COG5274, CYB5, Cytochrome b involved in lipid metabolism [Energy production and conversion / Lipid metabolism].
CDD:227602	444	EUK	Plants:5	COG5277, COG5277, Actin and related proteins [Cytoskeleton].
CDD:227603	207	miss	miss	COG5278, COG5278, Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms].
CDD:227606	833	PRK	Bacteria:8,nodiv:1	COG5281, COG5281, Phage-related minor tail protein [Function unknown].
CDD:227608	1213	PRK	Bacteria:7,Phages:1	COG5283, COG5283, Phage-related tail protein [Function unknown].
CDD:227609	299	EUKprk	Bacteria:5,Plants:1	COG5285, COG5285, Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism].
CDD:227614	715	PRK	Bacteria:16	COG5295, Hia, Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures].
CDD:227621	552	PRK	Bacteria:8	COG5305, COG5305, Predicted membrane protein [Function unknown].
CDD:227623	1024	EUKprk	Bacteria:1,Plants:4	COG5307, COG5307, SEC7 domain proteins [General function prediction only].
CDD:227637	570	EUK	Plants:4	COG5329, COG5329, Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms].
CDD:227638	364	PRK	Bacteria:4,nodiv:1	COG5330, COG5330, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227640	297	EUK	Plants:3	COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair].
CDD:227644	479	PRK	Bacteria:12	COG5339, COG5339, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227647	181	PRK	Bacteria:4,nodiv:1	COG5342, COG5342, Invasion protein B, involved in pathogenesis [General function prediction only].
CDD:227651	319	EUK	Plants:4	COG5347, COG5347, GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
CDD:227652	126	PRK	Bacteria:4,nodiv:1	COG5349, COG5349, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227659	458	PRK	Bacteria:6	COG5361, COG5361, Uncharacterized conserved protein [Function unknown].
CDD:227673	295	PRK	Bacteria:8	COG5383, COG5383, Uncharacterized protein conserved in bacteria [Function unknown].
CDD:227680	524	EUK	Plants:3	COG5391, COG5391, Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
CDD:227692	178	PRK	Bacteria:25,nodiv:2	COG5405, HslV, ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones].
CDD:227695	296	EUK	Plants:3	COG5408, COG5408, SPX domain-containing protein [Signal transduction mechanisms].
CDD:227698	460	EUK	Plants:3	COG5411, COG5411, Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].
CDD:227706	160	PRK	Bacteria:4	COG5419, COG5419, Uncharacterized conserved protein [Function unknown].
CDD:227708	480	PRK	Bacteria:3	COG5421, COG5421, Transposase [DNA replication, recombination, and repair].
CDD:227711	242	PRK	Bacteria:7	COG5424, COG5424, Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism].
CDD:227717	174	PRK	Bacteria:5,nodiv:1	COG5430, COG5430, Uncharacterized secreted protein [Function unknown].
CDD:227720	121	PRK	Bacteria:7	COG5433, COG5433, Transposase [DNA replication, recombination, and repair].
CDD:227721	542	EUKprk	Bacteria:5,Plants:1,nodiv:1	COG5434, PGU1, Endopygalactorunase [Cell envelope biogenesis, outer membrane].
CDD:227722	147	PRK	Bacteria:6	COG5435, COG5435, Uncharacterized conserved protein [Function unknown].
CDD:227725	385	PRK	Bacteria:5	COG5438, COG5438, Predicted multitransmembrane protein [Function unknown].
CDD:227731	565	PRK	Bacteria:5	COG5444, COG5444, Uncharacterized conserved protein [Function unknown].
CDD:227737	84	PRK	Bacteria:5,nodiv:1	COG5450, COG5450, Transcription regulator of the Arc/MetJ class [Transcription].
CDD:227744	63	PRK	Bacteria:8,nodiv:1	COG5457, COG5457, Uncharacterized conserved small protein [Function unknown].
CDD:227751	289	PRK	Bacteria:9	COG5464, COG5464, Uncharacterized conserved protein [Function unknown].
CDD:227757	96	PRK	Bacteria:5,nodiv:1	COG5470, COG5470, Uncharacterized conserved protein [Function unknown].
CDD:227763	488	PRK	Bacteria:4,nodiv:1	COG5476, COG5476, Uncharacterized conserved protein [Function unknown].
CDD:227765	141	EUKprk	Bacteria:3,Plants:2,nodiv:1	COG5478, COG5478, Predicted small integral membrane protein [Function unknown].
CDD:227766	556	PRK	Bacteria:5	COG5479, COG5479, Uncharacterized protein potentially involved in peptidoglycan biosynthesis [Cell envelope biogenesis, outer membrane].
CDD:227778	204	EUKprk	Bacteria:2,Plants:3	COG5491, VPS24, Conserved protein implicated in secretion [Cell motility and secretion].
CDD:227779	329	PRK	Bacteria:8	COG5492, COG5492, Bacterial surface proteins containing Ig-like domains [Cell motility and secretion].
CDD:227783	130	PRK	Bacteria:8	COG5496, COG5496, Predicted thioesterase [General function prediction only].
CDD:227784	228	PRK	Bacteria:5	COG5497, COG5497, Predicted secreted protein [Function unknown].
CDD:227789	135	PRK	Bacteria:4	COG5502, COG5502, Uncharacterized conserved protein [Function unknown].
CDD:227798	492	PRK	Bacteria:6	COG5511, COG5511, Bacteriophage capsid protein [General function prediction only].
CDD:227799	194	PRK	Bacteria:8	COG5512, COG5512, Zn-ribbon-containing, possibly RNA-binding protein and truncated derivatives [General function prediction only].
CDD:227806	562	PRK	Bacteria:7	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair].
CDD:227811	285	EUKprk	Bacteria:2,Plants:2	COG5524, COG5524, Bacteriorhodopsin [General function prediction only].
CDD:227812	611	PRK	Bacteria:8	COG5525, COG5525, Phage terminase, large subunit GpA [Replication, recombination and repair].
CDD:227818	237	EUKprk	Bacteria:2,Plants:3	COG5531, COG5531, SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics].
CDD:227829	420	EUKprk	Bacteria:2,Plants:3	COG5542, COG5542, Predicted integral membrane protein [Function unknown].
CDD:227837	125	PRK	Bacteria:3	COG5550, COG5550, Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones].
CDD:227838	261	PRK	Bacteria:6	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms].
CDD:227850	379	PRK	Bacteria:4,nodiv:1	COG5563, COG5563, Predicted integral membrane proteins containing uncharacterized repeats [Function unknown].
CDD:227861	271	EUK	Plants:3	COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
CDD:227863	156	EUK	Plants:3	COG5576, COG5576, Homeodomain-containing transcription factor [Transcription].
CDD:227864	145	PRK	Bacteria:4	COG5577, COG5577, Spore coat protein [Cell envelope biogenesis, outer membrane].
CDD:227865	208	PRK	Bacteria:6	COG5578, COG5578, Predicted integral membrane protein [Function unknown].
CDD:227868	233	PRK	Bacteria:10	COG5581, COG5581, c-di-GMP-binding protein [Signal transduction mechanisms].
CDD:227872	417	PRK	Bacteria:5	COG5585, COG5585, NAD+--asparagine ADP-ribosyltransferase [Signal transduction mechanisms].
CDD:227881	827	EUK	Plants:3	COG5594, COG5594, Uncharacterized integral membrane protein [Function unknown].
CDD:227885	526	PRK	Bacteria:3	COG5598, COG5598, Trimethylamine:corrinoid methyltransferase [Coenzyme metabolism].
CDD:227894	283	PRK	Bacteria:6	COG5607, COG5607, Uncharacterized conserved protein [Function unknown].
CDD:227903	152	PRK	Bacteria:1	COG5616, COG5616, Predicted integral membrane protein [Function unknown].
CDD:227904	801	PRK	Bacteria:3	COG5617, COG5617, Predicted integral membrane protein [Function unknown].
CDD:227919	302	PRK	Bacteria:3	COG5632, COG5632, N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane].
CDD:227922	824	PRK	Bacteria:4	COG5635, COG5635, Predicted NTPase (NACHT family) [Signal transduction mechanisms].
CDD:227928	498	EUK	Plants:4	COG5641, GAT1, GATA Zn-finger-containing transcription factor [Transcription].
CDD:227935	211	EUK	Plants:3	COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].
CDD:227937	536	PRK	Bacteria:7	COG5650, COG5650, Predicted integral membrane protein [Function unknown].
CDD:227938	490	EUKprk	Bacteria:7,Plants:1	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion].
CDD:227939	148	PRK	Bacteria:8	COG5652, COG5652, Predicted integral membrane protein [Function unknown].
CDD:227940	406	PRK	Bacteria:3,nodiv:1	COG5653, COG5653, Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane].
CDD:227941	163	PRK	Bacteria:4	COG5654, COG5654, Uncharacterized conserved protein [Function unknown].
CDD:227945	204	PRK	Bacteria:6	COG5658, COG5658, Predicted integral membrane protein [Function unknown].
CDD:227946	385	PRK	Bacteria:4	COG5659, COG5659, FOG: Transposase [DNA replication, recombination, and repair].
CDD:227949	256	PRK	Bacteria:10,nodiv:1	COG5662, COG5662, Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription].
CDD:214398	602	EUK	Vertebrates:257	MTH00004, ND5, NADH dehydrogenase subunit 5; Validated.
CDD:214404	70	EUK	Invertebrates:32	MTH00025, ATP8, ATP synthase F0 subunit 8; Validated.
CDD:177110	229	EUK	Invertebrates:29	MTH00035, ATP6, ATP synthase F0 subunit 6; Validated.
CDD:214408	54	EUK	Invertebrates:20	MTH00036, ATP8, ATP synthase F0 subunit 8; Validated.
CDD:214409	323	EUK	Invertebrates:29	MTH00040, ND1, NADH dehydrogenase subunit 1; Validated.
CDD:177116	349	EUK	Invertebrates:26	MTH00041, ND2, NADH dehydrogenase subunit 2; Validated.
CDD:177117	116	EUK	Invertebrates:24	MTH00042, ND3, NADH dehydrogenase subunit 3; Validated.
CDD:214410	98	EUK	Invertebrates:24	MTH00043, ND4L, NADH dehydrogenase subunit 4L; Validated.
CDD:214411	458	EUK	Invertebrates:27	MTH00044, ND4, NADH dehydrogenase subunit 4; Validated.
CDD:177120	162	EUK	Invertebrates:29	MTH00045, ND6, NADH dehydrogenase subunit 6; Validated.
CDD:177121	355	EUK	Invertebrates:32	MTH00046, CYTB, cytochrome b; Validated.
CDD:214412	194	EUK	Invertebrates:32	MTH00047, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:177124	215	EUK	Invertebrates:31	MTH00049, COX3, cytochrome c oxidase subunit III; Validated.
CDD:177125	170	EUK	Invertebrates:32	MTH00050, ATP6, ATP synthase F0 subunit 6; Validated.
CDD:177129	186	EUK	Invertebrates:24	MTH00057, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177130	293	EUK	Invertebrates:31	MTH00058, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:177131	289	EUK	Invertebrates:32	MTH00059, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177132	116	EUK	Invertebrates:30	MTH00060, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:177133	86	EUK	Invertebrates:31	MTH00061, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:214413	417	EUK	Invertebrates:33	MTH00062, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:214414	522	EUK	Invertebrates:31	MTH00063, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:177136	151	EUK	Invertebrates:31	MTH00064, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:214415	172	EUK	Vertebrates:67	MTH00065, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:214416	598	EUK	Vertebrates:71	MTH00066, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:177139	98	EUK	Vertebrates:63	MTH00067, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:214417	458	EUK	Vertebrates:76	MTH00068, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:177141	114	EUK	Vertebrates:60	MTH00069, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:177142	346	EUK	Vertebrates:72	MTH00070, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:164642	54	EUK	Vertebrates:56	MTH00072, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:177144	227	EUK	Vertebrates:69	MTH00073, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:177149	231	EUK	Invertebrates:40	MTH00080, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:177150	256	EUK	Invertebrates:39	MTH00083, COX3, cytochrome c oxidase subunit III; Provisional.
CDD:177151	355	EUK	Invertebrates:39	MTH00086, CYTB, cytochrome b; Provisional.
CDD:177152	195	EUK	Invertebrates:37	MTH00087, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:177153	284	EUK	Invertebrates:38	MTH00090, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:177154	273	EUK	Invertebrates:40	MTH00091, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177155	111	EUK	Invertebrates:38	MTH00092, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:177156	77	EUK	Invertebrates:34	MTH00093, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177157	403	EUK	Invertebrates:41	MTH00094, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:177158	527	EUK	Invertebrates:41	MTH00095, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:177159	121	EUK	Invertebrates:39	MTH00097, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177163	226	EUK	Mammals:181,Primates:40,Rodents:16	MTH00101, ATP6, ATP synthase F0 subunit 6; Validated.
CDD:214420	67	EUK	Mammals:166,Primates:41,Rodents:18	MTH00102, ATP8, ATP synthase F0 subunit 8; Validated.
CDD:177167	347	EUK	Mammals:215,Primates:47,Rodents:18	MTH00105, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177168	115	EUK	Mammals:178,Primates:40,Rodents:18	MTH00106, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:177169	98	EUK	Mammals:163,Primates:43,Rodents:19	MTH00107, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177170	602	EUK	Mammals:216,Primates:47,Rodents:18	MTH00108, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:214421	175	EUK	Mammals:196,Primates:47,Rodents:20	MTH00109, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177172	459	EUK	Mammals:203,Primates:47,Rodents:18	MTH00110, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:214422	323	EUK	Vertebrates:241	MTH00111, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:214423	346	EUK	Vertebrates:254	MTH00112, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177175	114	EUK	Vertebrates:186	MTH00113, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:214424	174	EUK	Vertebrates:241	MTH00115, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177178	227	EUK	Vertebrates:245	MTH00117, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:177179	261	EUK	Vertebrates:184	MTH00118, COX3, cytochrome c oxidase subunit III; Provisional.
CDD:214425	380	EUK	Vertebrates:235	MTH00119, CYTB, cytochrome b; Provisional.
CDD:177181	227	EUK	Vertebrates:194	MTH00120, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:214426	54	EUK	Vertebrates:167	MTH00123, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:214427	457	EUK	Vertebrates:245	MTH00124, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:177184	98	EUK	Vertebrates:195	MTH00125, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177185	98	EUK	Vertebrates:442	MTH00126, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177186	459	EUK	Vertebrates:493	MTH00127, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:177190	227	EUK	Vertebrates:471	MTH00132, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:177191	55	EUK	Vertebrates:417	MTH00133, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:177193	347	EUK	Vertebrates:512	MTH00135, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177194	116	EUK	Vertebrates:453	MTH00136, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:214428	611	EUK	Vertebrates:505	MTH00137, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:177196	173	EUK	Vertebrates:493	MTH00138, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:214430	228	EUK	Invertebrates:73	MTH00140, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:177199	259	EUK	Invertebrates:73	MTH00141, COX3, cytochrome c oxidase subunit III; Provisional.
CDD:177201	307	EUK	Invertebrates:73	MTH00143, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:214432	328	EUK	Invertebrates:66	MTH00144, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177203	379	EUK	Invertebrates:73	MTH00145, CYTB, cytochrome b; Provisional.
CDD:177204	51	EUK	Invertebrates:38	MTH00147, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:214433	117	EUK	Invertebrates:66	MTH00148, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:214434	97	EUK	Invertebrates:67	MTH00149, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:214435	417	EUK	Invertebrates:71	MTH00150, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:214436	565	EUK	Invertebrates:72	MTH00151, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:214437	163	EUK	Invertebrates:70	MTH00152, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177210	511	EUK	Invertebrates:252	MTH00153, COX1, cytochrome c oxidase subunit I; Provisional.
CDD:214438	227	EUK	Invertebrates:221	MTH00154, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:214439	255	EUK	Invertebrates:214	MTH00155, COX3, cytochrome c oxidase subunit III; Provisional.
CDD:214440	356	EUK	Invertebrates:226	MTH00156, CYTB, cytochrome b; Provisional.
CDD:214441	223	EUK	Invertebrates:220	MTH00157, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:177215	32	EUK	Invertebrates:159	MTH00158, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:214442	335	EUK	Invertebrates:230	MTH00160, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177217	113	EUK	Invertebrates:189	MTH00161, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:177218	89	EUK	Invertebrates:217	MTH00162, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:214443	445	EUK	Invertebrates:221	MTH00163, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:214444	573	EUK	Invertebrates:241	MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:214445	160	EUK	Invertebrates:221	MTH00166, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:177223	225	EUK	Invertebrates:23,Vertebrates:10	MTH00168, COX2, cytochrome c oxidase subunit II; Provisional.
CDD:214446	67	EUK	Invertebrates:20	MTH00169, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:177225	54	EUK	Invertebrates:8,Vertebrates:21	MTH00171, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:214448	231	EUK	Invertebrates:76	MTH00173, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:214449	229	EUK	Invertebrates:11	MTH00176, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:177230	227	EUK	Invertebrates:17,Vertebrates:23	MTH00179, ATP6, ATP synthase F0 subunit 6; Provisional.
CDD:214450	93	EUK	Invertebrates:22,Vertebrates:23	MTH00181, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177236	52	EUK	Invertebrates:9	MTH00186, ATP8, ATP synthase F0 subunit 8; Provisional.
CDD:177237	97	EUK	Invertebrates:11	MTH00188, ND4L, NADH dehydrogenase subunit 4L; Provisional.
CDD:177238	260	EUK	Invertebrates:25,Vertebrates:21	MTH00189, COX3, cytochrome c oxidase subunit III; Provisional.
CDD:177239	365	EUK	Invertebrates:25,Vertebrates:25	MTH00191, CYTB, cytochrome b; Provisional.
CDD:177241	306	EUK	Invertebrates:214	MTH00193, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:177244	323	EUK	Invertebrates:9	MTH00197, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:177246	347	EUK	Invertebrates:18,Vertebrates:24	MTH00200, ND2, NADH dehydrogenase subunit 2; Provisional.
CDD:214455	117	EUK	Invertebrates:10	MTH00202, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:214456	112	EUK	Invertebrates:26,Vertebrates:23	MTH00203, ND3, NADH dehydrogenase subunit 3; Provisional.
CDD:214457	448	EUK	Invertebrates:11	MTH00205, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:214458	450	EUK	Invertebrates:28,Vertebrates:23	MTH00206, ND4, NADH dehydrogenase subunit 4; Provisional.
CDD:177251	628	EUK	Invertebrates:29	MTH00208, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:177252	564	EUK	Invertebrates:9	MTH00209, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:214459	597	EUK	Invertebrates:25,Vertebrates:24	MTH00211, ND5, NADH dehydrogenase subunit 5; Provisional.
CDD:214460	160	EUK	Invertebrates:10	MTH00212, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:214461	168	EUK	Invertebrates:22,Vertebrates:23	MTH00214, ND6, NADH dehydrogenase subunit 6; Provisional.
CDD:214463	311	EUK	Invertebrates:22,Vertebrates:23	MTH00218, ND1, NADH dehydrogenase subunit 1; Provisional.
CDD:177260	512	EUK	Invertebrates:73	MTH00223, COX1, cytochrome c oxidase subunit I; Provisional.
CDD:222775	72	PRK	Phages:21	PHA00080, PHA00080, DksA-like zinc finger domain containing protein.
CDD:222788	131	PRK	Phages:24	PHA00415, 25, baseplate wedge subunit.
CDD:222789	193	PRK	Phages:31	PHA00428, PHA00428, tail tubular protein A.
CDD:222797	807	PRK	Phages:40	PHA00452, PHA00452, T3/T7-like RNA polymerase.
CDD:222798	315	PRK	Phages:26	PHA00454, PHA00454, ATP-dependent DNA ligase.
CDD:222816	212	PRK	Phages:25	PHA00911, 21, prohead core scaffolding protein and protease.
CDD:222826	107	PRK	Phages:13	PHA01627, PHA01627, DNA binding protein.
CDD:177369	881	PRK	Phages:20	PHA02528, 43, DNA polymerase; Provisional.
CDD:222855	278	PRK	Phages:16	PHA02529, O, capsid-scaffolding protein; Provisional.
CDD:222856	300	PRK	Phages:25	PHA02530, pseT, polynucleotide kinase; Provisional.
CDD:222857	514	PRK	Phages:27	PHA02531, 20, portal vertex protein; Provisional.
CDD:222858	534	PRK	Phages:26	PHA02533, 17, large terminase protein; Provisional.
CDD:222861	230	PRK	Phages:16	PHA02537, M, terminase endonuclease subunit; Provisional.
CDD:164934	348	PRK	Phages:16	PHA02538, N, capsid protein; Provisional.
CDD:222862	648	PRK	Phages:25	PHA02539, 18, tail sheath protein; Provisional.
CDD:222863	337	PRK	Phages:26	PHA02540, 61, DNA primase; Provisional.
CDD:222864	473	PRK	Phages:26	PHA02542, 41, 41 helicase; Provisional.
CDD:222865	125	PRK	Phages:26	PHA02543, regA, translation repressor protein; Provisional.
CDD:222866	316	PRK	Phages:25	PHA02544, 44, clamp loader, small subunit; Provisional.
CDD:177380	223	PRK	Phages:24	PHA02545, 45, sliding clamp; Provisional.
CDD:222867	340	PRK	Phages:24	PHA02546, 47, endonuclease subunit; Provisional.
CDD:222868	179	PRK	Phages:24	PHA02547, 55, RNA polymerase sigma factor; Provisional.
CDD:222869	304	PRK	Phages:26	PHA02550, 32, single-stranded DNA binding protein; Provisional.
CDD:177385	163	PRK	Phages:24	PHA02551, 19, tail tube protein; Provisional.
CDD:222870	151	PRK	Phages:26	PHA02552, 4, head completion protein; Provisional.
CDD:222871	611	PRK	Phages:26	PHA02553, 6, baseplate wedge subunit; Provisional.
CDD:177388	311	PRK	Phages:24	PHA02554, 13, neck protein; Provisional.
CDD:222872	216	PRK	Phages:26	PHA02555, 14, neck protein; Provisional.
CDD:222873	273	PRK	Phages:24	PHA02556, 15, tail sheath stabilizer and completion protein; Provisional.
CDD:222874	271	PRK	Phages:24	PHA02557, 22, prohead core protein; Provisional.
CDD:222875	501	PRK	Phages:26	PHA02558, uvsW, UvsW helicase; Provisional.
CDD:222876	216	PRK	Phages:22	PHA02559, 59, 59 protein; Provisional.
CDD:222877	351	PRK	Phages:15	PHA02561, D, tail protein; Provisional.
CDD:222878	562	PRK	Phages:22	PHA02562, 46, endonuclease subunit; Provisional.
CDD:222879	630	PRK	Phages:14	PHA02563, PHA02563, DNA polymerase; Provisional.
CDD:222881	684	PRK	Phages:14	PHA02566, alt, ADP-ribosyltransferase; Provisional.
CDD:222882	304	PRK	Phages:20	PHA02567, rnh, RnaseH; Provisional.
CDD:177400	109	PRK	Phages:19	PHA02571, a-gt.4, hypothetical protein; Provisional.
CDD:222885	227	PRK	Phages:19	PHA02575, 1, deoxynucleoside monophosphate kinase; Provisional.
CDD:222887	284	PRK	Phages:19	PHA02581, 9, baseplate wedge tail fiber connector; Provisional.
CDD:222889	218	PRK	Phages:19	PHA02583, 11, baseplate wedge subunit and tail pin; Provisional.
CDD:222890	1229	PRK	Phages:19	PHA02584, 34, long tail fiber, proximal subunit; Provisional.
CDD:222893	488	PRK	Phages:22	PHA02587, 30, DNA ligase; Provisional.
CDD:222895	378	PRK	Phages:19	PHA02589, rnlA, RNA ligase A; Provisional.
CDD:222896	439	PRK	Phages:21	PHA02592, 52, DNA topisomerase II medium subunit; Provisional.
CDD:222898	470	PRK	Phages:17	PHA02594, nadV, nicotinamide phosphoribosyl transferase; Provisional.
CDD:177432	454	PRK	Phages:19	PHA02607, wac, fibritin; Provisional.
CDD:222910	363	PRK	Viruses:22	PHA02614, PHA02614, Major capsid protein VP1; Provisional.
CDD:222912	647	PRK	Viruses:21	PHA02624, PHA02624, large T antigen; Provisional.
CDD:177443	675	PRK	Viruses:27	PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
CDD:222919	323	PRK	Viruses:25	PHA02688, PHA02688, ORF059 IMV protein VP55; Provisional.
CDD:165115	360	PRK	Viruses:2	PHA02748, PHA02748, viral inexin-like protein; Provisional.
CDD:222927	613	PRK	Viruses:96,nodiv:1	PHA02774, PHA02774, E1; Provisional.
CDD:222928	503	PRK	Viruses:99,nodiv:1	PHA02778, PHA02778, major capsid L1 protein; Provisional.
CDD:222950	648	PRK	Viruses:25	PHA02952, PHA02952, EEV maturation protein; Provisional.
CDD:222961	96	PRK	Viruses:27	PHA03005, PHA03005, sulfhydryl oxidase; Provisional.
CDD:222962	1004	PRK	Viruses:27	PHA03036, PHA03036, DNA polymerase; Provisional.
CDD:222968	438	PRK	Viruses:25	PHA03065, PHA03065, Hypothetical protein; Provisional.
CDD:222969	383	PRK	Viruses:25	PHA03067, PHA03067, hypothetical protein; Provisional.
CDD:177515	270	PRK	Viruses:24	PHA03068, PHA03068, DNA-binding phosphoprotein; Provisional.
CDD:177518	150	PRK	Viruses:25	PHA03073, PHA03073, late transcription factor VLTF-2; Provisional.
CDD:222971	219	PRK	Viruses:25	PHA03078, PHA03078, transcriptional elongation factor; Provisional.
CDD:222972	366	PRK	Viruses:25	PHA03080, PHA03080, putative virion core protein; Provisional.
CDD:222973	595	PRK	Viruses:25	PHA03081, PHA03081, putative metalloprotease; Provisional.
CDD:222975	334	PRK	Viruses:27	PHA03083, PHA03083, poxvirus myristoylprotein; Provisional.
CDD:222977	191	PRK	Viruses:20	PHA03089, PHA03089, late transcription factor VLTF-4; Provisional.
CDD:222979	185	PRK	Viruses:18	PHA03093, PHA03093, EEV glycoprotein; Provisional.
CDD:222980	471	PRK	Viruses:12	PHA03095, PHA03095, ankyrin-like protein; Provisional.
CDD:222981	284	PRK	Viruses:2	PHA03096, PHA03096, p28-like protein; Provisional.
CDD:222983	534	PRK	Viruses:16	PHA03098, PHA03098, kelch-like protein; Provisional.
CDD:222984	422	PRK	Viruses:13	PHA03100, PHA03100, ankyrin repeat protein; Provisional.
CDD:222985	314	PRK	Viruses:27	PHA03101, PHA03101, DNA topoisomerase type I; Provisional.
CDD:222986	153	PRK	Viruses:16	PHA03102, PHA03102, Small T antigen; Reviewed.
CDD:222990	141	PRK	Viruses:15	PHA03112, PHA03112, IL-18 binding protein; Provisional.
CDD:222996	286	PRK	Viruses:13	PHA03131, PHA03131, dUTPase; Provisional.
CDD:222997	580	PRK	Viruses:13	PHA03132, PHA03132, thymidine kinase; Provisional.
CDD:222999	835	PRK	Viruses:13	PHA03142, PHA03142, helicase-primase primase subunit BSLF1; Provisional.
CDD:223001	289	PRK	Viruses:13	PHA03148, PHA03148, hypothetical protein; Provisional.
CDD:223004	1028	PRK	Viruses:17	PHA03173, PHA03173, UL37 tegument protein; Provisional.
CDD:223013	180	PRK	Viruses:14	PHA03230, PHA03230, nuclear protein UL55; Provisional.
CDD:223014	829	PRK	Viruses:42	PHA03231, PHA03231, glycoprotein BALF4; Provisional.
CDD:223015	586	PRK	Viruses:19	PHA03232, PHA03232, DNA packaging protein UL32; Provisional.
CDD:223022	583	PRK	Viruses:19	PHA03248, PHA03248, DNA packaging tegument protein UL25; Provisional.
CDD:177569	316	PRK	Viruses:19	PHA03257, PHA03257, Capsid triplex subunit 2; Provisional.
CDD:223026	469	PRK	Viruses:19	PHA03261, PHA03261, Capsid triplex subunit 1; Provisional.
CDD:223028	332	PRK	Viruses:13	PHA03263, PHA03263, Capsid triplex subunit 1; Provisional.
CDD:223034	523	PRK	Viruses:19	PHA03293, PHA03293, deoxyribonuclease; Provisional.
CDD:223035	835	PRK	Viruses:18	PHA03294, PHA03294, envelope glycoprotein H; Provisional.
CDD:223036	714	PRK	Viruses:10	PHA03295, PHA03295, envelope glycoprotein H; Provisional.
CDD:223038	253	PRK	Viruses:10	PHA03302, PHA03302, envelope glycoprotein L; Provisional.
CDD:223039	1352	PRK	Viruses:17	PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
CDD:223040	782	PRK	Viruses:42	PHA03311, PHA03311, helicase-primase subunit BBLF4; Provisional.
CDD:223043	272	PRK	Viruses:17	PHA03323, PHA03323, nuclear egress membrane protein UL34; Provisional.
CDD:223045	275	PRK	Viruses:9	PHA03326, PHA03326, nuclear egress membrane protein; Provisional.
CDD:223046	316	PRK	Viruses:19	PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional.
CDD:177589	526	PRK	Viruses:17	PHA03348, PHA03348, tegument protein UL21; Provisional.
CDD:177590	343	PRK	Viruses:18	PHA03349, PHA03349, tegument protein UL16; Provisional.
CDD:223054	686	PRK	Viruses:19	PHA03359, PHA03359, UL17 tegument protein; Provisional.
CDD:223055	302	PRK	Viruses:19	PHA03361, PHA03361, UL7 tegument protein; Provisional.
CDD:223056	1189	PRK	Viruses:22	PHA03362, PHA03362, single-stranded binding protein UL29; Provisional.
CDD:223057	264	PRK	Viruses:22	PHA03364, PHA03364, hypothetical protein; Provisional.
CDD:177602	419	PRK	Viruses:11	PHA03365, PHA03365, hypothetical protein; Provisional.
CDD:223058	1304	PRK	Viruses:13	PHA03366, PHA03366, FGAM-synthase; Provisional.
CDD:223059	1115	PRK	Viruses:19	PHA03367, PHA03367, single-stranded DNA binding protein; Provisional.
CDD:223060	738	PRK	Viruses:19	PHA03368, PHA03368, DNA packaging terminase subunit 1; Provisional.
CDD:223063	730	PRK	Viruses:12	PHA03374, PHA03374, hypothetical protein; Provisional.
CDD:223067	432	PRK	Viruses:18	PHA03380, PHA03380, transactivating tegument protein VP16; Provisional.
CDD:223068	445	PRK	Viruses:21	PHA03384, PHA03384, early DNA-binding protein E2A; Provisional.
CDD:177623	267	PRK	Viruses:39	PHA03387, gp37, spherodin-like protein; Provisional.
CDD:223069	267	PRK	Viruses:49	PHA03390, pk1, serine/threonine-protein kinase 1; Provisional.
CDD:223070	395	PRK	Viruses:52	PHA03391, p47, viral transcription regulator p47; Provisional.
CDD:223071	507	PRK	Viruses:45	PHA03392, egt, ecdysteroid UDP-glucosyltransferase; Provisional.
CDD:223072	682	PRK	Viruses:47	PHA03393, odv-e66, occlusion-derived virus envelope protein E66; Provisional.
CDD:223073	865	PRK	Viruses:53	PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like protein; Provisional.
CDD:223074	493	PRK	Viruses:53	PHA03396, lef-9, late expression factor 9; Provisional.
CDD:177633	363	PRK	Viruses:53	PHA03397, vlf-1, very late expression factor 1; Provisional.
CDD:223075	303	PRK	Viruses:53	PHA03398, PHA03398, viral phosphatase superfamily protein; Provisional.
CDD:223076	200	PRK	Viruses:53	PHA03399, pif3, per os infectivity factor 3; Provisional.
CDD:177653	250	EUK	Plants:13	PLN00014, PLN00014, light-harvesting-like protein 3; Provisional.
CDD:215029	378	EUK	Plants:15	PLN00016, PLN00016, RNA-binding protein; Provisional.
CDD:215031	413	EUK	Plants:14	PLN00020, PLN00020, ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional.
CDD:177659	313	EUK	Plants:9	PLN00021, PLN00021, chlorophyllase.
CDD:177665	476	EUK	Plants:16	PLN00028, PLN00028, nitrate transmembrane transporter; Provisional.
CDD:215035	398	EUK	Plants:16	PLN00033, PLN00033, photosystem II stability/assembly factor; Provisional.
CDD:215038	233	EUK	Invertebrates:1,Plants:17	PLN00040, PLN00040, Protein MAK16 homolog; Provisional.
CDD:177688	263	EUK	Invertebrates:1,Plants:18	PLN00057, PLN00057, proliferating cell nuclear antigen; Provisional.
CDD:215046	262	EUK	Plants:13	PLN00066, PLN00066, PsbP domain-containing protein 4; Provisional.
CDD:215056	450	EUK	Plants:14	PLN00104, PLN00104, MYST -like histone acetyltransferase; Provisional.
CDD:215058	323	EUK	Plants:16	PLN00106, PLN00106, malate dehydrogenase.
CDD:215059	399	EUK	Plants:9	PLN00111, PLN00111, accumulation of photosystem one; Provisional.
CDD:215064	170	EUK	Plants:15	PLN00122, PLN00122, serine/threonine protein phosphatase 2A; Provisional.
CDD:215067	276	EUK	Plants:16	PLN00129, PLN00129, succinate dehydrogenase [ubiquinone] iron-sulfur subunit.
CDD:215073	815	EUK	Plants:9	PLN00142, PLN00142, sucrose synthase.
CDD:215075	130	EUK	Invertebrates:1,Plants:18	PLN00146, PLN00146, 40S ribosomal protein S15a; Provisional.
CDD:177755	130	EUK	Invertebrates:1,Plants:18	PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional.
CDD:215083	761	EUK	Plants:16	PLN00162, PLN00162, transport protein sec23; Provisional.
CDD:215084	480	EUK	Plants:2	PLN00164, PLN00164, glucosyltransferase; Provisional.
CDD:215090	333	EUK	Plants:8	PLN00176, PLN00176, galactinol synthase.
CDD:215091	390	EUK	Plants:15	PLN00179, PLN00179, acyl- [acyl-carrier protein] desaturase.
CDD:215095	457	EUK	Plants:16	PLN00191, PLN00191, enolase.
CDD:215101	519	EUK	Plants:16	PLN00203, PLN00203, glutamyl-tRNA reductase.
CDD:177880	344	EUK	Plants:9	PLN02236, PLN02236, choline kinase.
CDD:215132	189	EUK	Plants:14	PLN02238, PLN02238, hypoxanthine phosphoribosyltransferase.
CDD:177883	352	EUK	Plants:14	PLN02240, PLN02240, UDP-glucose 4-epimerase.
CDD:215133	436	EUK	Plants:14	PLN02241, PLN02241, glucose-1-phosphate adenylyltransferase.
CDD:215135	340	EUK	Plants:15	PLN02244, PLN02244, tocopherol O-methyltransferase.
CDD:215137	537	EUK	Plants:9	PLN02246, PLN02246, 4-coumarate--CoA ligase.
CDD:215138	1135	EUK	Plants:9	PLN02248, PLN02248, cellulose synthase-like protein.
CDD:215141	888	EUK	Plants:15	PLN02252, PLN02252, nitrate reductase [NADPH].
CDD:215144	304	EUK	Plants:16	PLN02256, PLN02256, arogenate dehydrogenase.
CDD:215145	590	EUK	Plants:9	PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
CDD:215155	371	EUK	Plants:15	PLN02275, PLN02275, transferase, transferring glycosyl groups.
CDD:215156	361	EUK	Plants:7	PLN02276, PLN02276, gibberellin 20-oxidase.
CDD:215159	334	EUK	Plants:15	PLN02285, PLN02285, methionyl-tRNA formyltransferase.
CDD:215160	576	EUK	Plants:15	PLN02286, PLN02286, arginine-tRNA ligase.
CDD:215162	394	EUK	Plants:13	PLN02288, PLN02288, mannose-6-phosphate isomerase.
CDD:177942	579	EUK	Plants:16	PLN02307, PLN02307, phosphoglucomutase.
CDD:215181	382	EUK	Plants:16	PLN02317, PLN02317, arogenate dehydratase.
CDD:215183	330	EUK	Plants:8	PLN02323, PLN02323, probable fructokinase.
CDD:215186	557	EUK	Plants:15	PLN02327, PLN02327, CTP synthase.
CDD:215190	465	EUK	Plants:11	PLN02332, PLN02332, membrane bound O-acyl transferase (MBOAT) family protein.
CDD:215192	229	EUK	Plants:16	PLN02334, PLN02334, ribulose-phosphate 3-epimerase.
CDD:177977	229	EUK	Plants:9	PLN02343, PLN02343, allene oxide cyclase.
CDD:177978	284	EUK	Plants:16	PLN02344, PLN02344, chorismate mutase.
CDD:215199	426	EUK	Plants:16	PLN02349, PLN02349, glycerol-3-phosphate acyltransferase.
CDD:215207	256	EUK	Plants:14	PLN02363, PLN02363, phosphoribosylanthranilate isomerase.
CDD:215208	308	EUK	Plants:16	PLN02366, PLN02366, spermidine synthase.
CDD:215211	583	EUK	Plants:16	PLN02371, PLN02371, phosphoglucosamine mutase family protein.
CDD:178008	413	EUK	Plants:9	PLN02382, PLN02382, probable sucrose-phosphatase.
CDD:215220	362	EUK	Plants:7	PLN02393, PLN02393, leucoanthocyanidin dioxygenase like protein.
CDD:215222	423	EUK	Plants:15	PLN02397, PLN02397, aspartate transaminase.
CDD:215233	332	EUK	Plants:16	PLN02424, PLN02424, ketopantoate hydroxymethyltransferase.
CDD:215236	349	EUK	Plants:15	PLN02428, PLN02428, lipoic acid synthase.
CDD:215237	345	EUK	Plants:16	PLN02433, PLN02433, uroporphyrinogen decarboxylase.
CDD:178053	237	EUK	Plants:12	PLN02434, PLN02434, fatty acid hydroxylase.
CDD:178056	813	EUK	Plants:16	PLN02437, PLN02437, ribonucleoside--diphosphate reductase large subunit.
CDD:215242	525	EUK	Plants:9	PLN02441, PLN02441, cytokinin dehydrogenase.
CDD:215246	758	EUK	Plants:13	PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
CDD:215247	459	EUK	Plants:7	PLN02448, PLN02448, UDP-glycosyltransferase family protein.
CDD:178068	485	EUK	Plants:16	PLN02449, PLN02449, ferrochelatase.
CDD:215250	455	EUK	Plants:15	PLN02456, PLN02456, citrate synthase.
CDD:215255	511	EUK	Plants:13	PLN02461, PLN02461, Probable pyruvate kinase.
CDD:215258	573	EUK	Plants:14	PLN02465, PLN02465, L-galactono-1,4-lactone dehydrogenase.
CDD:215265	328	EUK	Plants:8	PLN02478, PLN02478, alternative oxidase.
CDD:215269	335	EUK	Plants:11	PLN02489, PLN02489, homocysteine S-methyltransferase.
CDD:215278	553	EUK	Plants:16	PLN02502, PLN02502, lysyl-tRNA synthetase.
CDD:215287	355	EUK	Plants:13	PLN02524, PLN02524, S-adenosylmethionine decarboxylase.
CDD:178151	267	EUK	Plants:15	PLN02536, PLN02536, diaminopimelate epimerase.
CDD:178164	578	EUK	Plants:16	PLN02549, PLN02549, asparagine synthase (glutamine-hydrolyzing).
CDD:178166	521	EUK	Plants:16	PLN02551, PLN02551, aspartokinase.
CDD:215307	554	EUK	Plants:14	PLN02567, PLN02567, alpha,alpha-trehalase.
CDD:215314	496	EUK	Plants:16	PLN02576, PLN02576, protoporphyrinogen oxidase.
CDD:178196	249	EUK	Plants:16	PLN02584, PLN02584, 5'-methylthioadenosine nucleosidase.
CDD:215322	342	EUK	Plants:16	PLN02594, PLN02594, phosphatidate cytidylyltransferase.
CDD:215325	382	EUK	Plants:16	PLN02605, PLN02605, monogalactosyldiacylglycerol synthase.
CDD:178232	263	EUK	Plants:15	PLN02625, PLN02625, uroporphyrin-III C-methyltransferase.
CDD:215339	334	EUK	Plants:16	PLN02632, PLN02632, phytoene synthase.
CDD:215341	538	EUK	Plants:14	PLN02635, PLN02635, disproportionating enzyme.
CDD:215350	480	EUK	Plants:9	PLN02648, PLN02648, allene oxide synthase.
CDD:215351	560	EUK	Plants:16	PLN02649, PLN02649, glucose-6-phosphate isomerase.
CDD:178257	364	EUK	Plants:15	PLN02651, PLN02651, cysteine desulfurase.
CDD:178263	390	EUK	Plants:16	PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl reductase.
CDD:178266	284	EUK	Plants:15	PLN02660, PLN02660, pantoate--beta-alanine ligase.
CDD:215357	366	EUK	Plants:5	PLN02665, PLN02665, pectinesterase family protein.
CDD:215366	455	EUK	Plants:13	PLN02681, PLN02681, proline dehydrogenase.
CDD:178291	266	EUK	Plants:16	PLN02688, PLN02688, pyrroline-5-carboxylate reductase.
CDD:178309	267	EUK	Plants:15	PLN02707, PLN02707, Soluble inorganic pyrophosphatase.
CDD:178316	229	EUK	Plants:13	PLN02714, PLN02714, thiamin pyrophosphokinase.
CDD:178319	316	EUK	Plants:14	PLN02717, PLN02717, uridine nucleosidase.
CDD:215390	440	EUK	Plants:9	PLN02733, PLN02733, phosphatidylcholine-sterol O-acyltransferase.
CDD:215401	343	EUK	Plants:16	PLN02752, PLN02752, [acyl-carrier protein] S-malonyltransferase.
CDD:215412	629	EUK	Plants:7	PLN02769, PLN02769, Probable galacturonosyltransferase.
CDD:178374	286	EUK	Plants:16	PLN02775, PLN02775, Probable dihydrodipicolinate reductase.
CDD:215416	286	EUK	Plants:16	PLN02779, PLN02779, haloacid dehalogenase-like hydrolase family protein.
CDD:178380	315	EUK	Plants:15	PLN02783, PLN02783, diacylglycerol O-acyltransferase.
CDD:215423	320	EUK	Plants:14	PLN02789, PLN02789, farnesyltranstransferase.
CDD:215424	654	EUK	Plants:16	PLN02790, PLN02790, transketolase.
CDD:178392	505	EUK	Plants:13	PLN02795, PLN02795, allantoinase.
CDD:178408	211	EUK	Plants:14	PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
CDD:215438	403	EUK	Plants:14	PLN02818, PLN02818, tocopherol cyclase.
CDD:178418	336	EUK	Plants:15	PLN02823, PLN02823, spermine synthase.
CDD:178421	409	EUK	Plants:15	PLN02826, PLN02826, dihydroorotate dehydrogenase.
CDD:215444	615	EUK	Plants:13	PLN02830, PLN02830, UDP-sugar pyrophosphorylase.
CDD:215454	336	EUK	Plants:14	PLN02845, PLN02845, Branched-chain-amino-acid aminotransferase-like protein.
CDD:215457	491	EUK	Plants:16	PLN02852, PLN02852, ferredoxin-NADP+ reductase.
CDD:215458	492	EUK	Plants:16	PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha chain.
CDD:215469	465	EUK	Plants:16	PLN02871, PLN02871, UDP-sulfoquinovose:DAG sulfoquinovosyltransferase.
CDD:215471	274	EUK	Plants:16	PLN02873, PLN02873, coproporphyrinogen-III oxidase.
CDD:215472	398	EUK	Plants:14	PLN02875, PLN02875, 4-hydroxyphenylpyruvate dioxygenase.
CDD:215476	530	EUK	Plants:11	PLN02881, PLN02881, tetrahydrofolylpolyglutamate synthase.
CDD:178473	545	EUK	Plants:14	PLN02885, PLN02885, nicotinate phosphoribosyltransferase.
CDD:215485	562	EUK	Plants:16	PLN02895, PLN02895, phosphoacetylglucosamine mutase.
CDD:215487	936	EUK	Plants:16	PLN02900, PLN02900, alanyl-tRNA synthetase.
CDD:178499	296	EUK	Plants:15	PLN02911, PLN02911, inositol-phosphate phosphatase.
CDD:178512	220	EUK	Plants:16	PLN02924, PLN02924, thymidylate kinase.
CDD:215501	347	EUK	Plants:12	PLN02928, PLN02928, oxidoreductase family protein.
CDD:215502	301	EUK	Plants:14	PLN02929, PLN02929, NADH kinase.
CDD:215508	328	EUK	Plants:10	PLN02941, PLN02941, inositol-tetrakisphosphate 1-kinase.
CDD:178534	577	EUK	Plants:16	PLN02948, PLN02948, phosphoribosylaminoimidazole carboxylase.
CDD:178546	223	EUK	Plants:12	PLN02961, PLN02961, alanine-tRNA ligase.
CDD:215526	817	EUK	Plants:13	PLN02974, PLN02974, adenosylmethionine-8-amino-7-oxononanoate transaminase.
CDD:215528	478	EUK	Plants:15	PLN02977, PLN02977, glutathione synthetase.
CDD:215559	473	EUK	Plants:8	PLN03074, PLN03074, auxin influx permease; Provisional.
CDD:178624	296	EUK	Plants:8	PLN03075, PLN03075, nicotianamine synthase; Provisional.
CDD:215569	373	EUK	Plants:7	PLN03089, PLN03089, hypothetical protein; Provisional.
CDD:215577	403	EUK	Plants:14	PLN03103, PLN03103, GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional.
CDD:215582	206	EUK	Invertebrates:1,Plants:18	PLN03111, PLN03111, DNA-directed RNA polymerase II subunit family protein; Provisional.
CDD:215588	260	EUK	Plants:8	PLN03120, PLN03120, nucleic acid binding protein; Provisional.
CDD:215594	581	EUK	Plants:16	PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
CDD:178689	606	EUK	Plants:13	PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog; Provisional.
CDD:178691	431	EUK	Plants:5	PLN03146, PLN03146, aspartyl protease family protein; Provisional.
CDD:215615	346	EUK	Plants:11	PLN03180, PLN03180, reversibly glycosylated polypeptide; Provisional.
CDD:215617	429	EUK	Plants:9	PLN03182, PLN03182, xyloglucan 6-xylosyltransferase; Provisional.
CDD:215628	487	EUK	Plants:9	PLN03196, PLN03196, MOC1-like protein; Provisional.
CDD:215639	475	EUK	Plants:16	PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
CDD:234564	210	PRK	Bacteria:879,nodiv:1	PRK00001, rplC, 50S ribosomal protein L3; Validated.
CDD:234565	358	PRK	Bacteria:686,nodiv:2	PRK00002, aroB, 3-dehydroquinate synthase; Reviewed.
CDD:234566	105	PRK	Bacteria:841,nodiv:1	PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
CDD:234567	309	PRK	Bacteria:433	PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
CDD:234568	147	PRK	Bacteria:656,nodiv:2	PRK00006, fabZ, (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed.
CDD:234569	693	PRK	Bacteria:654,nodiv:1	PRK00007, PRK00007, elongation factor G; Reviewed.
CDD:234570	911	PRK	Bacteria:399	PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
CDD:178791	179	PRK	Bacteria:917,nodiv:1	PRK00010, rplE, 50S ribosomal protein L5; Validated.
CDD:234571	416	PRK	Bacteria:894,nodiv:2	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
CDD:234572	459	PRK	Bacteria:732,nodiv:2	PRK00012, gatA, aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed.
CDD:234573	542	PRK	Bacteria:817,nodiv:1	PRK00013, groEL, chaperonin GroEL; Reviewed.
CDD:234574	197	PRK	Bacteria:753,nodiv:2	PRK00015, rnhB, ribonuclease HII; Validated.
CDD:234575	159	PRK	Bacteria:418	PRK00016, PRK00016, metal-binding heat shock protein; Provisional.
CDD:234576	72	PRK	Bacteria:356,nodiv:1	PRK00019, rpmE, 50S ribosomal protein L31; Reviewed.
CDD:234577	244	PRK	Bacteria:793,nodiv:1	PRK00021, truA, tRNA pseudouridine synthase A; Validated.
CDD:234578	202	PRK	Bacteria:211,nodiv:1	PRK00022, lolB, outer membrane lipoprotein LolB; Provisional.
CDD:234579	225	PRK	Bacteria:527,nodiv:2	PRK00023, cmk, cytidylate kinase; Provisional.
CDD:178801	224	PRK	Bacteria:445,nodiv:1	PRK00024, PRK00024, hypothetical protein; Reviewed.
CDD:234580	380	PRK	Bacteria:309,nodiv:1	PRK00025, lpxB, lipid-A-disaccharide synthase; Reviewed.
CDD:234581	244	PRK	Bacteria:747,nodiv:1	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed.
CDD:234582	177	PRK	Bacteria:551,nodiv:1	PRK00028, infC, translation initiation factor IF-3; Reviewed.
CDD:234583	487	PRK	Bacteria:263,nodiv:1	PRK00029, PRK00029, hypothetical protein; Validated.
CDD:178807	195	PRK	Bacteria:221	PRK00031, lolA, lipoprotein chaperone; Reviewed.
CDD:234584	190	PRK	Bacteria:124	PRK00032, PRK00032, Maf-like protein; Reviewed.
CDD:178809	100	PRK	Bacteria:286	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed.
CDD:178810	95	PRK	Bacteria:492	PRK00034, gatC, aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed.
CDD:234585	333	PRK	Bacteria:435,nodiv:2	PRK00035, hemH, ferrochelatase; Reviewed.
CDD:234586	412	PRK	Bacteria:939,nodiv:1	PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
CDD:234587	164	PRK	Bacteria:617,nodiv:2	PRK00039, ruvC, Holliday junction resolvase; Reviewed.
CDD:234588	75	PRK	Bacteria:658,nodiv:1	PRK00040, rpsP, 30S ribosomal protein S16; Reviewed.
CDD:178815	93	PRK	Bacteria:212	PRK00041, PRK00041, hypothetical protein; Validated.
CDD:234589	250	PRK	Bacteria:809,nodiv:2	PRK00042, tpiA, triosephosphate isomerase; Provisional.
CDD:234590	212	PRK	Bacteria:298	PRK00043, thiE, thiamine-phosphate pyrophosphorylase; Reviewed.
CDD:234591	288	PRK	Bacteria:231,nodiv:1	PRK00044, psd, phosphatidylserine decarboxylase; Reviewed.
CDD:234592	423	PRK	Bacteria:606,nodiv:1	PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
CDD:234593	334	PRK	Bacteria:236	PRK00046, murB, UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional.
CDD:234594	498	PRK	Bacteria:313	PRK00047, glpK, glycerol kinase; Provisional.
CDD:234595	257	PRK	Bacteria:749,nodiv:2	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
CDD:234596	396	PRK	Bacteria:755,nodiv:1	PRK00049, PRK00049, elongation factor Tu; Reviewed.
CDD:234597	296	PRK	Bacteria:843,nodiv:2	PRK00050, PRK00050, 16S rRNA m(4)C1402 methyltranserfase; Provisional.
CDD:234598	125	PRK	Bacteria:288,nodiv:1	PRK00051, hisI, phosphoribosyl-AMP cyclohydrolase; Reviewed.
CDD:234599	269	PRK	Bacteria:677,nodiv:1	PRK00052, PRK00052, prolipoprotein diacylglyceryl transferase; Reviewed.
CDD:234600	363	PRK	Bacteria:353	PRK00053, alr, alanine racemase; Reviewed.
CDD:234601	250	PRK	Bacteria:121	PRK00054, PRK00054, dihydroorotate dehydrogenase electron transfer subunit; Reviewed.
CDD:234602	270	PRK	Bacteria:292	PRK00055, PRK00055, ribonuclease Z; Reviewed.
CDD:234603	236	PRK	Bacteria:249,nodiv:1	PRK00056, mtgA, monofunctional biosynthetic peptidoglycan transglycosylase; Provisional.
CDD:234604	213	PRK	Bacteria:174,nodiv:1	PRK00058, PRK00058, methionine sulfoxide reductase A; Provisional.
CDD:234606	154	PRK	Bacteria:732,nodiv:1	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase; Provisional.
CDD:234607	426	PRK	Bacteria:635,nodiv:1	PRK00062, PRK00062, glutamate-1-semialdehyde aminotransferase; Provisional.
CDD:234608	361	PRK	Bacteria:510,nodiv:1	PRK00064, recF, recombination protein F; Reviewed.
CDD:178836	315	PRK	Bacteria:116	PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
CDD:234609	970	PRK	Bacteria:52	PRK00068, PRK00068, hypothetical protein; Validated.
CDD:234610	126	PRK	Bacteria:547,nodiv:1	PRK00070, acpS, 4'-phosphopantetheinyl transferase; Provisional.
CDD:234611	203	PRK	Bacteria:443,nodiv:1	PRK00071, nadD, nicotinic acid mononucleotide adenylyltransferase; Provisional.
CDD:234612	295	PRK	Bacteria:652,nodiv:1	PRK00072, hemC, porphobilinogen deaminase; Reviewed.
CDD:234613	389	PRK	Bacteria:884,nodiv:2	PRK00073, pgk, phosphoglycerate kinase; Provisional.
CDD:234614	511	PRK	Bacteria:898,nodiv:2	PRK00074, guaA, GMP synthase; Reviewed.
CDD:234615	361	PRK	Bacteria:253,nodiv:1	PRK00075, cbiD, cobalt-precorrin-6A synthase; Reviewed.
CDD:234616	196	PRK	Bacteria:798,nodiv:2	PRK00076, recR, recombination protein RecR; Reviewed.
CDD:234617	425	PRK	Bacteria:913,nodiv:1	PRK00077, eno, enolase; Provisional.
CDD:234619	328	PRK	Bacteria:924,nodiv:2	PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
CDD:234620	194	PRK	Bacteria:620,nodiv:2	PRK00081, coaE, dephospho-CoA kinase; Reviewed.
CDD:234621	339	PRK	Bacteria:444,nodiv:1	PRK00082, hrcA, heat-inducible transcription repressor; Provisional.
CDD:178850	185	PRK	Bacteria:829,nodiv:2	PRK00083, frr, ribosome recycling factor; Reviewed.
CDD:178851	159	PRK	Bacteria:462	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed.
CDD:234622	247	PRK	Bacteria:496	PRK00085, recO, DNA repair protein RecO; Reviewed.
CDD:234623	647	PRK	Bacteria:33	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed.
CDD:234624	292	PRK	Bacteria:836,nodiv:2	PRK00089, era, GTPase Era; Reviewed.
CDD:234625	222	PRK	Bacteria:344	PRK00090, bioD, dithiobiotin synthetase; Reviewed.
CDD:234626	307	PRK	Bacteria:714,nodiv:2	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed.
CDD:234627	154	PRK	Bacteria:533,nodiv:1	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed.
CDD:234628	435	PRK	Bacteria:840,nodiv:1	PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
CDD:234629	325	PRK	Bacteria:716,nodiv:1	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated.
CDD:234630	617	PRK	Bacteria:550,nodiv:2	PRK00095, mutL, DNA mismatch repair protein; Reviewed.
CDD:234631	298	PRK	Bacteria:188	PRK00098, PRK00098, GTPase RsgA; Reviewed.
CDD:234632	172	PRK	Bacteria:913,nodiv:2	PRK00099, rplJ, 50S ribosomal protein L10; Reviewed.
CDD:234633	229	PRK	Bacteria:595,nodiv:1	PRK00102, rnc, ribonuclease III; Reviewed.
CDD:234634	157	PRK	Bacteria:525,nodiv:1	PRK00103, PRK00103, rRNA large subunit methyltransferase; Provisional.
CDD:234635	242	PRK	Bacteria:122	PRK00104, scpA, segregation and condensation protein A; Reviewed.
CDD:234636	335	PRK	Bacteria:266,nodiv:1	PRK00105, cobT, nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; Reviewed.
CDD:234637	187	PRK	Bacteria:655,nodiv:2	PRK00107, gidB, 16S rRNA methyltransferase GidB; Reviewed.
CDD:234638	344	PRK	Bacteria:846,nodiv:2	PRK00108, mraY, phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional.
CDD:234639	138	PRK	Bacteria:602,nodiv:1	PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed.
CDD:234640	245	PRK	Bacteria:703,nodiv:1	PRK00110, PRK00110, hypothetical protein; Validated.
CDD:234642	366	PRK	Bacteria:635	PRK00112, tgt, queuine tRNA-ribosyltransferase; Provisional.
CDD:234643	293	PRK	Bacteria:375	PRK00114, hslO, Hsp33-like chaperonin; Reviewed.
CDD:234644	346	PRK	Bacteria:568,nodiv:1	PRK00115, hemE, uroporphyrinogen decarboxylase; Validated.
CDD:234645	192	PRK	Bacteria:714,nodiv:2	PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
CDD:234646	157	PRK	Bacteria:233,nodiv:1	PRK00117, recX, recombination regulator RecX; Reviewed.
CDD:234647	104	PRK	Bacteria:154	PRK00118, PRK00118, putative DNA-binding protein; Validated.
CDD:234648	196	PRK	Bacteria:505,nodiv:2	PRK00120, PRK00120, dITP/XTP pyrophosphatase; Reviewed.
CDD:234649	202	PRK	Bacteria:606	PRK00121, trmB, tRNA (guanine-N(7)-)-methyltransferase; Reviewed.
CDD:234650	172	PRK	Bacteria:588,nodiv:2	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional.
CDD:178882	151	PRK	Bacteria:186,nodiv:1	PRK00124, PRK00124, hypothetical protein; Validated.
CDD:234651	278	PRK	Bacteria:127	PRK00125, pyrF, orotidine 5'-phosphate decarboxylase; Reviewed.
CDD:234652	286	PRK	Bacteria:135	PRK00128, ipk, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:234653	209	PRK	Bacteria:669,nodiv:1	PRK00129, upp, uracil phosphoribosyltransferase; Reviewed.
CDD:178886	290	PRK	Bacteria:33	PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
CDD:234654	175	PRK	Bacteria:298	PRK00131, aroK, shikimate kinase; Reviewed.
CDD:178888	130	PRK	Bacteria:911,nodiv:2	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
CDD:234655	673	PRK	Bacteria:406	PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
CDD:234657	188	PRK	Bacteria:106	PRK00135, scpB, segregation and condensation protein B; Reviewed.
CDD:234658	130	PRK	Bacteria:880,nodiv:1	PRK00136, rpsH, 30S ribosomal protein S8; Validated.
CDD:234659	147	PRK	Bacteria:852,nodiv:2	PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
CDD:234660	460	PRK	Bacteria:593,nodiv:2	PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional.
CDD:234661	141	PRK	Bacteria:850,nodiv:1	PRK00140, rplK, 50S ribosomal protein L11; Validated.
CDD:234663	314	PRK	Bacteria:296	PRK00142, PRK00142, putative rhodanese-related sulfurtransferase; Provisional.
CDD:234664	346	PRK	Bacteria:864,nodiv:2	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
CDD:234666	342	PRK	Bacteria:643,nodiv:2	PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional.
CDD:178901	194	PRK	Bacteria:88	PRK00148, PRK00148, Maf-like protein; Reviewed.
CDD:234667	401	PRK	Bacteria:829,nodiv:2	PRK00149, dnaA, chromosomal replication initiation protein; Reviewed.
CDD:234668	165	PRK	Bacteria:700,nodiv:1	PRK00150, def, peptide deformylase; Reviewed.
CDD:234669	104	PRK	Bacteria:566,nodiv:1	PRK00153, PRK00153, hypothetical protein; Validated.
CDD:234670	227	PRK	Bacteria:463	PRK00155, ispD, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; Reviewed.
CDD:234671	123	PRK	Bacteria:819,nodiv:1	PRK00157, rplL, 50S ribosomal protein L7/L12; Reviewed.
CDD:178908	108	PRK	Bacteria:109	PRK00162, glpE, thiosulfate sulfurtransferase; Validated.
CDD:234672	331	PRK	Bacteria:411	PRK00164, moaA, molybdenum cofactor biosynthesis protein A; Reviewed.
CDD:234673	275	PRK	Bacteria:339,nodiv:1	PRK00166, apaH, diadenosine tetraphosphatase; Reviewed.
CDD:234674	159	PRK	Bacteria:723,nodiv:1	PRK00168, coaD, phosphopantetheine adenylyltransferase; Provisional.
CDD:234675	201	PRK	Bacteria:186	PRK00170, PRK00170, azoreductase; Reviewed.
CDD:234676	65	PRK	Bacteria:835,nodiv:2	PRK00172, rpmI, 50S ribosomal protein L35; Reviewed.
CDD:178914	238	PRK	Bacteria:535,nodiv:2	PRK00173, rph, ribonuclease PH; Reviewed.
CDD:234677	637	PRK	Bacteria:384,nodiv:1	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional.
CDD:234678	379	PRK	Bacteria:240	PRK00175, metX, homoserine O-acetyltransferase; Provisional.
CDD:234679	548	PRK	Bacteria:432,nodiv:1	PRK00179, pgi, glucose-6-phosphate isomerase; Reviewed.
CDD:234680	402	PRK	Bacteria:454	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed.
CDD:234682	339	PRK	Bacteria:639	PRK00188, trpD, anthranilate phosphoribosyltransferase; Provisional.
CDD:234684	273	PRK	Bacteria:41	PRK00192, PRK00192, mannosyl-3-phosphoglycerate phosphatase; Reviewed.
CDD:178923	90	PRK	Bacteria:139	PRK00194, PRK00194, hypothetical protein; Validated.
CDD:234685	417	PRK	Bacteria:724,nodiv:1	PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
CDD:178925	94	PRK	Bacteria:291	PRK00199, ihfB, integration host factor subunit beta; Reviewed.
CDD:234686	137	PRK	Bacteria:571,nodiv:2	PRK00202, nusB, transcription antitermination protein NusB; Reviewed.
CDD:178927	150	PRK	Bacteria:355,nodiv:2	PRK00203, rnhA, ribonuclease H; Reviewed.
CDD:178928	128	PRK	Bacteria:138	PRK00207, PRK00207, sulfur transfer complex subunit TusD; Validated.
CDD:234687	250	PRK	Bacteria:562,nodiv:1	PRK00208, thiG, thiazole synthase; Reviewed.
CDD:178930	119	PRK	Bacteria:116	PRK00211, PRK00211, sulfur relay protein TusC; Validated.
CDD:234688	205	PRK	Bacteria:513	PRK00215, PRK00215, LexA repressor; Validated.
CDD:234689	239	PRK	Bacteria:402,nodiv:1	PRK00216, ubiE, ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed.
CDD:234690	207	PRK	Bacteria:223	PRK00218, PRK00218, putative lysogenization regulator; Reviewed.
CDD:234691	198	PRK	Bacteria:334,nodiv:1	PRK00220, PRK00220, putative glycerol-3-phosphate acyltransferase PlsY; Provisional.
CDD:234692	142	PRK	Bacteria:341	PRK00222, PRK00222, methionine sulfoxide reductase B; Provisional.
CDD:234693	157	PRK	Bacteria:623	PRK00226, greA, transcription elongation factor GreA; Reviewed.
CDD:234694	191	PRK	Bacteria:307,nodiv:1	PRK00228, PRK00228, hypothetical protein; Validated.
CDD:234695	230	PRK	Bacteria:421,nodiv:2	PRK00230, PRK00230, orotidine 5'-phosphate decarboxylase; Reviewed.
CDD:234696	332	PRK	Bacteria:217	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed.
CDD:234697	249	PRK	Bacteria:242	PRK00235, cobS, cobalamin synthase; Reviewed.
CDD:234698	297	PRK	Bacteria:397	PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
CDD:178943	88	PRK	Bacteria:839,nodiv:2	PRK00239, rpsT, 30S ribosomal protein S20; Reviewed.
CDD:234699	256	PRK	Bacteria:161	PRK00241, nudC, NADH pyrophosphatase; Reviewed.
CDD:234700	222	PRK	Bacteria:237,nodiv:1	PRK00249, flgH, flagellar basal body L-ring protein; Reviewed.
CDD:234701	865	PRK	Bacteria:952,nodiv:2	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
CDD:178948	108	PRK	Bacteria:118	PRK00253, fliE, flagellar hook-basal body protein FliE; Reviewed.
CDD:166874	381	PRK	Bacteria:25	PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase; Validated.
CDD:234703	278	PRK	Bacteria:500,nodiv:1	PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
CDD:234704	179	PRK	Bacteria:285,nodiv:2	PRK00259, PRK00259, intracellular septation protein A; Reviewed.
CDD:234705	463	PRK	Bacteria:915,nodiv:1	PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
CDD:234707	64	PRK	Bacteria:777,nodiv:2	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.
CDD:234708	272	PRK	Bacteria:866,nodiv:1	PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed.
CDD:178954	72	PRK	Bacteria:870,nodiv:2	PRK00276, infA, translation initiation factor IF-1; Validated.
CDD:178955	200	PRK	Bacteria:709,nodiv:2	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed.
CDD:234710	260	PRK	Bacteria:462,nodiv:1	PRK00278, trpC, indole-3-glycerol-phosphate synthase; Reviewed.
CDD:234711	215	PRK	Bacteria:698,nodiv:2	PRK00279, adk, adenylate kinase; Reviewed.
CDD:234712	268	PRK	Bacteria:606,nodiv:1	PRK00281, PRK00281, undecaprenyl pyrophosphate phosphatase; Reviewed.
CDD:234713	299	PRK	Bacteria:292	PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed.
CDD:178960	23	PRK	Bacteria:41	PRK00284, pqqA, coenzyme PQQ synthesis protein PqqA; Provisional.
CDD:178961	99	PRK	Bacteria:343,nodiv:2	PRK00285, ihfA, integration host factor subunit alpha; Reviewed.
CDD:234714	438	PRK	Bacteria:661,nodiv:1	PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
CDD:234715	627	PRK	Bacteria:967,nodiv:2	PRK00290, dnaK, molecular chaperone DnaK; Provisional.
CDD:234716	316	PRK	Bacteria:194,nodiv:1	PRK00292, glk, glucokinase; Provisional.
CDD:234717	571	PRK	Bacteria:172	PRK00293, dipZ, thiol:disulfide interchange protein precursor; Provisional.
CDD:234718	86	PRK	Bacteria:216	PRK00296, minE, cell division topological specificity factor MinE; Reviewed.
CDD:178967	81	PRK	Bacteria:136	PRK00299, PRK00299, sulfur transfer protein SirA; Reviewed.
CDD:234719	205	PRK	Bacteria:815,nodiv:2	PRK00300, gmk, guanylate kinase; Provisional.
CDD:234720	233	PRK	Bacteria:403	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed.
CDD:234721	505	PRK	Bacteria:343	PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed.
CDD:178971	66	PRK	Bacteria:753,nodiv:2	PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed.
CDD:234722	232	PRK	Bacteria:925,nodiv:1	PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
CDD:234723	264	PRK	Bacteria:691,nodiv:2	PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed.
CDD:178974	212	PRK	Bacteria:193,nodiv:1	PRK00312, pcm, protein-L-isoaspartate O-methyltransferase; Reviewed.
CDD:234724	193	PRK	Bacteria:137	PRK00315, PRK00315, potassium-transporting ATPase subunit C; Reviewed.
CDD:234725	193	PRK	Bacteria:218	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed.
CDD:234726	303	PRK	Bacteria:261	PRK00321, rdgC, recombination associated protein; Reviewed.
CDD:234727	359	PRK	Bacteria:26	PRK00325, algL, poly(beta-D-mannuronate) lyase; Provisional.
CDD:234728	139	PRK	Bacteria:505,nodiv:2	PRK00326, PRK00326, cell division protein MraZ; Reviewed.
CDD:178979	86	PRK	Bacteria:130	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated.
CDD:234729	604	PRK	Bacteria:797,nodiv:1	PRK00331, PRK00331, glucosamine--fructose-6-phosphate aminotransferase; Reviewed.
CDD:234731	271	PRK	Bacteria:268	PRK00343, ipk, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:234732	250	PRK	Bacteria:528,nodiv:2	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional.
CDD:234733	234	PRK	Bacteria:268,nodiv:1	PRK00347, PRK00347, putative DNA-binding transcriptional regulator; Reviewed.
CDD:234734	943	PRK	Bacteria:596,nodiv:1	PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
CDD:178985	92	PRK	Bacteria:886,nodiv:2	PRK00357, rpsS, 30S ribosomal protein S19; Reviewed.
CDD:234735	231	PRK	Bacteria:885,nodiv:2	PRK00358, pyrH, uridylate kinase; Provisional.
CDD:234736	76	PRK	Bacteria:828,nodiv:2	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed.
CDD:178988	95	PRK	Bacteria:763,nodiv:2	PRK00364, groES, co-chaperonin GroES; Reviewed.
CDD:234737	360	PRK	Bacteria:693,nodiv:1	PRK00366, ispG, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed.
CDD:178991	204	PRK	Bacteria:119	PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed.
CDD:234739	160	PRK	Bacteria:443,nodiv:1	PRK00376, lspA, lipoprotein signal peptidase; Reviewed.
CDD:178993	334	PRK	Bacteria:170	PRK00378, PRK00378, nucleoid-associated protein NdpA; Validated.
CDD:234741	281	PRK	Bacteria:577,nodiv:1	PRK00380, panC, pantoate--beta-alanine ligase; Reviewed.
CDD:234742	359	PRK	Bacteria:489,nodiv:1	PRK00389, gcvT, glycine cleavage system aminomethyltransferase T; Reviewed.
CDD:234743	805	PRK	Bacteria:949,nodiv:1	PRK00390, leuS, leucyl-tRNA synthetase; Validated.
CDD:178997	79	PRK	Bacteria:883,nodiv:2	PRK00391, rpsR, 30S ribosomal protein S18; Reviewed.
CDD:234744	69	PRK	Bacteria:794,nodiv:2	PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed.
CDD:234745	197	PRK	Bacteria:234	PRK00393, ribA, GTP cyclohydrolase II; Reviewed.
CDD:234746	179	PRK	Bacteria:77	PRK00394, PRK00394, transcription factor; Reviewed.
CDD:179001	79	PRK	Bacteria:291,nodiv:1	PRK00395, hfq, RNA-binding protein Hfq; Provisional.
CDD:234747	46	PRK	Bacteria:59	PRK00398, rpoP, DNA-directed RNA polymerase subunit P; Provisional.
CDD:179004	44	PRK	Bacteria:743,nodiv:1	PRK00399, rpmH, 50S ribosomal protein L34; Reviewed.
CDD:179005	105	PRK	Bacteria:303,nodiv:1	PRK00400, hisE, phosphoribosyl-ATP pyrophosphatase; Validated.
CDD:234748	418	PRK	Bacteria:165	PRK00402, PRK00402, 3-isopropylmalate dehydratase large subunit; Reviewed.
CDD:234749	1112	PRK	Bacteria:945,nodiv:2	PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
CDD:179008	139	PRK	Bacteria:18	PRK00407, PRK00407, hypothetical protein; Provisional.
CDD:234750	782	PRK	Bacteria:138	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed.
CDD:234751	394	PRK	Bacteria:54	PRK00411, cdc6, cell division control protein 6; Reviewed.
CDD:234752	638	PRK	Bacteria:767,nodiv:2	PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
CDD:179013	59	PRK	Bacteria:74	PRK00415, rps27e, 30S ribosomal protein S27e; Reviewed.
CDD:234753	177	PRK	Bacteria:563,nodiv:1	PRK00416, dcd, deoxycytidine triphosphate deaminase; Reviewed.
CDD:234754	62	PRK	Bacteria:97	PRK00418, PRK00418, DNA gyrase inhibitor; Reviewed.
CDD:234755	376	PRK	Bacteria:44	PRK00419, PRK00419, DNA primase small subunit; Reviewed.
CDD:234756	112	PRK	Bacteria:37	PRK00420, PRK00420, hypothetical protein; Validated.
CDD:234757	461	PRK	Bacteria:749,nodiv:1	PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase; Provisional.
CDD:234758	310	PRK	Bacteria:64	PRK00423, tfb, transcription initiation factor IIB; Reviewed.
CDD:179020	95	PRK	Bacteria:184	PRK00430, fis, global DNA-binding transcriptional dual regulator Fis; Provisional.
CDD:234759	177	PRK	Bacteria:151	PRK00431, PRK00431, RNase III inhibitor; Provisional.
CDD:234760	50	PRK	Bacteria:48	PRK00432, PRK00432, 30S ribosomal protein S27ae; Validated.
CDD:179023	88	PRK	Bacteria:60	PRK00435, ef1B, elongation factor 1-beta; Validated.
CDD:234761	343	PRK	Bacteria:612	PRK00436, argC, N-acetyl-gamma-glutamyl-phosphate reductase; Validated.
CDD:234762	163	PRK	Bacteria:86	PRK00439, leuD, 3-isopropylmalate dehydratase small subunit; Reviewed.
CDD:234763	319	PRK	Bacteria:57	PRK00440, rfc, replication factor C small subunit; Reviewed.
CDD:179028	261	PRK	Bacteria:232	PRK00443, nagB, glucosamine-6-phosphate deaminase; Provisional.
CDD:234765	105	PRK	Bacteria:174	PRK00446, cyaY, frataxin-like protein; Provisional.
CDD:234767	1437	PRK	Bacteria:182	PRK00448, polC, DNA polymerase III PolC; Validated.
CDD:234768	274	PRK	Bacteria:649,nodiv:2	PRK00450, dapF, diaminopimelate epimerase; Provisional.
CDD:234769	447	PRK	Bacteria:246,nodiv:1	PRK00451, PRK00451, glycine dehydrogenase subunit 1; Validated.
CDD:179034	108	PRK	Bacteria:823,nodiv:2	PRK00453, rpsF, 30S ribosomal protein S6; Reviewed.
CDD:234770	196	PRK	Bacteria:696,nodiv:1	PRK00454, engB, GTP-binding protein YsxC; Reviewed.
CDD:234771	202	PRK	Bacteria:796,nodiv:2	PRK00455, pyrE, orotate phosphoribosyltransferase; Validated.
CDD:234772	127	PRK	Bacteria:19	PRK00458, PRK00458, S-adenosylmethionine decarboxylase proenzyme; Provisional.
CDD:234773	87	PRK	Bacteria:23	PRK00461, rpmC, 50S ribosomal protein L29; Reviewed.
CDD:234774	154	PRK	Bacteria:723,nodiv:1	PRK00464, nrdR, transcriptional regulator NrdR; Validated.
CDD:179039	37	PRK	Bacteria:527	PRK00465, rpmJ, 50S ribosomal protein L36; Reviewed.
CDD:179041	134	PRK	Bacteria:78	PRK00474, rps9p, 30S ribosomal protein S9P; Reviewed.
CDD:234775	588	PRK	Bacteria:932,nodiv:1	PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
CDD:234777	242	PRK	Bacteria:313	PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
CDD:234778	491	PRK	Bacteria:812,nodiv:1	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
CDD:234779	464	PRK	Bacteria:633,nodiv:2	PRK00485, fumC, fumarate hydratase; Reviewed.
CDD:234780	339	PRK	Bacteria:893,nodiv:2	PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha; Validated.
CDD:234781	287	PRK	Bacteria:434	PRK00489, hisG, ATP phosphoribosyltransferase; Reviewed.
CDD:234782	114	PRK	Bacteria:180	PRK00499, rnpA, ribonuclease P; Reviewed.
CDD:234783	50	PRK	Bacteria:243	PRK00504, rpmG, 50S ribosomal protein L33; Validated.
CDD:234784	221	PRK	Bacteria:282	PRK00507, PRK00507, deoxyribose-phosphate aldolase; Provisional.
CDD:234785	399	PRK	Bacteria:547,nodiv:1	PRK00509, PRK00509, argininosuccinate synthase; Provisional.
CDD:179052	214	PRK	Bacteria:92	PRK00513, minC, septum formation inhibitor; Reviewed.
CDD:234786	250	PRK	Bacteria:570	PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
CDD:234787	120	PRK	Bacteria:666,nodiv:1	PRK00521, rbfA, ribosome-binding factor A; Validated.
CDD:179055	167	PRK	Bacteria:211	PRK00522, tpx, lipid hydroperoxide peroxidase; Provisional.
CDD:179057	71	PRK	Bacteria:127,nodiv:1	PRK00528, rpmE, 50S ribosomal protein L31; Reviewed.
CDD:234788	186	PRK	Bacteria:894,nodiv:2	PRK00529, PRK00529, elongation factor P; Validated.
CDD:234789	414	PRK	Bacteria:159	PRK00549, PRK00549, competence damage-inducible protein A; Provisional.
CDD:234790	168	PRK	Bacteria:915,nodiv:2	PRK00550, rpsE, 30S ribosomal protein S5; Validated.
CDD:234791	194	PRK	Bacteria:14	PRK00556, minC, septum formation inhibitor; Reviewed.
CDD:234792	598	PRK	Bacteria:799,nodiv:2	PRK00558, uvrC, excinuclease ABC subunit C; Validated.
CDD:234793	112	PRK	Bacteria:893,nodiv:1	PRK00565, rplV, 50S ribosomal protein L22; Reviewed.
CDD:234794	1156	PRK	Bacteria:913,nodiv:2	PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional.
CDD:234795	134	PRK	Bacteria:202	PRK00567, mscL, large-conductance mechanosensitive channel; Reviewed.
CDD:234796	135	PRK	Bacteria:561,nodiv:2	PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated.
CDD:234797	92	PRK	Bacteria:32	PRK00575, tatA, twin arginine translocase protein A; Provisional.
CDD:234799	367	PRK	Bacteria:339	PRK00578, prfB, peptide chain release factor 2; Validated.
CDD:234801	359	PRK	Bacteria:872,nodiv:2	PRK00591, prfA, peptide chain release factor 1; Validated.
CDD:179075	53	PRK	Bacteria:692	PRK00595, rpmG, 50S ribosomal protein L33; Validated.
CDD:179076	102	PRK	Bacteria:856,nodiv:1	PRK00596, rpsJ, 30S ribosomal protein S10; Reviewed.
CDD:234802	150	PRK	Bacteria:418,nodiv:2	PRK00601, dut, deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional.
CDD:234804	791	PRK	Bacteria:897,nodiv:1	PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta; Reviewed.
CDD:179080	205	PRK	Bacteria:26	PRK00642, PRK00642, inorganic pyrophosphatase; Provisional.
CDD:234807	191	PRK	Bacteria:37	PRK00648, PRK00648, Maf-like protein; Reviewed.
CDD:234808	325	PRK	Bacteria:349,nodiv:2	PRK00652, lpxK, tetraacyldisaccharide 4'-kinase; Reviewed.
CDD:234809	466	PRK	Bacteria:343,nodiv:1	PRK00654, glgA, glycogen synthase; Provisional.
CDD:179085	134	PRK	Bacteria:667,nodiv:2	PRK00668, ndk, mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated.
CDD:234811	228	PRK	Bacteria:148,nodiv:1	PRK00685, PRK00685, metal-dependent hydrolase; Provisional.
CDD:234813	388	PRK	Bacteria:632,nodiv:2	PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
CDD:234814	205	PRK	Bacteria:469	PRK00698, tmk, thymidylate kinase; Validated.
CDD:234815	439	PRK	Bacteria:271,nodiv:1	PRK00701, PRK00701, manganese transport protein MntH; Reviewed.
CDD:234816	220	PRK	Bacteria:547,nodiv:2	PRK00702, PRK00702, ribose-5-phosphate isomerase A; Provisional.
CDD:234817	160	PRK	Bacteria:33	PRK00704, PRK00704, photosystem I reaction center protein subunit XI; Provisional.
CDD:234819	416	PRK	Bacteria:226,nodiv:1	PRK00711, PRK00711, D-amino acid dehydrogenase small subunit; Validated.
CDD:234820	156	PRK	Bacteria:385,nodiv:1	PRK00714, PRK00714, RNA pyrophosphohydrolase; Reviewed.
CDD:234821	378	PRK	Bacteria:151	PRK00719, PRK00719, alkanesulfonate monooxygenase; Provisional.
CDD:234822	78	PRK	Bacteria:46	PRK00720, tatA, twin arginine translocase protein A; Provisional.
CDD:179097	297	PRK	Bacteria:37	PRK00723, PRK00723, phosphatidylserine decarboxylase; Provisional.
CDD:234823	263	PRK	Bacteria:270,nodiv:1	PRK00724, PRK00724, formate dehydrogenase accessory protein; Reviewed.
CDD:234824	425	PRK	Bacteria:194	PRK00725, glgC, glucose-1-phosphate adenylyltransferase; Provisional.
CDD:234825	357	PRK	Bacteria:755,nodiv:2	PRK00726, murG, undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional.
CDD:234827	666	PRK	Bacteria:306,nodiv:1	PRK00733, hppA, membrane-bound proton-translocating pyrophosphatase; Validated.
CDD:179105	526	PRK	Bacteria:435,nodiv:1	PRK00741, prfC, peptide chain release factor 3; Provisional.
CDD:234828	354	PRK	Bacteria:277,nodiv:1	PRK00742, PRK00742, chemotaxis-specific methylesterase; Provisional.
CDD:179108	233	PRK	Bacteria:529,nodiv:1	PRK00748, PRK00748, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated.
CDD:234829	510	PRK	Bacteria:192	PRK00750, lysK, lysyl-tRNA synthetase; Reviewed.
CDD:179112	184	PRK	Bacteria:56	PRK00758, PRK00758, GMP synthase subunit A; Validated.
CDD:179115	197	PRK	Bacteria:144,nodiv:1	PRK00767, PRK00767, transcriptional regulator BetI; Validated.
CDD:234831	268	PRK	Bacteria:329	PRK00768, nadE, NAD synthetase; Reviewed.
CDD:179118	437	PRK	Bacteria:88	PRK00771, PRK00771, signal recognition particle protein Srp54; Provisional.
CDD:234832	358	PRK	Bacteria:589,nodiv:1	PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
CDD:234833	76	PRK	Bacteria:50	PRK00773, rplX, 50S ribosomal protein LX; Validated.
CDD:234834	153	PRK	Bacteria:50	PRK00777, PRK00777, phosphopantetheine adenylyltransferase; Provisional.
CDD:234835	304	PRK	Bacteria:446	PRK00779, PRK00779, ornithine carbamoyltransferase; Provisional.
CDD:234836	267	PRK	Bacteria:19	PRK00782, PRK00782, hypothetical protein; Provisional.
CDD:234837	263	PRK	Bacteria:65	PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional.
CDD:234838	488	PRK	Bacteria:390	PRK00784, PRK00784, cobyric acid synthase; Provisional.
CDD:179126	109	PRK	Bacteria:34,nodiv:1	PRK00790, fliE, flagellar hook-basal body protein FliE; Reviewed.
CDD:179127	132	PRK	Bacteria:55,nodiv:1	PRK00794, flbT, flagellar biosynthesis repressor FlbT; Reviewed.
CDD:234840	188	PRK	Bacteria:194,nodiv:2	PRK00802, PRK00802, 3-methyladenine DNA glycosylase; Reviewed.
CDD:179131	52	PRK	Bacteria:50	PRK00807, PRK00807, 50S ribosomal protein L24e; Validated.
CDD:179133	144	PRK	Bacteria:22	PRK00809, PRK00809, hypothetical protein; Provisional.
CDD:234842	113	PRK	Bacteria:22	PRK00810, nifW, nitrogenase stabilizing/protective protein; Provisional.
CDD:234843	283	PRK	Bacteria:330	PRK00811, PRK00811, spermidine synthase; Provisional.
CDD:234844	350	PRK	Bacteria:141	PRK00816, rnfD, electron transport complex protein RnfD; Reviewed.
CDD:179136	179	PRK	Bacteria:69	PRK00819, PRK00819, RNA 2'-phosphotransferase; Reviewed.
CDD:234845	97	PRK	Bacteria:224,nodiv:1	PRK00823, phhB, pterin-4-alpha-carbinolamine dehydratase; Validated.
CDD:179138	41	PRK	Bacteria:242,nodiv:1	PRK00831, rpmJ, 50S ribosomal protein L36; Validated.
CDD:179139	350	PRK	Bacteria:53	PRK00843, egsA, NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed.
CDD:234846	407	PRK	Bacteria:103	PRK00844, glgC, glucose-1-phosphate adenylyltransferase; Provisional.
CDD:234847	217	PRK	Bacteria:233	PRK00847, thyX, FAD-dependent thymidylate synthase; Reviewed.
CDD:179143	459	PRK	Bacteria:625,nodiv:1	PRK00855, PRK00855, argininosuccinate lyase; Provisional.
CDD:234849	305	PRK	Bacteria:828,nodiv:1	PRK00856, pyrB, aspartate carbamoyltransferase catalytic subunit; Provisional.
CDD:234850	300	PRK	Bacteria:9	PRK00861, PRK00861, putative lipid kinase; Reviewed.
CDD:234851	261	PRK	Bacteria:521,nodiv:1	PRK00865, PRK00865, glutamate racemase; Provisional.
CDD:179147	302	PRK	Bacteria:33	PRK00870, PRK00870, haloalkane dehalogenase; Provisional.
CDD:179149	157	PRK	Bacteria:13	PRK00872, PRK00872, hypothetical protein; Provisional.
CDD:179150	326	PRK	Bacteria:24	PRK00876, nadE, NAD synthetase; Reviewed.
CDD:234853	425	PRK	Bacteria:674	PRK00877, hisD, bifunctional histidinal dehydrogenase/ histidinol dehydrogenase; Reviewed.
CDD:234854	513	PRK	Bacteria:730,nodiv:2	PRK00881, purH, bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional.
CDD:234855	194	PRK	Bacteria:94	PRK00884, PRK00884, Maf-like protein; Reviewed.
CDD:234856	420	PRK	Bacteria:684,nodiv:2	PRK00885, PRK00885, phosphoribosylamine--glycine ligase; Provisional.
CDD:234857	240	PRK	Bacteria:68	PRK00886, PRK00886, 2-phosphosulfolactate phosphatase; Provisional.
CDD:179156	105	PRK	Bacteria:166	PRK00888, ftsB, cell division protein FtsB; Reviewed.
CDD:234858	343	PRK	Bacteria:450,nodiv:2	PRK00892, lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional.
CDD:234859	152	PRK	Bacteria:250	PRK00893, PRK00893, aspartate carbamoyltransferase regulatory subunit; Reviewed.
CDD:234861	552	PRK	Bacteria:487	PRK00911, PRK00911, dihydroxy-acid dehydratase; Provisional.
CDD:234862	237	PRK	Bacteria:11	PRK00912, PRK00912, ribonuclease P protein component 3; Provisional.
CDD:234863	483	PRK	Bacteria:554,nodiv:1	PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional.
CDD:234864	513	PRK	Bacteria:552	PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
CDD:179167	307	PRK	Bacteria:51	PRK00919, PRK00919, GMP synthase subunit B; Validated.
CDD:234865	126	PRK	Bacteria:36	PRK00923, PRK00923, sirohydrochlorin cobaltochelatase; Reviewed.
CDD:179169	276	PRK	Bacteria:170,nodiv:1	PRK00924, PRK00924, 5-keto-4-deoxyuronate isomerase; Provisional.
CDD:234866	333	PRK	Bacteria:679,nodiv:2	PRK00927, PRK00927, tryptophanyl-tRNA synthetase; Reviewed.
CDD:234867	165	PRK	Bacteria:23	PRK00933, PRK00933, ribosomal biogenesis protein; Validated.
CDD:234868	285	PRK	Bacteria:29	PRK00934, PRK00934, ribose-phosphate pyrophosphokinase; Provisional.
CDD:179173	99	PRK	Bacteria:67	PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
CDD:179174	781	PRK	Bacteria:27	PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated.
CDD:234869	283	PRK	Bacteria:629,nodiv:1	PRK00942, PRK00942, acetylglutamate kinase; Provisional.
CDD:234870	347	PRK	Bacteria:167	PRK00943, PRK00943, selenophosphate synthetase; Provisional.
CDD:234871	195	PRK	Bacteria:20,nodiv:1	PRK00944, PRK00944, hypothetical protein; Provisional.
CDD:179177	171	PRK	Bacteria:22	PRK00945, PRK00945, acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional.
CDD:234872	361	PRK	Bacteria:31	PRK00950, PRK00950, histidinol-phosphate aminotransferase; Validated.
CDD:234873	195	PRK	Bacteria:482,nodiv:1	PRK00951, hisB, imidazoleglycerol-phosphate dehydratase; Validated.
CDD:234874	620	PRK	Bacteria:49	PRK00955, PRK00955, hypothetical protein; Provisional.
CDD:179181	208	PRK	Bacteria:20	PRK00956, thyA, thymidylate synthase; Provisional.
CDD:234875	305	PRK	Bacteria:23	PRK00957, PRK00957, methionine synthase; Provisional.
CDD:234876	517	PRK	Bacteria:20	PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
CDD:179185	165	PRK	Bacteria:19	PRK00962, PRK00962, hypothetical protein; Provisional.
CDD:234877	225	PRK	Bacteria:36	PRK00964, PRK00964, tetrahydromethanopterin S-methyltransferase subunit A; Provisional.
CDD:179187	96	PRK	Bacteria:24	PRK00965, PRK00965, tetrahydromethanopterin S-methyltransferase subunit B; Provisional.
CDD:179188	105	PRK	Bacteria:45	PRK00967, PRK00967, hypothetical protein; Provisional.
CDD:234878	240	PRK	Bacteria:32	PRK00968, PRK00968, tetrahydromethanopterin S-methyltransferase subunit D; Provisional.
CDD:234879	508	PRK	Bacteria:32	PRK00969, PRK00969, hypothetical protein; Provisional.
CDD:234880	307	PRK	Bacteria:277	PRK00971, PRK00971, glutaminase; Provisional.
CDD:234881	292	PRK	Bacteria:32	PRK00972, PRK00972, tetrahydromethanopterin S-methyltransferase subunit E; Provisional.
CDD:179193	446	PRK	Bacteria:28	PRK00973, PRK00973, glucose-6-phosphate isomerase; Provisional.
CDD:234882	326	PRK	Bacteria:31	PRK00976, PRK00976, hypothetical protein; Provisional.
CDD:179195	80	PRK	Bacteria:388,nodiv:2	PRK00977, PRK00977, exodeoxyribonuclease VII small subunit; Provisional.
CDD:234883	308	PRK	Bacteria:39	PRK00979, PRK00979, tetrahydromethanopterin S-methyltransferase subunit H; Provisional.
CDD:179197	78	PRK	Bacteria:798,nodiv:2	PRK00982, acpP, acyl carrier protein; Provisional.
CDD:234884	341	PRK	Bacteria:216	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed.
CDD:234885	277	PRK	Bacteria:35	PRK00994, PRK00994, F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional.
CDD:234886	304	PRK	Bacteria:135	PRK00996, PRK00996, ribonuclease HIII; Provisional.
CDD:179205	99	PRK	Bacteria:48	PRK01018, PRK01018, 50S ribosomal protein L30e; Reviewed.
CDD:234888	167	PRK	Bacteria:26	PRK01022, PRK01022, hypothetical protein; Provisional.
CDD:179208	77	PRK	Bacteria:26	PRK01026, PRK01026, tetrahydromethanopterin S-methyltransferase subunit G; Provisional.
CDD:234890	264	PRK	Bacteria:32	PRK01030, PRK01030, tetrahydromethanopterin S-methyltransferase subunit C; Provisional.
CDD:234891	258	PRK	Bacteria:23	PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit HisF; Provisional.
CDD:234893	298	PRK	Bacteria:549,nodiv:1	PRK01045, ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed.
CDD:234894	346	PRK	Bacteria:131	PRK01059, PRK01059, ATP:guanido phosphotransferase; Provisional.
CDD:179214	281	PRK	Bacteria:291	PRK01060, PRK01060, endonuclease IV; Provisional.
CDD:179217	419	PRK	Bacteria:124	PRK01076, PRK01076, L-rhamnose isomerase; Provisional.
CDD:234896	451	PRK	Bacteria:267	PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase; Validated.
CDD:234897	440	PRK	Bacteria:50	PRK01096, PRK01096, deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional.
CDD:179220	62	PRK	Bacteria:53	PRK01099, rpoK, DNA-directed RNA polymerase subunit K; Provisional.
CDD:234899	274	PRK	Bacteria:568,nodiv:1	PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated.
CDD:234900	590	PRK	Bacteria:36	PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional.
CDD:234901	60	PRK	Bacteria:561,nodiv:2	PRK01110, rpmF, 50S ribosomal protein L32; Validated.
CDD:234903	247	PRK	Bacteria:81	PRK01115, PRK01115, DNA polymerase sliding clamp; Validated.
CDD:234904	430	PRK	Bacteria:771,nodiv:1	PRK01117, PRK01117, adenylosuccinate synthetase; Provisional.
CDD:234905	679	PRK	Bacteria:284,nodiv:1	PRK01122, PRK01122, potassium-transporting ATPase subunit B; Provisional.
CDD:234906	282	PRK	Bacteria:47	PRK01123, PRK01123, shikimate kinase; Provisional.
CDD:234907	221	PRK	Bacteria:232	PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase; Provisional.
CDD:234908	163	PRK	Bacteria:66	PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
CDD:234909	85	PRK	Bacteria:73	PRK01146, PRK01146, DNA-directed RNA polymerase subunit L; Provisional.
CDD:179234	58	PRK	Bacteria:67	PRK01151, rps17E, 30S ribosomal protein S17e; Validated.
CDD:179235	174	PRK	Bacteria:52	PRK01153, PRK01153, nicotinamide-nucleotide adenylyltransferase; Provisional.
CDD:234910	230	PRK	Bacteria:18	PRK01158, PRK01158, phosphoglycolate phosphatase; Provisional.
CDD:179239	99	PRK	Bacteria:60	PRK01178, rps24e, 30S ribosomal protein S24e; Reviewed.
CDD:234914	184	PRK	Bacteria:21	PRK01184, PRK01184, hypothetical protein; Provisional.
CDD:234915	120	PRK	Bacteria:66	PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
CDD:234916	89	PRK	Bacteria:70	PRK01192, PRK01192, 50S ribosomal protein L31e; Reviewed.
CDD:234917	352	PRK	Bacteria:78	PRK01198, PRK01198, V-type ATP synthase subunit C; Provisional.
CDD:234918	127	PRK	Bacteria:534,nodiv:1	PRK01202, PRK01202, glycine cleavage system protein H; Provisional.
CDD:234919	312	PRK	Bacteria:241	PRK01209, cobD, cobalamin biosynthesis protein; Provisional.
CDD:234920	301	PRK	Bacteria:507	PRK01212, PRK01212, homoserine kinase; Provisional.
CDD:234921	724	PRK	Bacteria:410,nodiv:1	PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase II; Provisional.
CDD:179250	264	PRK	Bacteria:21	PRK01215, PRK01215, competence damage-inducible protein A; Provisional.
CDD:179253	99	PRK	Bacteria:31	PRK01220, PRK01220, malonate decarboxylase subunit delta; Provisional.
CDD:234922	312	PRK	Bacteria:30	PRK01221, PRK01221, putative deoxyhypusine synthase; Provisional.
CDD:234923	210	PRK	Bacteria:263	PRK01222, PRK01222, N-(5'-phosphoribosyl)anthranilate isomerase; Provisional.
CDD:234924	208	PRK	Bacteria:48	PRK01229, PRK01229, N-glycosylase/DNA lyase; Provisional.
CDD:179257	295	PRK	Bacteria:47,nodiv:1	PRK01231, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:234925	682	PRK	Bacteria:607,nodiv:1	PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
CDD:234927	289	PRK	Bacteria:37	PRK01237, PRK01237, triphosphoribosyl-dephospho-CoA synthase; Validated.
CDD:179261	50	PRK	Bacteria:66	PRK01242, rpl39e, 50S ribosomal protein L39e; Validated.
CDD:179262	176	PRK	Bacteria:295,nodiv:1	PRK01250, PRK01250, inorganic pyrophosphatase; Provisional.
CDD:179263	54	PRK	Bacteria:45	PRK01253, PRK01253, preprotein translocase subunit SecG; Reviewed.
CDD:234929	309	PRK	Bacteria:478,nodiv:2	PRK01259, PRK01259, ribose-phosphate pyrophosphokinase; Provisional.
CDD:234932	482	PRK	Bacteria:192	PRK01269, PRK01269, tRNA s(4)U8 sulfurtransferase; Provisional.
CDD:179270	389	PRK	Bacteria:78	PRK01278, argD, acetylornithine transaminase protein; Provisional.
CDD:234933	155	PRK	Bacteria:57	PRK01285, PRK01285, pyruvoyl-dependent arginine decarboxylase; Reviewed.
CDD:234934	336	PRK	Bacteria:184,nodiv:1	PRK01286, PRK01286, deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional.
CDD:234936	207	PRK	Bacteria:46	PRK01293, PRK01293, phosphoribosyl-dephospho-CoA transferase; Provisional.
CDD:234937	336	PRK	Bacteria:52	PRK01294, PRK01294, lipase chaperone; Provisional.
CDD:234939	240	PRK	Bacteria:263,nodiv:1	PRK01305, PRK01305, arginyl-tRNA-protein transferase; Provisional.
CDD:167208	104	PRK	Bacteria:21	PRK01310, PRK01310, hypothetical protein; Validated.
CDD:234942	521	PRK	Bacteria:361,nodiv:1	PRK01318, PRK01318, membrane protein insertase; Provisional.
CDD:179280	242	PRK	Bacteria:46	PRK01322, PRK01322, 6-carboxyhexanoate--CoA ligase; Provisional.
CDD:234943	57	PRK	Bacteria:30	PRK01343, PRK01343, zinc-binding protein; Provisional.
CDD:234944	317	PRK	Bacteria:46	PRK01345, PRK01345, heat shock protein HtpX; Provisional.
CDD:234945	411	PRK	Bacteria:42	PRK01346, PRK01346, hypothetical protein; Provisional.
CDD:234947	214	PRK	Bacteria:256	PRK01362, PRK01362, putative translaldolase; Provisional.
CDD:179287	137	PRK	Bacteria:19	PRK01371, PRK01371, sec-independent translocase; Provisional.
CDD:234948	304	PRK	Bacteria:384,nodiv:1	PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
CDD:179289	99	PRK	Bacteria:128,nodiv:1	PRK01381, PRK01381, Trp operon repressor; Provisional.
CDD:234949	406	PRK	Bacteria:228	PRK01388, PRK01388, arginine deiminase; Provisional.
CDD:234950	460	PRK	Bacteria:79	PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:234951	180	PRK	Bacteria:75	PRK01392, citX, 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed.
CDD:179293	104	PRK	Bacteria:51	PRK01395, PRK01395, V-type ATP synthase subunit F; Provisional.
CDD:234952	328	PRK	Bacteria:55,nodiv:1	PRK01402, hslO, Hsp33-like chaperonin; Reviewed.
CDD:234953	476	PRK	Bacteria:941,nodiv:2	PRK01406, gltX, glutamyl-tRNA synthetase; Reviewed.
CDD:179297	480	PRK	Bacteria:19	PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:234956	435	PRK	Bacteria:752,nodiv:2	PRK01490, tig, trigger factor; Provisional.
CDD:234959	304	PRK	Bacteria:45	PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
CDD:234960	394	PRK	Bacteria:203,nodiv:1	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional.
CDD:234964	507	PRK	Bacteria:1004,nodiv:1	PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
CDD:234966	154	PRK	Bacteria:76	PRK01617, PRK01617, hypothetical protein; Provisional.
CDD:179313	286	PRK	Bacteria:138	PRK01637, PRK01637, hypothetical protein; Reviewed.
CDD:179314	200	PRK	Bacteria:536,nodiv:1	PRK01641, leuD, isopropylmalate isomerase small subunit; Provisional.
CDD:234967	483	PRK	Bacteria:231	PRK01642, cls, cardiolipin synthetase; Reviewed.
CDD:234968	428	PRK	Bacteria:225,nodiv:1	PRK01663, PRK01663, C4-dicarboxylate transporter DctA; Reviewed.
CDD:234969	87	PRK	Bacteria:374	PRK01678, rpmE2, 50S ribosomal protein L31 type B; Reviewed.
CDD:234970	258	PRK	Bacteria:85,nodiv:1	PRK01683, PRK01683, trans-aconitate 2-methyltransferase; Provisional.
CDD:234971	215	PRK	Bacteria:322	PRK01686, hisG, ATP phosphoribosyltransferase catalytic subunit; Reviewed.
CDD:234972	351	PRK	Bacteria:113	PRK01688, PRK01688, histidinol-phosphate aminotransferase; Provisional.
CDD:234973	64	PRK	Bacteria:213,nodiv:1	PRK01712, PRK01712, carbon storage regulator; Provisional.
CDD:234974	320	PRK	Bacteria:64	PRK01722, PRK01722, formimidoylglutamase; Provisional.
CDD:234975	239	PRK	Bacteria:80	PRK01723, PRK01723, 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed.
CDD:179327	114	PRK	Bacteria:131	PRK01732, rnpA, ribonuclease P; Reviewed.
CDD:234976	190	PRK	Bacteria:117	PRK01736, PRK01736, hypothetical protein; Reviewed.
CDD:234977	332	PRK	Bacteria:16	PRK01741, PRK01741, cell division protein ZipA; Provisional.
CDD:234978	662	PRK	Bacteria:188	PRK01747, mnmC, bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed.
CDD:234979	176	PRK	Bacteria:142	PRK01749, PRK01749, disulfide bond formation protein B; Provisional.
CDD:234981	456	PRK	Bacteria:194	PRK01766, PRK01766, multidrug efflux protein; Reviewed.
CDD:179334	171	PRK	Bacteria:89	PRK01770, PRK01770, sec-independent translocase; Provisional.
CDD:234982	95	PRK	Bacteria:112	PRK01777, PRK01777, hypothetical protein; Validated.
CDD:179338	143	PRK	Bacteria:120	PRK01816, PRK01816, hypothetical protein; Provisional.
CDD:234983	133	PRK	Bacteria:93	PRK01821, PRK01821, hypothetical protein; Provisional.
CDD:234984	264	PRK	Bacteria:529,nodiv:2	PRK01827, thyA, thymidylate synthase; Reviewed.
CDD:234986	303	PRK	Bacteria:53	PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
CDD:179345	157	PRK	Bacteria:202	PRK01885, greB, transcription elongation factor GreB; Reviewed.
CDD:234988	356	PRK	Bacteria:68	PRK01889, PRK01889, GTPase RsgA; Reviewed.
CDD:234989	133	PRK	Bacteria:18	PRK01903, rnpA, ribonuclease P; Reviewed.
CDD:179350	205	PRK	Bacteria:140	PRK01908, PRK01908, electron transport complex protein RnfG; Validated.
CDD:179352	292	PRK	Bacteria:19	PRK01911, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:234992	169	PRK	Bacteria:49	PRK01919, tatB, sec-independent translocase; Provisional.
CDD:234993	333	PRK	Bacteria:438,nodiv:1	PRK01966, ddl, D-alanyl-alanine synthetase A; Reviewed.
CDD:179358	152	PRK	Bacteria:17	PRK02001, PRK02001, hypothetical protein; Validated.
CDD:234995	498	PRK	Bacteria:49	PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:179362	88	PRK	Bacteria:32	PRK02079, PRK02079, pyrroloquinoline quinone biosynthesis protein PqqD; Provisional.
CDD:234996	253	PRK	Bacteria:732,nodiv:1	PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit HisF; Provisional.
CDD:234997	241	PRK	Bacteria:343	PRK02090, PRK02090, phosphoadenosine phosphosulfate reductase; Provisional.
CDD:234999	255	PRK	Bacteria:358	PRK02101, PRK02101, hypothetical protein; Validated.
CDD:179366	331	PRK	Bacteria:197	PRK02102, PRK02102, ornithine carbamoyltransferase; Validated.
CDD:179367	105	PRK	Bacteria:40	PRK02103, PRK02103, malonate decarboxylase subunit delta; Provisional.
CDD:235000	560	PRK	Bacteria:214,nodiv:1	PRK02106, PRK02106, choline dehydrogenase; Validated.
CDD:235001	523	PRK	Bacteria:177	PRK02107, PRK02107, glutamate--cysteine ligase; Provisional.
CDD:235003	297	PRK	Bacteria:65	PRK02114, PRK02114, formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional.
CDD:235005	652	PRK	Bacteria:26	PRK02122, PRK02122, glucosamine-6-phosphate deaminase-like protein; Validated.
CDD:235006	334	PRK	Bacteria:22	PRK02126, PRK02126, ribonuclease Z; Provisional.
CDD:235007	249	PRK	Bacteria:100	PRK02134, PRK02134, hypothetical protein; Provisional.
CDD:235008	201	PRK	Bacteria:54	PRK02135, PRK02135, hypothetical protein; Provisional.
CDD:179379	291	PRK	Bacteria:53	PRK02155, ppnK, NAD(+)/NADH kinase family protein; Provisional.
CDD:235011	301	PRK	Bacteria:166	PRK02190, PRK02190, agmatinase; Provisional.
CDD:179382	201	PRK	Bacteria:42	PRK02195, PRK02195, V-type ATP synthase subunit D; Provisional.
CDD:235012	357	PRK	Bacteria:21	PRK02201, PRK02201, putative inner membrane protein translocase component YidC; Provisional.
CDD:179385	880	PRK	Bacteria:12	PRK02224, PRK02224, chromosome segregation protein; Provisional.
CDD:235014	238	PRK	Bacteria:60	PRK02227, PRK02227, hypothetical protein; Provisional.
CDD:179387	100	PRK	Bacteria:27	PRK02228, PRK02228, V-type ATP synthase subunit F; Provisional.
CDD:235015	195	PRK	Bacteria:165	PRK02234, recU, Holliday junction-specific endonuclease; Reviewed.
CDD:235016	109	PRK	Bacteria:184,nodiv:1	PRK02237, PRK02237, hypothetical protein; Provisional.
CDD:179391	254	PRK	Bacteria:28	PRK02240, PRK02240, GTP cyclohydrolase III; Provisional.
CDD:179392	343	PRK	Bacteria:28	PRK02249, PRK02249, DNA primase large subunit; Validated.
CDD:179395	167	PRK	Bacteria:27	PRK02253, PRK02253, deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional.
CDD:235018	462	PRK	Bacteria:84	PRK02256, PRK02256, putative aminopeptidase 1; Provisional.
CDD:235019	288	PRK	Bacteria:36	PRK02259, PRK02259, aspartoacylase; Provisional.
CDD:179399	158	PRK	Bacteria:406	PRK02260, PRK02260, S-ribosylhomocysteinase; Provisional.
CDD:179400	137	PRK	Bacteria:35	PRK02261, PRK02261, methylaspartate mutase subunit S; Provisional.
CDD:235020	317	PRK	Bacteria:77	PRK02264, PRK02264, N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional.
CDD:179402	246	PRK	Bacteria:60	PRK02265, PRK02265, acetoacetate decarboxylase; Provisional.
CDD:235021	141	PRK	Bacteria:20	PRK02268, PRK02268, hypothetical protein; Provisional.
CDD:235022	325	PRK	Bacteria:41	PRK02271, PRK02271, methylenetetrahydromethanopterin reductase; Provisional.
CDD:235023	200	PRK	Bacteria:48	PRK02277, PRK02277, orotate phosphoribosyltransferase-like protein; Provisional.
CDD:235024	171	PRK	Bacteria:58	PRK02287, PRK02287, hypothetical protein; Provisional.
CDD:235025	344	PRK	Bacteria:66	PRK02290, PRK02290, 3-dehydroquinate synthase; Provisional.
CDD:235026	188	PRK	Bacteria:20	PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
CDD:235028	175	PRK	Bacteria:755,nodiv:1	PRK02304, PRK02304, adenine phosphoribosyltransferase; Provisional.
CDD:235029	303	PRK	Bacteria:59	PRK02308, uvsE, putative UV damage endonuclease; Provisional.
CDD:235030	233	PRK	Bacteria:139	PRK02315, PRK02315, adaptor protein; Provisional.
CDD:235031	381	PRK	Bacteria:184	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional.
CDD:235032	737	PRK	Bacteria:23	PRK02362, PRK02362, ski2-like helicase; Provisional.
CDD:235033	129	PRK	Bacteria:160	PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed.
CDD:179417	443	PRK	Bacteria:16	PRK02382, PRK02382, dihydroorotase; Provisional.
CDD:179418	296	PRK	Bacteria:29	PRK02391, PRK02391, heat shock protein HtpX; Provisional.
CDD:235034	279	PRK	Bacteria:16	PRK02395, PRK02395, hypothetical protein; Provisional.
CDD:179420	406	PRK	Bacteria:91	PRK02399, PRK02399, hypothetical protein; Provisional.
CDD:235035	343	PRK	Bacteria:344,nodiv:1	PRK02406, PRK02406, DNA polymerase IV; Validated.
CDD:235036	253	PRK	Bacteria:153	PRK02412, aroD, 3-dehydroquinate dehydratase; Provisional.
CDD:235037	435	PRK	Bacteria:761,nodiv:1	PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional.
CDD:235038	245	PRK	Bacteria:49	PRK02436, xerD, site-specific tyrosine recombinase XerD-like protein; Reviewed.
CDD:179427	752	PRK	Bacteria:53	PRK02471, PRK02471, bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional.
CDD:235041	447	PRK	Bacteria:137	PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:235042	294	PRK	Bacteria:57	PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
CDD:179430	163	PRK	Bacteria:85	PRK02487, PRK02487, hypothetical protein; Provisional.
CDD:235043	347	PRK	Bacteria:32,nodiv:1	PRK02492, PRK02492, deoxyhypusine synthase-like protein; Provisional.
CDD:235045	310	PRK	Bacteria:68	PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
CDD:235046	422	PRK	Bacteria:28	PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
CDD:235047	973	PRK	Bacteria:16	PRK02509, PRK02509, hypothetical protein; Provisional.
CDD:235048	132	PRK	Bacteria:22	PRK02515, psbU, photosystem II complex extrinsic protein precursor U; Provisional.
CDD:235049	312	PRK	Bacteria:36	PRK02534, PRK02534, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:179441	188	PRK	Bacteria:39	PRK02542, PRK02542, photosystem I assembly protein Ycf4; Provisional.
CDD:179443	154	PRK	Bacteria:51	PRK02551, PRK02551, flavoprotein NrdI; Provisional.
CDD:235051	44	PRK	Bacteria:37	PRK02561, psbF, cytochrome b559 subunit beta; Provisional.
CDD:235052	1331	PRK	Bacteria:38	PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional.
CDD:235054	347	PRK	Bacteria:46	PRK02615, PRK02615, thiamine-phosphate pyrophosphorylase; Provisional.
CDD:235056	396	PRK	Bacteria:203	PRK02627, PRK02627, acetylornithine aminotransferase; Provisional.
CDD:235057	679	PRK	Bacteria:97	PRK02628, nadE, NAD synthetase; Reviewed.
CDD:179455	305	PRK	Bacteria:37	PRK02645, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:179456	305	PRK	Bacteria:36	PRK02649, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:235058	375	PRK	Bacteria:37	PRK02654, PRK02654, putative inner membrane protein translocase component YidC; Provisional.
CDD:179460	312	PRK	Bacteria:39	PRK02693, PRK02693, apocytochrome f; Reviewed.
CDD:235059	459	PRK	Bacteria:36	PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:235060	119	PRK	Bacteria:33	PRK02710, PRK02710, plastocyanin; Provisional.
CDD:235061	320	PRK	Bacteria:16	PRK02714, PRK02714, O-succinylbenzoate synthase; Provisional.
CDD:235063	200	PRK	Bacteria:14	PRK02726, PRK02726, molybdopterin-guanine dinucleotide biosynthesis protein A; Provisional.
CDD:235064	367	PRK	Bacteria:178,nodiv:1	PRK02731, PRK02731, histidinol-phosphate aminotransferase; Validated.
CDD:235066	345	PRK	Bacteria:39	PRK02746, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional.
CDD:179469	295	PRK	Bacteria:17	PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
CDD:235067	203	PRK	Bacteria:269	PRK02759, PRK02759, bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed.
CDD:235068	380	PRK	Bacteria:21	PRK02769, PRK02769, histidine decarboxylase; Provisional.
CDD:235069	139	PRK	Bacteria:22	PRK02770, PRK02770, S-adenosylmethionine decarboxylase proenzyme; Provisional.
CDD:179473	419	PRK	Bacteria:68,nodiv:1	PRK02794, PRK02794, DNA polymerase IV; Provisional.
CDD:235070	322	PRK	Bacteria:108	PRK02797, PRK02797, 4-alpha-L-fucosyltransferase; Provisional.
CDD:235071	101	PRK	Bacteria:124	PRK02801, PRK02801, primosomal replication protein N; Provisional.
CDD:235073	428	PRK	Bacteria:146	PRK02813, PRK02813, putative aminopeptidase 2; Provisional.
CDD:179478	243	PRK	Bacteria:39	PRK02816, PRK02816, phycocyanobilin:ferredoxin oxidoreductase; Validated.
CDD:235075	133	PRK	Bacteria:143	PRK02833, PRK02833, phosphate-starvation-inducible protein PsiE; Provisional.
CDD:235076	427	PRK	Bacteria:85	PRK02842, PRK02842, light-independent protochlorophyllide reductase subunit N; Provisional.
CDD:235077	161	PRK	Bacteria:83,nodiv:1	PRK02853, PRK02853, hypothetical protein; Provisional.
CDD:235078	369	PRK	Bacteria:41	PRK02858, PRK02858, germination protease; Provisional.
CDD:179486	429	PRK	Bacteria:54	PRK02862, glgC, glucose-1-phosphate adenylyltransferase; Provisional.
CDD:235079	147	PRK	Bacteria:143	PRK02866, PRK02866, cyanate hydratase; Validated.
CDD:235080	245	PRK	Bacteria:95	PRK02868, PRK02868, hypothetical protein; Provisional.
CDD:235082	635	PRK	Bacteria:65	PRK02888, PRK02888, nitrous-oxide reductase; Validated.
CDD:235083	427	PRK	Bacteria:60	PRK02889, tolB, translocation protein TolB; Provisional.
CDD:179494	100	PRK	Bacteria:91	PRK02898, PRK02898, cobalt transport protein CbiN; Provisional.
CDD:179495	197	PRK	Bacteria:35	PRK02899, PRK02899, adaptor protein; Provisional.
CDD:235084	327	PRK	Bacteria:52	PRK02901, PRK02901, O-succinylbenzoate synthase; Provisional.
CDD:179497	105	PRK	Bacteria:129	PRK02909, PRK02909, transcriptional activator FlhD; Provisional.
CDD:235085	519	PRK	Bacteria:86	PRK02910, PRK02910, light-independent protochlorophyllide reductase subunit B; Provisional.
CDD:179499	150	PRK	Bacteria:110	PRK02913, PRK02913, hypothetical protein; Provisional.
CDD:235087	466	PRK	Bacteria:205	PRK02925, PRK02925, glucuronate isomerase; Reviewed.
CDD:179503	499	PRK	Bacteria:189	PRK02929, PRK02929, L-arabinose isomerase; Provisional.
CDD:179504	110	PRK	Bacteria:44	PRK02935, PRK02935, hypothetical protein; Provisional.
CDD:179505	377	PRK	Bacteria:46	PRK02936, argD, acetylornithine aminotransferase; Provisional.
CDD:235088	167	PRK	Bacteria:92	PRK02943, PRK02943, SecA regulator SecM; Provisional.
CDD:235089	575	PRK	Bacteria:177	PRK02946, aceK, bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated.
CDD:179510	246	PRK	Bacteria:71	PRK02947, PRK02947, hypothetical protein; Provisional.
CDD:235090	309	PRK	Bacteria:105	PRK02951, PRK02951, DNA replication terminus site-binding protein; Provisional.
CDD:179513	68	PRK	Bacteria:44	PRK02955, PRK02955, small acid-soluble spore protein SspI; Provisional.
CDD:235091	73	PRK	Bacteria:69	PRK02958, tatA, twin arginine translocase protein A; Provisional.
CDD:235092	316	PRK	Bacteria:64	PRK02963, PRK02963, carbon starvation induced protein; Validated.
CDD:235093	139	PRK	Bacteria:86	PRK02967, PRK02967, nickel responsive regulator; Provisional.
CDD:235094	129	PRK	Bacteria:82	PRK02971, PRK02971, 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional.
CDD:179518	450	PRK	Bacteria:102	PRK02975, PRK02975, putative common antigen polymerase; Provisional.
CDD:235095	1094	PRK	Bacteria:43	PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
CDD:235096	441	PRK	Bacteria:159	PRK02991, PRK02991, D-serine dehydratase; Provisional.
CDD:235097	726	PRK	Bacteria:232	PRK02999, PRK02999, malate synthase G; Provisional.
CDD:179524	283	PRK	Bacteria:56	PRK03001, PRK03001, M48 family peptidase; Provisional.
CDD:179525	472	PRK	Bacteria:67	PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
CDD:235098	428	PRK	Bacteria:53	PRK03007, PRK03007, deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional.
CDD:235099	358	PRK	Bacteria:124	PRK03011, PRK03011, butyrate kinase; Provisional.
CDD:235100	122	PRK	Bacteria:15	PRK03031, rnpA, ribonuclease P; Reviewed.
CDD:235101	856	PRK	Bacteria:63	PRK03059, PRK03059, PII uridylyl-transferase; Provisional.
CDD:235103	378	PRK	Bacteria:195	PRK03080, PRK03080, phosphoserine aminotransferase; Provisional.
CDD:179535	304	PRK	Bacteria:83	PRK03092, PRK03092, ribose-phosphate pyrophosphokinase; Provisional.
CDD:179538	136	PRK	Bacteria:26	PRK03100, PRK03100, sec-independent translocase; Provisional.
CDD:235104	409	PRK	Bacteria:13	PRK03103, PRK03103, DNA polymerase IV; Reviewed.
CDD:179541	169	PRK	Bacteria:29	PRK03114, PRK03114, NTPase; Reviewed.
CDD:235105	127	PRK	Bacteria:71	PRK03124, PRK03124, S-adenosylmethionine decarboxylase proenzyme; Provisional.
CDD:179543	514	PRK	Bacteria:65	PRK03137, PRK03137, 1-pyrroline-5-carboxylate dehydrogenase; Provisional.
CDD:179544	259	PRK	Bacteria:32	PRK03140, PRK03140, phosphatidylserine decarboxylase; Provisional.
CDD:235106	359	PRK	Bacteria:66	PRK03158, PRK03158, histidinol-phosphate aminotransferase; Provisional.
CDD:235107	292	PRK	Bacteria:785,nodiv:1	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.
CDD:235108	508	PRK	Bacteria:46	PRK03180, ligB, ATP-dependent DNA ligase; Reviewed.
CDD:235109	272	PRK	Bacteria:44	PRK03187, tgl, transglutaminase; Provisional.
CDD:235110	300	PRK	Bacteria:61	PRK03188, PRK03188, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:235111	320	PRK	Bacteria:412	PRK03202, PRK03202, 6-phosphofructokinase; Provisional.
CDD:235112	398	PRK	Bacteria:68	PRK03244, argD, acetylornithine aminotransferase; Provisional.
CDD:235113	298	PRK	Bacteria:61	PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
CDD:235114	224	PRK	Bacteria:96	PRK03298, PRK03298, hypothetical protein; Provisional.
CDD:235115	368	PRK	Bacteria:93	PRK03317, PRK03317, histidinol-phosphate aminotransferase; Provisional.
CDD:179559	352	PRK	Bacteria:47	PRK03321, PRK03321, putative aminotransferase; Provisional.
CDD:179560	395	PRK	Bacteria:38	PRK03333, coaE, dephospho-CoA kinase/protein folding accessory domain-containing protein; Provisional.
CDD:235116	168	PRK	Bacteria:44	PRK03341, PRK03341, arginine repressor; Provisional.
CDD:235117	368	PRK	Bacteria:106	PRK03343, PRK03343, transaldolase; Validated.
CDD:235118	454	PRK	Bacteria:45	PRK03348, PRK03348, DNA polymerase IV; Provisional.
CDD:179564	346	PRK	Bacteria:31	PRK03352, PRK03352, DNA polymerase IV; Validated.
CDD:235119	217	PRK	Bacteria:127	PRK03353, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional.
CDD:235121	306	PRK	Bacteria:66	PRK03372, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:235122	292	PRK	Bacteria:120	PRK03378, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:235123	774	PRK	Bacteria:42	PRK03381, PRK03381, PII uridylyl-transferase; Provisional.
CDD:235124	333	PRK	Bacteria:94	PRK03427, PRK03427, cell division protein ZipA; Provisional.
CDD:235125	157	PRK	Bacteria:117	PRK03430, PRK03430, hypothetical protein; Validated.
CDD:179579	344	PRK	Bacteria:70	PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
CDD:235127	144	PRK	Bacteria:91	PRK03467, PRK03467, hypothetical protein; Provisional.
CDD:179584	264	PRK	Bacteria:44	PRK03501, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:179585	228	PRK	Bacteria:94	PRK03511, minC, septum formation inhibitor; Reviewed.
CDD:235128	315	PRK	Bacteria:138	PRK03522, rumB, 23S rRNA methyluridine methyltransferase; Reviewed.
CDD:235129	188	PRK	Bacteria:45	PRK03537, PRK03537, molybdate ABC transporter periplasmic molybdate-binding protein; Provisional.
CDD:179591	390	PRK	Bacteria:135	PRK03545, PRK03545, putative arabinose transporter; Provisional.
CDD:235131	621	PRK	Bacteria:79	PRK03562, PRK03562, glutathione-regulated potassium-efflux system protein KefC; Provisional.
CDD:179595	309	PRK	Bacteria:104	PRK03564, PRK03564, formate dehydrogenase accessory protein FdhE; Provisional.
CDD:179596	144	PRK	Bacteria:101	PRK03573, PRK03573, transcriptional regulator SlyA; Provisional.
CDD:235133	176	PRK	Bacteria:45	PRK03578, hscB, co-chaperone HscB; Provisional.
CDD:235134	655	PRK	Bacteria:135,nodiv:1	PRK03584, PRK03584, acetoacetyl-CoA synthetase; Provisional.
CDD:235135	295	PRK	Bacteria:30,Environmental:1,nodiv:2	PRK03592, PRK03592, haloalkane dehalogenase; Provisional.
CDD:235136	331	PRK	Bacteria:101	PRK03598, PRK03598, putative efflux pump membrane fusion protein; Provisional.
CDD:179603	134	PRK	Bacteria:237	PRK03600, nrdI, ribonucleotide reductase stimulatory protein; Reviewed.
CDD:235137	275	PRK	Bacteria:93	PRK03601, PRK03601, transcriptional regulator HdfR; Provisional.
CDD:235138	312	PRK	Bacteria:33	PRK03604, moaC, bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional.
CDD:179606	162	PRK	Bacteria:138	PRK03606, PRK03606, ureidoglycolate hydrolase; Provisional.
CDD:235139	521	PRK	Bacteria:102	PRK03612, PRK03612, spermidine synthase; Provisional.
CDD:235140	219	PRK	Bacteria:336	PRK03619, PRK03619, phosphoribosylformylglycinamidine synthase I; Provisional.
CDD:235141	303	PRK	Bacteria:104,nodiv:1	PRK03620, PRK03620, 5-dehydro-4-deoxyglucarate dehydratase; Provisional.
CDD:235142	140	PRK	Bacteria:139	PRK03624, PRK03624, putative acetyltransferase; Provisional.
CDD:179615	274	PRK	Bacteria:105	PRK03634, PRK03634, rhamnulose-1-phosphate aldolase; Provisional.
CDD:235144	294	PRK	Bacteria:285,nodiv:1	PRK03635, PRK03635, chromosome replication initiation inhibitor protein; Validated.
CDD:235145	179	PRK	Bacteria:50	PRK03636, PRK03636, hypothetical protein; Provisional.
CDD:235146	483	PRK	Bacteria:46	PRK03640, PRK03640, O-succinylbenzoic acid--CoA ligase; Provisional.
CDD:235147	471	PRK	Bacteria:88	PRK03643, PRK03643, altronate oxidoreductase; Provisional.
CDD:179626	146	PRK	Bacteria:81	PRK03660, PRK03660, anti-sigma F factor; Provisional.
CDD:179627	164	PRK	Bacteria:89	PRK03661, PRK03661, hypothetical protein; Validated.
CDD:179628	271	PRK	Bacteria:62	PRK03669, PRK03669, mannosyl-3-phosphoglycerate phosphatase; Reviewed.
CDD:179631	243	PRK	Bacteria:102	PRK03692, PRK03692, putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional.
CDD:235150	248	PRK	Bacteria:94	PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
CDD:235151	394	PRK	Bacteria:107	PRK03699, PRK03699, putative transporter; Provisional.
CDD:179637	166	PRK	Bacteria:121	PRK03719, PRK03719, ecotin; Provisional.
CDD:235153	171	PRK	Bacteria:87	PRK03731, aroL, shikimate kinase II; Reviewed.
CDD:235154	552	PRK	Bacteria:237,nodiv:1	PRK03739, PRK03739, 2-isopropylmalate synthase; Validated.
CDD:179641	332	PRK	Bacteria:30	PRK03743, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Validated.
CDD:179642	191	PRK	Bacteria:129	PRK03757, PRK03757, hypothetical protein; Provisional.
CDD:235156	184	PRK	Bacteria:105	PRK03759, PRK03759, isopentenyl-diphosphate delta-isomerase; Provisional.
CDD:235158	778	PRK	Bacteria:121	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional.
CDD:179646	103	PRK	Bacteria:29	PRK03762, PRK03762, hypothetical protein; Provisional.
CDD:179647	200	PRK	Bacteria:145,nodiv:1	PRK03767, PRK03767, NAD(P)H:quinone oxidoreductase; Provisional.
CDD:235159	331	PRK	Bacteria:105	PRK03784, PRK03784, vtamin B12-transporter permease; Provisional.
CDD:235160	448	PRK	Bacteria:62,nodiv:1	PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:179651	438	PRK	Bacteria:115	PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:235162	401	PRK	Bacteria:27	PRK03815, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:235163	351	PRK	Bacteria:17	PRK03817, PRK03817, galactokinase; Provisional.
CDD:179654	552	PRK	Bacteria:110	PRK03818, PRK03818, putative transporter; Validated.
CDD:235165	195	PRK	Bacteria:127	PRK03826, PRK03826, 5'-nucleotidase; Provisional.
CDD:179658	73	PRK	Bacteria:54	PRK03830, PRK03830, small acid-soluble spore protein Tlp; Provisional.
CDD:235166	241	PRK	Bacteria:72	PRK03837, PRK03837, transcriptional regulator NanR; Provisional.
CDD:179661	198	PRK	Bacteria:124	PRK03846, PRK03846, adenylylsulfate kinase; Provisional.
CDD:235167	375	PRK	Bacteria:75,nodiv:1	PRK03854, opgC, glucans biosynthesis protein; Provisional.
CDD:179663	396	PRK	Bacteria:26	PRK03858, PRK03858, DNA polymerase IV; Validated.
CDD:235168	410	PRK	Bacteria:21	PRK03868, PRK03868, glucose-6-phosphate isomerase; Provisional.
CDD:235169	96	PRK	Bacteria:27	PRK03879, PRK03879, ribonuclease P protein component 1; Validated.
CDD:235170	467	PRK	Bacteria:39	PRK03881, PRK03881, hypothetical protein; Provisional.
CDD:179669	142	PRK	Bacteria:50	PRK03902, PRK03902, manganese transport transcriptional regulator; Provisional.
CDD:235171	274	PRK	Bacteria:27	PRK03903, PRK03903, transaldolase; Provisional.
CDD:235172	385	PRK	Bacteria:222	PRK03906, PRK03906, mannonate dehydratase; Provisional.
CDD:179673	331	PRK	Bacteria:180	PRK03910, PRK03910, D-cysteine desulfhydrase; Validated.
CDD:235174	260	PRK	Bacteria:21	PRK03911, PRK03911, heat-inducible transcription repressor; Provisional.
CDD:235175	880	PRK	Bacteria:10	PRK03918, PRK03918, chromosome segregation protein; Provisional.
CDD:179676	113	PRK	Bacteria:48	PRK03922, PRK03922, hypothetical protein; Provisional.
CDD:235176	450	PRK	Bacteria:548	PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
CDD:235177	265	PRK	Bacteria:27	PRK03934, PRK03934, phosphatidylserine decarboxylase; Provisional.
CDD:179681	307	PRK	Bacteria:27	PRK03946, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional.
CDD:235179	140	PRK	Bacteria:45	PRK03947, PRK03947, prefoldin subunit alpha; Reviewed.
CDD:179684	131	PRK	Bacteria:28	PRK03955, PRK03955, hypothetical protein; Reviewed.
CDD:179685	100	PRK	Bacteria:24	PRK03957, PRK03957, V-type ATP synthase subunit F; Provisional.
CDD:235181	176	PRK	Bacteria:32	PRK03958, PRK03958, tRNA 2'-O-methylase; Reviewed.
CDD:235182	399	PRK	Bacteria:11	PRK03968, PRK03968, DNA primase large subunit; Validated.
CDD:179690	141	PRK	Bacteria:35	PRK03975, tfx, putative transcriptional regulator; Provisional.
CDD:235183	90	PRK	Bacteria:64	PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
CDD:235184	463	PRK	Bacteria:25	PRK03979, PRK03979, ADP-specific phosphofructokinase; Provisional.
CDD:235185	292	PRK	Bacteria:75	PRK03980, PRK03980, flap endonuclease-1; Provisional.
CDD:235186	288	PRK	Bacteria:26	PRK03982, PRK03982, heat shock protein HtpX; Provisional.
CDD:235187	244	PRK	Bacteria:31	PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
CDD:235188	262	PRK	Bacteria:78	PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated.
CDD:235189	138	PRK	Bacteria:54	PRK03988, PRK03988, translation initiation factor IF-2 subunit beta; Validated.
CDD:235190	613	PRK	Bacteria:56	PRK03991, PRK03991, threonyl-tRNA synthetase; Validated.
CDD:179699	389	PRK	Bacteria:72	PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional.
CDD:235191	267	PRK	Bacteria:52	PRK03995, PRK03995, hypothetical protein; Provisional.
CDD:235192	241	PRK	Bacteria:83	PRK03996, PRK03996, proteasome subunit alpha; Provisional.
CDD:235193	129	PRK	Bacteria:75	PRK03999, PRK03999, translation initiation factor IF-5A; Provisional.
CDD:235194	411	PRK	Bacteria:81	PRK04000, PRK04000, translation initiation factor IF-2 subunit gamma; Validated.
CDD:235195	586	PRK	Bacteria:77	PRK04004, PRK04004, translation initiation factor IF-2; Validated.
CDD:235196	111	PRK	Bacteria:83	PRK04005, PRK04005, 50S ribosomal protein L18e; Provisional.
CDD:235197	70	PRK	Bacteria:86	PRK04007, rps28e, 30S ribosomal protein S28e; Validated.
CDD:235198	411	PRK	Bacteria:81	PRK04011, PRK04011, peptide chain release factor 1; Provisional.
CDD:179708	100	PRK	Bacteria:72	PRK04012, PRK04012, translation initiation factor IF-1A; Provisional.
CDD:235199	91	PRK	Bacteria:58	PRK04015, PRK04015, DNA/RNA-binding protein albA; Provisional.
CDD:235200	62	PRK	Bacteria:82	PRK04016, PRK04016, DNA-directed RNA polymerase subunit N; Provisional.
CDD:179711	132	PRK	Bacteria:16	PRK04017, PRK04017, hypothetical protein; Provisional.
CDD:179712	330	PRK	Bacteria:84	PRK04019, rplP0, acidic ribosomal protein P0; Validated.
CDD:235201	204	PRK	Bacteria:83	PRK04020, rps2P, 30S ribosomal protein S2; Provisional.
CDD:235202	1121	PRK	Bacteria:38	PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
CDD:235203	412	PRK	Bacteria:50	PRK04024, PRK04024, cofactor-independent phosphoglycerate mutase; Provisional.
CDD:235204	195	PRK	Bacteria:85	PRK04027, PRK04027, 30S ribosomal protein S7P; Reviewed.
CDD:235205	630	PRK	Bacteria:77	PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E; Validated.
CDD:235206	408	PRK	Bacteria:79	PRK04031, PRK04031, DNA primase; Provisional.
CDD:235207	159	PRK	Bacteria:59	PRK04032, PRK04032, hypothetical protein; Provisional.
CDD:179721	130	PRK	Bacteria:81	PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed.
CDD:235208	504	PRK	Bacteria:55	PRK04036, PRK04036, DNA polymerase II small subunit; Validated.
CDD:235209	134	PRK	Bacteria:85	PRK04038, rps19p, 30S ribosomal protein S19P; Provisional.
CDD:235210	188	PRK	Bacteria:51	PRK04040, PRK04040, adenylate kinase; Provisional.
CDD:235211	254	PRK	Bacteria:80	PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
CDD:235212	419	PRK	Bacteria:27	PRK04043, tolB, translocation protein TolB; Provisional.
CDD:235213	211	PRK	Bacteria:80	PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
CDD:179728	222	PRK	Bacteria:84	PRK04046, PRK04046, translation initiation factor IF-6; Provisional.
CDD:235214	127	PRK	Bacteria:86	PRK04049, PRK04049, 30S ribosomal protein S8e; Validated.
CDD:179730	177	PRK	Bacteria:80	PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
CDD:235215	149	PRK	Bacteria:76	PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
CDD:179732	180	PRK	Bacteria:27	PRK04056, PRK04056, Maf-like protein; Reviewed.
CDD:235216	203	PRK	Bacteria:85	PRK04057, PRK04057, 30S ribosomal protein S3Ae; Validated.
CDD:179734	88	PRK	Bacteria:40	PRK04059, rpl34e, 50S ribosomal protein L34e; Validated.
CDD:235217	161	PRK	Bacteria:66	PRK04069, PRK04069, serine-protein kinase RsbW; Provisional.
CDD:235218	207	PRK	Bacteria:26	PRK04081, PRK04081, hypothetical protein; Provisional.
CDD:235219	158	PRK	Bacteria:20	PRK04098, PRK04098, sec-independent translocase; Provisional.
CDD:179739	273	PRK	Bacteria:20	PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
CDD:179740	139	PRK	Bacteria:48	PRK04101, PRK04101, fosfomycin resistance protein FosB; Provisional.
CDD:235220	137	PRK	Bacteria:30	PRK04115, PRK04115, hypothetical protein; Provisional.
CDD:235221	548	PRK	Bacteria:171	PRK04123, PRK04123, ribulokinase; Provisional.
CDD:179745	395	PRK	Bacteria:35	PRK04135, PRK04135, cofactor-independent phosphoglycerate mutase; Provisional.
CDD:179746	48	PRK	Bacteria:73	PRK04136, rpl40e, 50S ribosomal protein L40e; Provisional.
CDD:235224	317	PRK	Bacteria:38	PRK04140, PRK04140, hypothetical protein; Provisional.
CDD:235225	264	PRK	Bacteria:46	PRK04143, PRK04143, hypothetical protein; Provisional.
CDD:179749	293	PRK	Bacteria:100	PRK04147, PRK04147, N-acetylneuraminate lyase; Provisional.
CDD:235226	134	PRK	Bacteria:16	PRK04148, PRK04148, hypothetical protein; Provisional.
CDD:235227	391	PRK	Bacteria:115	PRK04149, sat, sulfate adenylyltransferase; Reviewed.
CDD:179752	197	PRK	Bacteria:34	PRK04151, PRK04151, IMP cyclohydrolase; Provisional.
CDD:235228	287	PRK	Bacteria:79	PRK04155, PRK04155, chaperone protein HchA; Provisional.
CDD:235229	567	PRK	Bacteria:74	PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
CDD:235230	256	PRK	Bacteria:187	PRK04158, PRK04158, transcriptional repressor CodY; Validated.
CDD:235231	258	PRK	Bacteria:68	PRK04160, PRK04160, diphthine synthase; Provisional.
CDD:235233	235	PRK	Bacteria:46	PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional.
CDD:235234	181	PRK	Bacteria:87	PRK04164, PRK04164, hypothetical protein; Provisional.
CDD:235235	450	PRK	Bacteria:56	PRK04165, PRK04165, acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional.
CDD:235236	334	PRK	Bacteria:27	PRK04168, PRK04168, molybdate ABC transporter periplasmic substrate-binding protein; Provisional.
CDD:235237	232	PRK	Bacteria:155	PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like protein; Reviewed.
CDD:235238	222	PRK	Bacteria:47	PRK04171, PRK04171, ribosome biogenesis protein; Provisional.
CDD:235239	489	PRK	Bacteria:89	PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha; Provisional.
CDD:235240	456	PRK	Bacteria:353	PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
CDD:179766	122	PRK	Bacteria:82	PRK04175, rpl7ae, 50S ribosomal protein L7Ae; Validated.
CDD:235241	257	PRK	Bacteria:86	PRK04176, PRK04176, ribulose-1,5-biphosphate synthetase; Provisional.
CDD:235242	62	PRK	Bacteria:74	PRK04179, rpl37e, 50S ribosomal protein L37e; Reviewed.
CDD:179769	293	PRK	Bacteria:370	PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
CDD:235243	257	PRK	Bacteria:27	PRK04181, PRK04181, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:235244	180	PRK	Bacteria:92	PRK04182, PRK04182, cytidylate kinase; Provisional.
CDD:235245	419	PRK	Bacteria:75	PRK04183, PRK04183, glutamyl-tRNA(Gln) amidotransferase subunit D; Validated.
CDD:235246	535	PRK	Bacteria:61	PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
CDD:179774	191	PRK	Bacteria:14	PRK04190, PRK04190, glucose-6-phosphate isomerase; Provisional.
CDD:235247	207	PRK	Bacteria:74	PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
CDD:235248	586	PRK	Bacteria:182	PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
CDD:235249	392	PRK	Bacteria:128	PRK04194, PRK04194, hypothetical protein; Provisional.
CDD:235250	482	PRK	Bacteria:69	PRK04195, PRK04195, replication factor C large subunit; Provisional.
CDD:235251	460	PRK	Bacteria:160	PRK04196, PRK04196, V-type ATP synthase subunit B; Provisional.
CDD:235252	172	PRK	Bacteria:86	PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
CDD:179781	395	PRK	Bacteria:40	PRK04200, PRK04200, cofactor-independent phosphoglycerate mutase; Provisional.
CDD:235253	265	PRK	Bacteria:124	PRK04201, PRK04201, zinc transporter ZupT; Provisional.
CDD:235254	215	PRK	Bacteria:77	PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
CDD:235255	343	PRK	Bacteria:116	PRK04204, PRK04204, RNA 3'-terminal-phosphate cyclase; Provisional.
CDD:179786	341	PRK	Bacteria:90	PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase; Provisional.
CDD:179787	468	PRK	Bacteria:120	PRK04208, rbcL, ribulose bisophosphate carboxylase; Reviewed.
CDD:235256	601	PRK	Bacteria:244	PRK04210, PRK04210, phosphoenolpyruvate carboxykinase; Provisional.
CDD:235257	145	PRK	Bacteria:83	PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
CDD:179790	201	PRK	Bacteria:36	PRK04213, PRK04213, GTP-binding protein; Provisional.
CDD:235259	177	PRK	Bacteria:82	PRK04219, rpl5p, 50S ribosomal protein L5P; Reviewed.
CDD:179793	301	PRK	Bacteria:21	PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
CDD:179794	153	PRK	Bacteria:74	PRK04223, rpl22p, 50S ribosomal protein L22P; Reviewed.
CDD:235260	337	PRK	Bacteria:80	PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
CDD:235262	196	PRK	Bacteria:48	PRK04235, PRK04235, hypothetical protein; Provisional.
CDD:179798	110	PRK	Bacteria:63	PRK04239, PRK04239, hypothetical protein; Provisional.
CDD:235263	196	PRK	Bacteria:83	PRK04243, PRK04243, 50S ribosomal protein L15e; Validated.
CDD:235264	238	PRK	Bacteria:35	PRK04247, PRK04247, hypothetical protein; Provisional.
CDD:235266	347	PRK	Bacteria:70	PRK04262, PRK04262, hypothetical protein; Provisional.
CDD:235267	226	PRK	Bacteria:86	PRK04266, PRK04266, fibrillarin; Provisional.
CDD:179806	300	PRK	Bacteria:61	PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p; Reviewed.
CDD:235268	271	PRK	Bacteria:47	PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42; Provisional.
CDD:235270	298	PRK	Bacteria:41	PRK04286, PRK04286, hypothetical protein; Provisional.
CDD:235271	115	PRK	Bacteria:71	PRK04290, PRK04290, 30S ribosomal protein S6e; Validated.
CDD:179812	333	PRK	Bacteria:54	PRK04293, PRK04293, adenylosuccinate synthetase; Provisional.
CDD:235272	190	PRK	Bacteria:428,nodiv:2	PRK04296, PRK04296, thymidine kinase; Provisional.
CDD:235273	317	PRK	Bacteria:78	PRK04301, radA, DNA repair and recombination protein RadA; Validated.
CDD:235274	223	PRK	Bacteria:73	PRK04302, PRK04302, triosephosphate isomerase; Provisional.
CDD:235275	98	PRK	Bacteria:80	PRK04306, PRK04306, 50S ribosomal protein L21e; Reviewed.
CDD:235277	383	PRK	Bacteria:65	PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated.
CDD:235278	464	PRK	Bacteria:259	PRK04311, PRK04311, selenocysteine synthase; Provisional.
CDD:179820	237	PRK	Bacteria:84	PRK04313, PRK04313, 30S ribosomal protein S4e; Validated.
CDD:235279	570	PRK	Bacteria:83	PRK04319, PRK04319, acetyl-CoA synthetase; Provisional.
CDD:235280	113	PRK	Bacteria:80	PRK04322, PRK04322, peptidyl-tRNA hydrolase; Provisional.
CDD:179823	91	PRK	Bacteria:134	PRK04323, PRK04323, hypothetical protein; Provisional.
CDD:179825	330	PRK	Bacteria:30	PRK04326, PRK04326, methionine synthase; Provisional.
CDD:235282	88	PRK	Bacteria:64	PRK04330, PRK04330, hypothetical protein; Provisional.
CDD:235284	251	PRK	Bacteria:72	PRK04334, PRK04334, hypothetical protein; Provisional.
CDD:179831	87	PRK	Bacteria:15	PRK04337, PRK04337, 50S ribosomal protein L35Ae; Validated.
CDD:235286	382	PRK	Bacteria:70	PRK04338, PRK04338, N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional.
CDD:235287	367	PRK	Bacteria:85	PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
CDD:235288	397	PRK	Bacteria:859,nodiv:1	PRK04346, PRK04346, tryptophan synthase subunit beta; Validated.
CDD:235289	490	PRK	Bacteria:73	PRK04350, PRK04350, thymidine phosphorylase; Provisional.
CDD:235290	149	PRK	Bacteria:135	PRK04351, PRK04351, hypothetical protein; Provisional.
CDD:235291	217	PRK	Bacteria:52	PRK04358, PRK04358, hypothetical protein; Provisional.
CDD:235292	481	PRK	Bacteria:282,nodiv:1	PRK04366, PRK04366, glycine dehydrogenase subunit 2; Validated.
CDD:235293	296	PRK	Bacteria:539,nodiv:1	PRK04375, PRK04375, protoheme IX farnesyltransferase; Provisional.
CDD:179841	90	PRK	Bacteria:103	PRK04387, PRK04387, hypothetical protein; Provisional.
CDD:179847	185	PRK	Bacteria:105	PRK04424, PRK04424, fatty acid biosynthesis transcriptional regulator; Provisional.
CDD:179848	147	PRK	Bacteria:100	PRK04435, PRK04435, hypothetical protein; Provisional.
CDD:235298	399	PRK	Bacteria:129	PRK04439, PRK04439, S-adenosylmethionine synthetase; Provisional.
CDD:235299	348	PRK	Bacteria:26	PRK04443, PRK04443, acetyl-lysine deacetylase; Provisional.
CDD:235300	351	PRK	Bacteria:102	PRK04447, PRK04447, hypothetical protein; Provisional.
CDD:235301	319	PRK	Bacteria:55	PRK04452, PRK04452, acetyl-CoA decarbonylase/synthase complex subunit delta; Provisional.
CDD:235302	463	PRK	Bacteria:26	PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed.
CDD:179855	137	PRK	Bacteria:32	PRK04460, PRK04460, nickel responsive regulator; Provisional.
CDD:235306	398	PRK	Bacteria:26	PRK04531, PRK04531, acetylglutamate kinase; Provisional.
CDD:179863	189	PRK	Bacteria:122	PRK04542, PRK04542, elongation factor P; Provisional.
CDD:235310	537	PRK	Bacteria:194	PRK04750, ubiB, putative ubiquinone biosynthesis protein UbiB; Reviewed.
CDD:179876	246	PRK	Bacteria:101	PRK04761, ppnK, inorganic polyphosphate/ATP-NAD kinase; Reviewed.
CDD:179877	569	PRK	Bacteria:149	PRK04778, PRK04778, septation ring formation regulator EzrA; Provisional.
CDD:235312	448	PRK	Bacteria:41	PRK04792, tolB, translocation protein TolB; Provisional.
CDD:179880	221	PRK	Bacteria:36	PRK04804, minC, septum formation inhibitor; Reviewed.
CDD:235313	503	PRK	Bacteria:116	PRK04813, PRK04813, D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional.
CDD:179883	455	PRK	Bacteria:144	PRK04833, PRK04833, argininosuccinate lyase; Provisional.
CDD:235314	423	PRK	Bacteria:145	PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
CDD:235315	903	PRK	Bacteria:97	PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
CDD:179886	160	PRK	Bacteria:133	PRK04860, PRK04860, hypothetical protein; Provisional.
CDD:235316	1486	PRK	Bacteria:130	PRK04863, mukB, cell division protein MukB; Provisional.
CDD:179888	356	PRK	Bacteria:72	PRK04870, PRK04870, histidinol-phosphate aminotransferase; Provisional.
CDD:235317	265	PRK	Bacteria:145	PRK04885, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional.
CDD:235318	298	PRK	Bacteria:76	PRK04897, PRK04897, heat shock protein HtpX; Provisional.
CDD:235319	956	PRK	Bacteria:193	PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
CDD:179892	433	PRK	Bacteria:30	PRK04922, tolB, translocation protein TolB; Provisional.
CDD:235320	503	PRK	Bacteria:110	PRK04926, dgt, deoxyguanosinetriphosphate triphosphohydrolase; Provisional.
CDD:179895	184	PRK	Bacteria:105	PRK04930, PRK04930, glutathione-regulated potassium-efflux system ancillary protein KefG; Provisional.
CDD:179896	180	PRK	Bacteria:128	PRK04940, PRK04940, hypothetical protein; Provisional.
CDD:235321	181	PRK	Bacteria:146	PRK04946, PRK04946, hypothetical protein; Provisional.
CDD:179898	251	PRK	Bacteria:153	PRK04949, PRK04949, putative sulfate transport protein CysZ; Validated.
CDD:235322	213	PRK	Bacteria:152	PRK04950, PRK04950, ProP expression regulator; Provisional.
CDD:235323	111	PRK	Bacteria:108	PRK04960, PRK04960, universal stress protein UspB; Provisional.
CDD:179902	377	PRK	Bacteria:82	PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase; Provisional.
CDD:179903	72	PRK	Bacteria:100	PRK04966, PRK04966, hypothetical protein; Provisional.
CDD:235324	181	PRK	Bacteria:131	PRK04968, PRK04968, SecY interacting protein Syd; Provisional.
CDD:235325	818	PRK	Bacteria:197	PRK04974, PRK04974, glycerol-3-phosphate acyltransferase; Validated.
CDD:235326	202	PRK	Bacteria:88	PRK04976, torD, chaperone protein TorD; Validated.
CDD:179908	102	PRK	Bacteria:116	PRK04980, PRK04980, hypothetical protein; Provisional.
CDD:179909	239	PRK	Bacteria:151	PRK04984, PRK04984, fatty acid metabolism regulator; Provisional.
CDD:235327	130	PRK	Bacteria:122	PRK04987, PRK04987, fumarate reductase subunit C; Provisional.
CDD:179912	88	PRK	Bacteria:153	PRK04998, PRK04998, hypothetical protein; Provisional.
CDD:235329	884	PRK	Bacteria:131	PRK05007, PRK05007, PII uridylyl-transferase; Provisional.
CDD:179914	171	PRK	Bacteria:122	PRK05014, hscB, co-chaperone HscB; Provisional.
CDD:235330	424	PRK	Bacteria:155	PRK05015, PRK05015, aminopeptidase B; Provisional.
CDD:235331	509	PRK	Bacteria:146	PRK05022, PRK05022, anaerobic nitric oxide reductase transcription regulator; Provisional.
CDD:235332	362	PRK	Bacteria:217	PRK05031, PRK05031, tRNA (uracil-5-)-methyltransferase; Validated.
CDD:235333	312	PRK	Bacteria:196,nodiv:1	PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
CDD:235334	695	PRK	Bacteria:152	PRK05035, PRK05035, electron transport complex protein RnfC; Provisional.
CDD:179920	644	PRK	Bacteria:138	PRK05054, PRK05054, exoribonuclease II; Provisional.
CDD:179922	156	PRK	Bacteria:150,nodiv:1	PRK05066, PRK05066, arginine repressor; Provisional.
CDD:179923	218	PRK	Bacteria:170	PRK05070, PRK05070, DNA mismatch repair protein; Provisional.
CDD:235336	173	PRK	Bacteria:128	PRK05074, PRK05074, inosine/xanthosine triphosphatase; Reviewed.
CDD:235337	414	PRK	Bacteria:112	PRK05077, frsA, fermentation/respiration switch protein; Reviewed.
CDD:235338	291	PRK	Bacteria:92	PRK05082, PRK05082, N-acetylmannosamine kinase; Provisional.
CDD:235339	357	PRK	Bacteria:88	PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed.
CDD:179929	78	PRK	Bacteria:123	PRK05087, PRK05087, D-alanine--poly(phosphoribitol) ligase subunit 2; Validated.
CDD:235341	188	PRK	Bacteria:202	PRK05089, PRK05089, cytochrome C oxidase assembly protein; Provisional.
CDD:179931	95	PRK	Bacteria:119	PRK05090, PRK05090, hypothetical protein; Validated.
CDD:235342	931	PRK	Bacteria:82,nodiv:1	PRK05092, PRK05092, PII uridylyl-transferase; Provisional.
CDD:179933	403	PRK	Bacteria:186	PRK05093, argD, bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed.
CDD:179934	107	PRK	Bacteria:122	PRK05094, PRK05094, dsDNA-mimic protein; Reviewed.
CDD:235343	346	PRK	Bacteria:126	PRK05096, PRK05096, guanosine 5'-monophosphate oxidoreductase; Provisional.
CDD:235344	150	PRK	Bacteria:127	PRK05097, PRK05097, Ter macrodomain organizer matS-binding protein; Provisional.
CDD:179937	382	PRK	Bacteria:120	PRK05101, PRK05101, galactokinase; Provisional.
CDD:235345	322	PRK	Bacteria:139	PRK05105, PRK05105, O-succinylbenzoate synthase; Provisional.
CDD:235346	383	PRK	Bacteria:162	PRK05111, PRK05111, acetylornithine deacetylase; Provisional.
CDD:235347	191	PRK	Bacteria:162	PRK05113, PRK05113, electron transport complex protein RnfB; Provisional.
CDD:179941	59	PRK	Bacteria:111	PRK05114, PRK05114, hypothetical protein; Provisional.
CDD:235348	399	PRK	Bacteria:108	PRK05122, PRK05122, major facilitator superfamily transporter; Provisional.
CDD:235349	474	PRK	Bacteria:144	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
CDD:235350	233	PRK	Bacteria:370,nodiv:1	PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional.
CDD:235351	435	PRK	Bacteria:88,nodiv:1	PRK05137, tolB, translocation protein TolB; Provisional.
CDD:235353	246	PRK	Bacteria:125	PRK05157, PRK05157, pyrroloquinoline quinone biosynthesis protein PqqC; Provisional.
CDD:235354	437	PRK	Bacteria:128	PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
CDD:235355	124	PRK	Bacteria:948,nodiv:2	PRK05163, rpsL, 30S ribosomal protein S12; Validated.
CDD:179951	211	PRK	Bacteria:239,nodiv:1	PRK05168, PRK05168, ribonuclease T; Provisional.
CDD:235356	147	PRK	Bacteria:271,nodiv:1	PRK05170, PRK05170, hypothetical protein; Provisional.
CDD:179953	172	PRK	Bacteria:313,nodiv:2	PRK05174, PRK05174, 3-hydroxydecanoyl-(acyl carrier protein) dehydratase; Validated.
CDD:235357	239	PRK	Bacteria:37,nodiv:1	PRK05177, minC, septum formation inhibitor; Reviewed.
CDD:235358	122	PRK	Bacteria:903,nodiv:2	PRK05179, rpsM, 30S ribosomal protein S13; Validated.
CDD:235359	310	PRK	Bacteria:981,nodiv:2	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional.
CDD:235360	616	PRK	Bacteria:251	PRK05183, hscA, chaperone protein HscA; Provisional.
CDD:235361	302	PRK	Bacteria:119	PRK05184, PRK05184, pyrroloquinoline quinone biosynthesis protein PqqB; Provisional.
CDD:179959	114	PRK	Bacteria:896,nodiv:2	PRK05185, rplT, 50S ribosomal protein L20; Provisional.
CDD:235362	618	PRK	Bacteria:909,nodiv:2	PRK05192, PRK05192, tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated.
CDD:235363	264	PRK	Bacteria:550,nodiv:2	PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional.
CDD:235364	443	PRK	Bacteria:614,nodiv:2	PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional.
CDD:235365	176	PRK	Bacteria:361	PRK05205, PRK05205, bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase; Provisional.
CDD:179964	168	PRK	Bacteria:231	PRK05208, PRK05208, hypothetical protein; Provisional.
CDD:235366	613	PRK	Bacteria:632,nodiv:1	PRK05218, PRK05218, heat shock protein 90; Provisional.
CDD:235367	758	PRK	Bacteria:515,nodiv:1	PRK05222, PRK05222, 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional.
CDD:235368	487	PRK	Bacteria:172	PRK05225, PRK05225, ketol-acid reductoisomerase; Validated.
CDD:235369	319	PRK	Bacteria:152	PRK05231, PRK05231, homoserine kinase; Provisional.
CDD:179969	142	PRK	Bacteria:302,nodiv:2	PRK05234, mgsA, methylglyoxal synthase; Validated.
CDD:235370	177	PRK	Bacteria:148	PRK05244, PRK05244, Der GTPase activator; Provisional.
CDD:235371	316	PRK	Bacteria:403,nodiv:2	PRK05246, PRK05246, glutathione synthetase; Provisional.
CDD:235372	121	PRK	Bacteria:134	PRK05248, PRK05248, hypothetical protein; Provisional.
CDD:235373	461	PRK	Bacteria:220,nodiv:1	PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase; Provisional.
CDD:235374	384	PRK	Bacteria:862,nodiv:1	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated.
CDD:235375	301	PRK	Bacteria:478,nodiv:1	PRK05253, PRK05253, sulfate adenylyltransferase subunit 2; Provisional.
CDD:235376	224	PRK	Bacteria:557,nodiv:2	PRK05254, PRK05254, uracil-DNA glycosylase; Provisional.
CDD:235377	171	PRK	Bacteria:264	PRK05255, PRK05255, hypothetical protein; Provisional.
CDD:235378	238	PRK	Bacteria:131	PRK05256, PRK05256, condesin subunit E; Provisional.
CDD:179979	494	PRK	Bacteria:274,nodiv:1	PRK05257, PRK05257, malate:quinone oxidoreductase; Validated.
CDD:179980	440	PRK	Bacteria:131	PRK05260, PRK05260, condesin subunit F; Provisional.
CDD:235379	785	PRK	Bacteria:219	PRK05261, PRK05261, putative phosphoketolase; Provisional.
CDD:235380	239	PRK	Bacteria:541,nodiv:2	PRK05265, PRK05265, pyridoxine 5'-phosphate synthase; Provisional.
CDD:235381	318	PRK	Bacteria:331	PRK05269, PRK05269, transaldolase B; Provisional.
CDD:235382	493	PRK	Bacteria:114	PRK05270, PRK05270, galactose-1-phosphate uridylyltransferase; Provisional.
CDD:235383	147	PRK	Bacteria:610	PRK05273, PRK05273, D-tyrosyl-tRNA(Tyr) deacylase; Provisional.
CDD:235384	326	PRK	Bacteria:127	PRK05274, PRK05274, 2-keto-3-deoxygluconate permease; Provisional.
CDD:235385	438	PRK	Bacteria:120	PRK05277, PRK05277, chloride channel protein; Provisional.
CDD:235386	441	PRK	Bacteria:263	PRK05279, PRK05279, N-acetylglutamate synthase; Validated.
CDD:179990	233	PRK	Bacteria:116	PRK05282, PRK05282, (alpha)-aspartyl dipeptidase; Validated.
CDD:235387	257	PRK	Bacteria:154,nodiv:1	PRK05283, PRK05283, deoxyribose-phosphate aldolase; Provisional.
CDD:235388	344	PRK	Bacteria:555,nodiv:2	PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
CDD:235389	250	PRK	Bacteria:219,nodiv:1	PRK05287, PRK05287, hypothetical protein; Provisional.
CDD:235390	262	PRK	Bacteria:510,nodiv:2	PRK05289, PRK05289, UDP-N-acetylglucosamine acyltransferase; Provisional.
CDD:235391	546	PRK	Bacteria:282	PRK05290, PRK05290, hybrid cluster protein; Provisional.
CDD:235392	449	PRK	Bacteria:794,nodiv:1	PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
CDD:179997	380	PRK	Bacteria:91	PRK05293, glgC, glucose-1-phosphate adenylyltransferase; Provisional.
CDD:235393	1066	PRK	Bacteria:688,nodiv:1	PRK05294, carB, carbamoyl phosphate synthase large subunit; Reviewed.
CDD:235394	1290	PRK	Bacteria:345,nodiv:1	PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase; Provisional.
CDD:235395	652	PRK	Bacteria:992,nodiv:1	PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
CDD:235396	258	PRK	Bacteria:872,nodiv:2	PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
CDD:235397	378	PRK	Bacteria:128	PRK05301, PRK05301, pyrroloquinoline quinone biosynthesis protein PqqE; Provisional.
CDD:235398	156	PRK	Bacteria:980,nodiv:2	PRK05302, PRK05302, 30S ribosomal protein S7; Validated.
CDD:235399	367	PRK	Bacteria:381,nodiv:1	PRK05303, flgI, flagellar basal body P-ring protein; Provisional.
CDD:235400	206	PRK	Bacteria:247,nodiv:1	PRK05305, PRK05305, phosphatidylserine decarboxylase; Provisional.
CDD:235401	746	PRK	Bacteria:916,nodiv:1	PRK05306, infB, translation initiation factor IF-2; Validated.
CDD:180007	128	PRK	Bacteria:926,nodiv:1	PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
CDD:235402	336	PRK	Bacteria:64,nodiv:1	PRK05312, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional.
CDD:180009	452	PRK	Bacteria:188	PRK05313, PRK05313, hypothetical protein; Provisional.
CDD:235403	432	PRK	Bacteria:65	PRK05318, PRK05318, deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional.
CDD:235404	205	PRK	Bacteria:914,nodiv:1	PRK05319, rplD, 50S ribosomal protein L4; Provisional.
CDD:235405	257	PRK	Bacteria:55	PRK05320, PRK05320, rhodanese superfamily protein; Provisional.
CDD:235406	400	PRK	Bacteria:298,nodiv:1	PRK05321, PRK05321, nicotinate phosphoribosyltransferase; Provisional.
CDD:235407	387	PRK	Bacteria:79	PRK05322, PRK05322, galactokinase; Provisional.
CDD:235408	329	PRK	Bacteria:179	PRK05324, PRK05324, succinylglutamate desuccinylase; Provisional.
CDD:235409	401	PRK	Bacteria:356	PRK05325, PRK05325, hypothetical protein; Provisional.
CDD:235410	562	PRK	Bacteria:237,nodiv:1	PRK05326, PRK05326, potassium/proton antiporter; Reviewed.
CDD:235411	203	PRK	Bacteria:946,nodiv:1	PRK05327, rpsD, 30S ribosomal protein S4; Validated.
CDD:235412	422	PRK	Bacteria:149	PRK05329, PRK05329, anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated.
CDD:235413	300	PRK	Bacteria:454,nodiv:2	PRK05330, PRK05330, coproporphyrinogen III oxidase; Provisional.
CDD:235414	334	PRK	Bacteria:674,nodiv:2	PRK05331, PRK05331, putative phosphate acyltransferase; Provisional.
CDD:235415	285	PRK	Bacteria:40	PRK05333, PRK05333, NAD-dependent deacetylase; Provisional.
CDD:235416	436	PRK	Bacteria:299,nodiv:1	PRK05335, PRK05335, tRNA (uracil-5-)-methyltransferase Gid; Reviewed.
CDD:235417	337	PRK	Bacteria:258,nodiv:1	PRK05337, PRK05337, beta-hexosaminidase; Provisional.
CDD:235418	116	PRK	Bacteria:898,nodiv:2	PRK05338, rplS, 50S ribosomal protein L19; Provisional.
CDD:235419	269	PRK	Bacteria:495	PRK05339, PRK05339, PEP synthetase regulatory protein; Provisional.
CDD:235420	241	PRK	Bacteria:259,nodiv:1	PRK05340, PRK05340, UDP-2,3-diacylglucosamine hydrolase; Provisional.
CDD:235421	438	PRK	Bacteria:130	PRK05341, PRK05341, homogentisate 1,2-dioxygenase; Provisional.
CDD:235422	412	PRK	Bacteria:911,nodiv:1	PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional.
CDD:235423	256	PRK	Bacteria:144	PRK05346, PRK05346, Na(+)-translocating NADH-quinone reductase subunit C; Provisional.
CDD:235424	554	PRK	Bacteria:446	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional.
CDD:235425	405	PRK	Bacteria:139	PRK05349, PRK05349, Na(+)-translocating NADH-quinone reductase subunit B; Provisional.
CDD:180033	82	PRK	Bacteria:74	PRK05350, PRK05350, acyl carrier protein; Provisional.
CDD:235426	448	PRK	Bacteria:153	PRK05352, PRK05352, Na(+)-translocating NADH-quinone reductase subunit A; Provisional.
CDD:235427	634	PRK	Bacteria:317	PRK05354, PRK05354, arginine decarboxylase; Provisional.
CDD:235428	360	PRK	Bacteria:491,nodiv:1	PRK05355, PRK05355, 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional.
CDD:235429	181	PRK	Bacteria:385,nodiv:1	PRK05359, PRK05359, oligoribonuclease; Provisional.
CDD:235430	394	PRK	Bacteria:375	PRK05362, PRK05362, phosphopentomutase; Provisional.
CDD:235431	280	PRK	Bacteria:316,nodiv:1	PRK05363, PRK05363, TMAO/DMSO reductase; Reviewed.
CDD:180040	195	PRK	Bacteria:140,nodiv:1	PRK05365, PRK05365, malonic semialdehyde reductase; Provisional.
CDD:235432	954	PRK	Bacteria:464	PRK05367, PRK05367, glycine dehydrogenase; Provisional.
CDD:235433	302	PRK	Bacteria:307,nodiv:1	PRK05368, PRK05368, homoserine O-succinyltransferase; Provisional.
CDD:235434	447	PRK	Bacteria:204	PRK05370, PRK05370, argininosuccinate synthase; Validated.
CDD:235435	767	PRK	Bacteria:120	PRK05371, PRK05371, x-prolyl-dipeptidyl aminopeptidase; Provisional.
CDD:180045	296	PRK	Bacteria:75	PRK05377, PRK05377, fructose-1,6-bisphosphate aldolase; Reviewed.
CDD:235436	340	PRK	Bacteria:42	PRK05379, PRK05379, bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional.
CDD:235437	533	PRK	Bacteria:1041,nodiv:1	PRK05380, pyrG, CTP synthetase; Validated.
CDD:235438	359	PRK	Bacteria:960,nodiv:2	PRK05382, PRK05382, chorismate synthase; Validated.
CDD:235439	327	PRK	Bacteria:781,nodiv:2	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional.
CDD:235440	353	PRK	Bacteria:127	PRK05387, PRK05387, histidinol-phosphate aminotransferase; Provisional.
CDD:235441	395	PRK	Bacteria:469	PRK05388, argJ, bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein; Validated.
CDD:235442	305	PRK	Bacteria:63	PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
CDD:235443	146	PRK	Bacteria:562,nodiv:1	PRK05395, PRK05395, 3-dehydroquinate dehydratase; Provisional.
CDD:180054	341	PRK	Bacteria:249,nodiv:1	PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
CDD:180055	416	PRK	Bacteria:80	PRK05398, PRK05398, formyl-coenzyme A transferase; Provisional.
CDD:235444	854	PRK	Bacteria:768,nodiv:2	PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
CDD:235445	726	PRK	Bacteria:404	PRK05402, PRK05402, glycogen branching enzyme; Provisional.
CDD:235446	246	PRK	Bacteria:331,nodiv:1	PRK05406, PRK05406, LamB/YcsF family protein; Provisional.
CDD:180059	90	PRK	Bacteria:336,nodiv:1	PRK05408, PRK05408, oxidative damage protection protein; Provisional.
CDD:235447	281	PRK	Bacteria:149	PRK05409, PRK05409, hypothetical protein; Provisional.
CDD:180061	161	PRK	Bacteria:424,nodiv:1	PRK05412, PRK05412, putative nucleotide-binding protein; Reviewed.
CDD:235448	556	PRK	Bacteria:417,nodiv:1	PRK05414, PRK05414, urocanate hydratase; Provisional.
CDD:235449	341	PRK	Bacteria:195,nodiv:1	PRK05415, PRK05415, hypothetical protein; Provisional.
CDD:235450	288	PRK	Bacteria:624	PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
CDD:235451	191	PRK	Bacteria:41	PRK05417, PRK05417, glutathione-dependent formaldehyde-activating enzyme; Provisional.
CDD:235452	205	PRK	Bacteria:225,nodiv:1	PRK05419, PRK05419, putative sulfite oxidase subunit YedZ; Reviewed.
CDD:235453	231	PRK	Bacteria:148	PRK05420, PRK05420, aquaporin Z; Provisional.
CDD:235454	263	PRK	Bacteria:135	PRK05421, PRK05421, hypothetical protein; Provisional.
CDD:235455	148	PRK	Bacteria:912,nodiv:2	PRK05422, smpB, SsrA-binding protein; Validated.
CDD:180070	104	PRK	Bacteria:137	PRK05423, PRK05423, hypothetical protein; Provisional.
CDD:180071	230	PRK	Bacteria:900,nodiv:2	PRK05424, rplA, 50S ribosomal protein L1; Validated.
CDD:235456	327	PRK	Bacteria:252	PRK05425, PRK05425, asparagine synthetase AsnA; Provisional.
CDD:235457	189	PRK	Bacteria:877,nodiv:2	PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
CDD:235458	308	PRK	Bacteria:195	PRK05427, PRK05427, putative manganese-dependent inorganic pyrophosphatase; Provisional.
CDD:235459	308	PRK	Bacteria:314,nodiv:1	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional.
CDD:235460	372	PRK	Bacteria:623,nodiv:1	PRK05429, PRK05429, gamma-glutamyl kinase; Provisional.
CDD:235461	425	PRK	Bacteria:988,nodiv:2	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
CDD:235462	600	PRK	Bacteria:967,nodiv:1	PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
CDD:235463	507	PRK	Bacteria:548,nodiv:1	PRK05434, PRK05434, phosphoglyceromutase; Provisional.
CDD:235464	82	PRK	Bacteria:948,nodiv:2	PRK05435, rpmA, 50S ribosomal protein L27; Validated.
CDD:235465	352	PRK	Bacteria:321	PRK05437, PRK05437, isopentenyl pyrophosphate isomerase; Provisional.
CDD:235466	311	PRK	Bacteria:399,nodiv:2	PRK05439, PRK05439, pantothenate kinase; Provisional.
CDD:235467	299	PRK	Bacteria:316	PRK05441, murQ, N-acetylmuramic acid-6-phosphate etherase; Reviewed.
CDD:235468	326	PRK	Bacteria:218,nodiv:1	PRK05442, PRK05442, malate dehydrogenase; Provisional.
CDD:235469	691	PRK	Bacteria:573,nodiv:1	PRK05443, PRK05443, polyphosphate kinase; Provisional.
CDD:235470	580	PRK	Bacteria:700,nodiv:1	PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional.
CDD:180087	164	PRK	Bacteria:114	PRK05445, PRK05445, hypothetical protein; Validated.
CDD:235471	354	PRK	Bacteria:210	PRK05446, PRK05446, imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional.
CDD:235472	385	PRK	Bacteria:739,nodiv:1	PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional.
CDD:180090	126	PRK	Bacteria:476,nodiv:2	PRK05449, PRK05449, aspartate alpha-decarboxylase; Provisional.
CDD:235473	245	PRK	Bacteria:449,nodiv:1	PRK05450, PRK05450, 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional.
CDD:235474	345	PRK	Bacteria:374,nodiv:2	PRK05451, PRK05451, dihydroorotase; Provisional.
CDD:235476	605	PRK	Bacteria:229	PRK05454, PRK05454, glucosyltransferase MdoH; Provisional.
CDD:235477	172	PRK	Bacteria:674,nodiv:2	PRK05456, PRK05456, ATP-dependent protease subunit HslV; Provisional.
CDD:235478	284	PRK	Bacteria:260	PRK05457, PRK05457, heat shock protein HtpX; Provisional.
CDD:235479	326	PRK	Bacteria:136	PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase; Provisional.
CDD:180098	127	PRK	Bacteria:345,nodiv:1	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed.
CDD:235480	266	PRK	Bacteria:161	PRK05462, PRK05462, S-adenosylmethionine decarboxylase; Provisional.
CDD:180100	262	PRK	Bacteria:122,nodiv:1	PRK05463, PRK05463, hypothetical protein; Provisional.
CDD:235481	409	PRK	Bacteria:157	PRK05464, PRK05464, Na(+)-translocating NADH-quinone reductase subunit F; Provisional.
CDD:235482	260	PRK	Bacteria:180	PRK05465, PRK05465, ethanolamine ammonia-lyase small subunit; Provisional.
CDD:235483	226	PRK	Bacteria:172	PRK05467, PRK05467, Fe(II)-dependent oxygenase superfamily protein; Provisional.
CDD:235484	408	PRK	Bacteria:333	PRK05469, PRK05469, peptidase T; Provisional.
CDD:180105	118	PRK	Bacteria:135	PRK05470, PRK05470, fumarate reductase subunit D; Provisional.
CDD:235485	252	PRK	Bacteria:105	PRK05471, PRK05471, CDP-diacylglycerol pyrophosphatase; Provisional.
CDD:235486	213	PRK	Bacteria:310	PRK05472, PRK05472, redox-sensing transcriptional repressor Rex; Provisional.
CDD:180108	86	PRK	Bacteria:218	PRK05473, PRK05473, hypothetical protein; Provisional.
CDD:235487	437	PRK	Bacteria:223,nodiv:1	PRK05474, PRK05474, xylose isomerase; Provisional.
CDD:235488	425	PRK	Bacteria:548,nodiv:2	PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase; Provisional.
CDD:235489	474	PRK	Bacteria:735,nodiv:2	PRK05477, gatB, aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated.
CDD:235490	466	PRK	Bacteria:596,nodiv:1	PRK05478, PRK05478, isopropylmalate isomerase large subunit; Validated.
CDD:235491	330	PRK	Bacteria:621	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
CDD:235492	209	PRK	Bacteria:365,nodiv:1	PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
CDD:235493	289	PRK	Bacteria:807,nodiv:2	PRK05481, PRK05481, lipoyl synthase; Provisional.
CDD:235494	559	PRK	Bacteria:393	PRK05482, PRK05482, potassium-transporting ATPase subunit A; Provisional.
CDD:180117	122	PRK	Bacteria:876,nodiv:1	PRK05483, rplN, 50S ribosomal protein L14; Validated.
CDD:235495	178	PRK	Bacteria:894,nodiv:2	PRK05498, rplF, 50S ribosomal protein L6; Validated.
CDD:180120	632	PRK	Bacteria:91	PRK05506, PRK05506, bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional.
CDD:235496	180	PRK	Bacteria:68	PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
CDD:235497	156	PRK	Bacteria:31	PRK05528, PRK05528, methionine sulfoxide reductase A; Provisional.
CDD:235499	283	PRK	Bacteria:63,nodiv:1	PRK05550, PRK05550, bifunctional methionine sulfoxide reductase B/A protein; Provisional.
CDD:235500	248	PRK	Bacteria:317	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated.
CDD:235501	631	PRK	Bacteria:653,nodiv:2	PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
CDD:235502	805	PRK	Bacteria:944,nodiv:2	PRK05560, PRK05560, DNA gyrase subunit A; Validated.
CDD:235503	742	PRK	Bacteria:603,nodiv:1	PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
CDD:235504	223	PRK	Bacteria:20	PRK05562, PRK05562, precorrin-2 dehydrogenase; Provisional.
CDD:235505	559	PRK	Bacteria:185	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated.
CDD:235506	247	PRK	Bacteria:90	PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:235507	486	PRK	Bacteria:430,nodiv:1	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed.
CDD:235509	148	PRK	Bacteria:240	PRK05571, PRK05571, ribose-5-phosphate isomerase B; Provisional.
CDD:180137	252	PRK	Bacteria:61	PRK05572, PRK05572, sporulation sigma factor SigF; Validated.
CDD:235510	103	PRK	Bacteria:810,nodiv:1	PRK05573, rplU, 50S ribosomal protein L21; Validated.
CDD:235511	340	PRK	Bacteria:361	PRK05574, holA, DNA polymerase III subunit delta; Reviewed.
CDD:235512	229	PRK	Bacteria:89	PRK05576, PRK05576, cobalt-precorrin-2 C(20)-methyltransferase; Validated.
CDD:180142	131	PRK	Bacteria:122,nodiv:1	PRK05578, PRK05578, cytidine deaminase; Validated.
CDD:235513	399	PRK	Bacteria:367,nodiv:1	PRK05579, PRK05579, bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated.
CDD:235514	679	PRK	Bacteria:474,nodiv:1	PRK05580, PRK05580, primosome assembly protein PriA; Validated.
CDD:235515	220	PRK	Bacteria:344	PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated.
CDD:235516	650	PRK	Bacteria:237	PRK05582, PRK05582, DNA topoisomerase I; Validated.
CDD:180148	230	PRK	Bacteria:304	PRK05584, PRK05584, 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated.
CDD:235518	106	PRK	Bacteria:301	PRK05585, yajC, preprotein translocase subunit YajC; Validated.
CDD:235521	166	PRK	Bacteria:33	PRK05590, PRK05590, hypothetical protein; Provisional.
CDD:235522	113	PRK	Bacteria:832,nodiv:1	PRK05591, rplQ, 50S ribosomal protein L17; Validated.
CDD:235523	146	PRK	Bacteria:855,nodiv:2	PRK05592, rplO, 50S ribosomal protein L15; Reviewed.
CDD:235524	117	PRK	Bacteria:842,nodiv:1	PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
CDD:235530	186	PRK	Bacteria:22,nodiv:1	PRK05602, PRK05602, RNA polymerase sigma factor; Reviewed.
CDD:235531	573	PRK	Bacteria:18	PRK05605, PRK05605, long-chain-fatty-acid--CoA ligase; Validated.
CDD:180161	181	PRK	Bacteria:514	PRK05609, nusG, transcription antitermination protein NusG; Validated.
CDD:235532	84	PRK	Bacteria:770,nodiv:2	PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed.
CDD:180163	59	PRK	Bacteria:680,nodiv:2	PRK05611, rpmD, 50S ribosomal protein L30; Reviewed.
CDD:180164	419	PRK	Bacteria:326	PRK05614, gltA, type II citrate synthase; Reviewed.
CDD:235533	342	PRK	Bacteria:132,nodiv:1	PRK05617, PRK05617, 3-hydroxyisobutyryl-CoA hydrolase; Provisional.
CDD:235534	197	PRK	Bacteria:518,nodiv:1	PRK05618, PRK05618, 50S ribosomal protein L25/general stress protein Ctc; Reviewed.
CDD:235535	284	PRK	Bacteria:707,nodiv:1	PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated.
CDD:180169	217	PRK	Bacteria:46	PRK05625, PRK05625, 5-amino-6-(5-phosphoribosylamino)uracil reductase; Validated.
CDD:180170	89	PRK	Bacteria:830,nodiv:1	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed.
CDD:235536	305	PRK	Bacteria:411	PRK05627, PRK05627, bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed.
CDD:180172	375	PRK	Bacteria:53	PRK05628, PRK05628, coproporphyrinogen III oxidase; Validated.
CDD:235537	684	PRK	Bacteria:267	PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
CDD:235538	185	PRK	Bacteria:11	PRK05634, PRK05634, nucleosidase; Provisional.
CDD:235541	367	PRK	Bacteria:718,nodiv:2	PRK05643, PRK05643, DNA polymerase III subunit beta; Validated.
CDD:235542	638	PRK	Bacteria:425	PRK05644, gyrB, DNA gyrase subunit B; Validated.
CDD:235544	200	PRK	Bacteria:397,nodiv:2	PRK05647, purN, phosphoribosylglycinamide formyltransferase; Reviewed.
CDD:235545	270	PRK	Bacteria:22	PRK05650, PRK05650, short chain dehydrogenase; Provisional.
CDD:235546	246	PRK	Bacteria:303	PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated.
CDD:235547	292	PRK	Bacteria:418	PRK05654, PRK05654, acetyl-CoA carboxylase subunit beta; Validated.
CDD:235548	325	PRK	Bacteria:146	PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
CDD:235549	619	PRK	Bacteria:348,nodiv:1	PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
CDD:235550	378	PRK	Bacteria:152	PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
CDD:180188	330	PRK	Bacteria:23	PRK05664, PRK05664, threonine-phosphate decarboxylase; Reviewed.
CDD:235551	580	PRK	Bacteria:539	PRK05667, dnaG, DNA primase; Validated.
CDD:235552	189	PRK	Bacteria:348	PRK05670, PRK05670, anthranilate synthase component II; Provisional.
CDD:235553	1046	PRK	Bacteria:111	PRK05672, dnaE2, error-prone DNA polymerase; Validated.
CDD:235554	1135	PRK	Bacteria:451	PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
CDD:180194	291	PRK	Bacteria:445	PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha; Validated.
CDD:235555	195	PRK	Bacteria:270	PRK05679, PRK05679, pyridoxamine 5'-phosphate oxidase; Provisional.
CDD:180196	137	PRK	Bacteria:160	PRK05680, flgB, flagellar basal body rod protein FlgB; Reviewed.
CDD:235556	135	PRK	Bacteria:279,nodiv:1	PRK05681, flgC, flagellar basal body rod protein FlgC; Reviewed.
CDD:235557	407	PRK	Bacteria:290	PRK05682, flgE, flagellar hook protein FlgE; Validated.
CDD:235559	312	PRK	Bacteria:140	PRK05684, flgJ, flagellar rod assembly protein/muramidase FlgJ; Validated.
CDD:235560	132	PRK	Bacteria:164	PRK05685, fliS, flagellar protein FliS; Validated.
CDD:235561	339	PRK	Bacteria:370,nodiv:1	PRK05686, fliG, flagellar motor switch protein G; Validated.
CDD:235562	246	PRK	Bacteria:172	PRK05687, fliH, flagellar assembly protein H; Validated.
CDD:235563	147	PRK	Bacteria:105	PRK05689, fliJ, flagellar biosynthesis chaperone; Validated.
CDD:180204	245	PRK	Bacteria:180,nodiv:1	PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB; Provisional.
CDD:180206	287	PRK	Bacteria:101	PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
CDD:180207	170	PRK	Bacteria:56	PRK05696, fliL, flagellar basal body-associated protein FliL; Reviewed.
CDD:235565	137	PRK	Bacteria:55	PRK05697, PRK05697, flagellar basal body-associated protein FliL-like protein; Validated.
CDD:235566	245	PRK	Bacteria:462,nodiv:1	PRK05699, fliP, flagellar biosynthesis protein FliP; Reviewed.
CDD:235567	89	PRK	Bacteria:212	PRK05700, fliQ, flagellar biosynthesis protein FliQ; Validated.
CDD:235568	242	PRK	Bacteria:259,nodiv:1	PRK05701, fliR, flagellar biosynthesis protein FliR; Reviewed.
CDD:235569	359	PRK	Bacteria:347	PRK05702, flhB, flagellar biosynthesis protein FlhB; Reviewed.
CDD:235570	424	PRK	Bacteria:132	PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
CDD:235571	407	PRK	Bacteria:314	PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated.
CDD:235573	299	PRK	Bacteria:294	PRK05710, PRK05710, glutamyl-Q tRNA(Asp) synthetase; Reviewed.
CDD:235574	240	PRK	Bacteria:219	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional.
CDD:180218	100	PRK	Bacteria:371	PRK05715, PRK05715, NADH:ubiquinone oxidoreductase subunit K; Validated.
CDD:235576	252	PRK	Bacteria:444	PRK05716, PRK05716, methionine aminopeptidase; Validated.
CDD:235577	212	PRK	Bacteria:179	PRK05718, PRK05718, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional.
CDD:235578	344	PRK	Bacteria:139	PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
CDD:235579	495	PRK	Bacteria:630,nodiv:1	PRK05722, PRK05722, glucose-6-phosphate 1-dehydrogenase; Validated.
CDD:235580	319	PRK	Bacteria:523,nodiv:1	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated.
CDD:235581	142	PRK	Bacteria:246,nodiv:1	PRK05728, PRK05728, DNA polymerase III subunit chi; Validated.
CDD:235582	874	PRK	Bacteria:869,nodiv:1	PRK05729, valS, valyl-tRNA synthetase; Reviewed.
CDD:235583	318	PRK	Bacteria:283	PRK05731, PRK05731, thiamine monophosphate kinase; Provisional.
CDD:235584	395	PRK	Bacteria:136	PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated.
CDD:235586	92	PRK	Bacteria:878,nodiv:1	PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
CDD:235587	92	PRK	Bacteria:272	PRK05740, secE, preprotein translocase subunit SecE; Reviewed.
CDD:235588	912	PRK	Bacteria:609,nodiv:1	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
CDD:180232	448	PRK	Bacteria:119	PRK05748, PRK05748, replicative DNA helicase; Provisional.
CDD:235589	425	PRK	Bacteria:278	PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed.
CDD:180234	156	PRK	Bacteria:377,nodiv:1	PRK05751, PRK05751, preprotein translocase subunit SecB; Validated.
CDD:180236	137	PRK	Bacteria:128	PRK05753, PRK05753, nucleoside diphosphate kinase regulator; Provisional.
CDD:235591	880	PRK	Bacteria:709,nodiv:2	PRK05755, PRK05755, DNA polymerase I; Provisional.
CDD:235592	286	PRK	Bacteria:156,nodiv:1	PRK05756, PRK05756, pyridoxamine kinase; Validated.
CDD:235593	177	PRK	Bacteria:497,nodiv:1	PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated.
CDD:180240	156	PRK	Bacteria:442,nodiv:1	PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
CDD:235594	787	PRK	Bacteria:36	PRK05761, PRK05761, DNA polymerase I; Reviewed.
CDD:235595	786	PRK	Bacteria:191	PRK05762, PRK05762, DNA polymerase II; Reviewed.
CDD:235596	393	PRK	Bacteria:363,nodiv:1	PRK05764, PRK05764, aspartate aminotransferase; Provisional.
CDD:235598	52	PRK	Bacteria:69	PRK05766, rps14P, 30S ribosomal protein S14P; Reviewed.
CDD:180247	92	PRK	Bacteria:75	PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
CDD:235599	441	PRK	Bacteria:38	PRK05769, PRK05769, 4-aminobutyrate aminotransferase; Provisional.
CDD:235600	646	PRK	Bacteria:119	PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
CDD:235601	219	PRK	Bacteria:17	PRK05773, PRK05773, 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated.
CDD:235602	670	PRK	Bacteria:21	PRK05776, PRK05776, DNA topoisomerase I; Provisional.
CDD:235603	476	PRK	Bacteria:404,nodiv:2	PRK05777, PRK05777, NADH:ubiquinone oxidoreductase subunit N; Provisional.
CDD:235604	301	PRK	Bacteria:97	PRK05778, PRK05778, 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated.
CDD:180256	486	PRK	Bacteria:17	PRK05784, PRK05784, phosphoribosylamine--glycine ligase; Provisional.
CDD:235609	210	PRK	Bacteria:91	PRK05787, PRK05787, cobalt-precorrin-6Y C(5)-methyltransferase; Validated.
CDD:235610	315	PRK	Bacteria:84	PRK05788, PRK05788, cobalamin biosynthesis protein CbiG; Validated.
CDD:180261	393	PRK	Bacteria:279	PRK05790, PRK05790, putative acyltransferase; Provisional.
CDD:180263	374	PRK	Bacteria:26	PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
CDD:235612	170	PRK	Bacteria:152	PRK05800, cobU, adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated.
CDD:235613	320	PRK	Bacteria:31	PRK05802, PRK05802, hypothetical protein; Provisional.
CDD:180266	233	PRK	Bacteria:69	PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
CDD:180269	282	PRK	Bacteria:65	PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
CDD:235615	462	PRK	Bacteria:568	PRK05812, secD, preprotein translocase subunit SecD; Reviewed.
CDD:235616	219	PRK	Bacteria:40	PRK05813, PRK05813, single-stranded DNA-binding protein; Provisional.
CDD:235617	227	PRK	Bacteria:758,nodiv:1	PRK05815, PRK05815, F0F1 ATP synthase subunit A; Validated.
CDD:180275	235	PRK	Bacteria:267	PRK05819, deoD, purine nucleoside phosphorylase; Reviewed.
CDD:180276	440	PRK	Bacteria:200	PRK05820, deoA, thymidine phosphorylase; Reviewed.
CDD:235619	465	PRK	Bacteria:314	PRK05826, PRK05826, pyruvate kinase; Provisional.
CDD:180279	194	PRK	Bacteria:19	PRK05834, PRK05834, hypothetical protein; Provisional.
CDD:235622	497	PRK	Bacteria:344	PRK05846, PRK05846, NADH:ubiquinone oxidoreductase subunit M; Reviewed.
CDD:235623	783	PRK	Bacteria:17	PRK05849, PRK05849, hypothetical protein; Provisional.
CDD:235624	578	PRK	Bacteria:21	PRK05850, PRK05850, acyl-CoA synthetase; Validated.
CDD:235628	582	PRK	Bacteria:51	PRK05855, PRK05855, short chain dehydrogenase; Validated.
CDD:235633	296	PRK	Bacteria:29	PRK05872, PRK05872, short chain dehydrogenase; Provisional.
CDD:235634	405	PRK	Bacteria:25	PRK05877, PRK05877, aminodeoxychorismate synthase component I; Provisional.
CDD:235637	164	PRK	Bacteria:550,nodiv:1	PRK05888, PRK05888, NADH dehydrogenase subunit I; Provisional.
CDD:235639	586	PRK	Bacteria:517,nodiv:1	PRK05899, PRK05899, transketolase; Reviewed.
CDD:235640	509	PRK	Bacteria:101	PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
CDD:235645	408	PRK	Bacteria:854,nodiv:1	PRK05912, PRK05912, tyrosyl-tRNA synthetase; Validated.
CDD:180312	204	PRK	Bacteria:146	PRK05920, PRK05920, aromatic acid decarboxylase; Validated.
CDD:235647	249	PRK	Bacteria:211	PRK05928, hemD, uroporphyrinogen-III synthase; Reviewed.
CDD:235648	455	PRK	Bacteria:374	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
CDD:180318	94	PRK	Bacteria:168	PRK05943, PRK05943, 50S ribosomal protein L25; Reviewed.
CDD:235652	232	PRK	Bacteria:401,nodiv:1	PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit; Reviewed.
CDD:235653	381	PRK	Bacteria:12	PRK05952, PRK05952, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:235655	385	PRK	Bacteria:310	PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
CDD:235656	423	PRK	Bacteria:101	PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional.
CDD:235658	860	PRK	Bacteria:52,nodiv:1	PRK05972, ligD, ATP-dependent DNA ligase; Reviewed.
CDD:235659	80	PRK	Bacteria:138,nodiv:1	PRK05974, PRK05974, phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed.
CDD:168324	351	PRK	Bacteria:22	PRK05975, PRK05975, 3-carboxy-cis,cis-muconate cycloisomerase; Provisional.
CDD:235660	472	PRK	Bacteria:92	PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
CDD:180334	148	PRK	Bacteria:32	PRK05978, PRK05978, hypothetical protein; Provisional.
CDD:180337	391	PRK	Bacteria:29,nodiv:1	PRK05985, PRK05985, cytosine deaminase; Provisional.
CDD:235662	191	PRK	Bacteria:279	PRK05986, PRK05986, cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated.
CDD:180339	156	PRK	Bacteria:39,nodiv:1	PRK05988, PRK05988, formate dehydrogenase subunit gamma; Validated.
CDD:235663	1244	PRK	Bacteria:130	PRK05989, cobN, cobaltochelatase subunit CobN; Reviewed.
CDD:180341	241	PRK	Bacteria:61	PRK05990, PRK05990, precorrin-2 C(20)-methyltransferase; Reviewed.
CDD:235664	262	PRK	Bacteria:58,nodiv:1	PRK05995, PRK05995, enoyl-CoA hydratase; Provisional.
CDD:235665	423	PRK	Bacteria:22	PRK05996, motB, flagellar motor protein MotB; Validated.
CDD:235666	450	PRK	Bacteria:36,nodiv:1	PRK06002, fliI, flagellum-specific ATP synthase; Validated.
CDD:168340	126	PRK	Bacteria:34,nodiv:1	PRK06003, flgB, flagellar basal body rod protein FlgB; Reviewed.
CDD:235667	127	PRK	Bacteria:24	PRK06004, flgB, flagellar basal body rod protein FlgB; Reviewed.
CDD:180347	160	PRK	Bacteria:23,nodiv:1	PRK06005, flgA, flagellar basal body P-ring biosynthesis protein FlgA; Reviewed.
CDD:235668	542	PRK	Bacteria:380	PRK06007, fliF, flagellar MS-ring protein; Reviewed.
CDD:235669	348	PRK	Bacteria:34	PRK06008, flgL, flagellar hook-associated protein FlgL; Validated.
CDD:235670	140	PRK	Bacteria:33	PRK06009, flgD, flagellar basal body rod modification protein; Reviewed.
CDD:235671	88	PRK	Bacteria:48	PRK06010, fliQ, flagellar biosynthesis protein FliQ; Reviewed.
CDD:235672	697	PRK	Bacteria:413,nodiv:1	PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
CDD:235674	372	PRK	Bacteria:590,nodiv:1	PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed.
CDD:235676	286	PRK	Bacteria:374,nodiv:1	PRK06027, purU, formyltetrahydrofolate deformylase; Reviewed.
CDD:235677	185	PRK	Bacteria:161	PRK06029, PRK06029, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional.
CDD:235679	199	PRK	Bacteria:30	PRK06032, fliH, flagellar assembly protein H; Validated.
CDD:235680	279	PRK	Bacteria:23	PRK06034, PRK06034, hypothetical protein; Provisional.
CDD:235681	975	PRK	Bacteria:337	PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
CDD:235682	553	PRK	Bacteria:37	PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
CDD:235683	154	PRK	Bacteria:78	PRK06049, rpl30p, 50S ribosomal protein L30P; Reviewed.
CDD:235685	443	PRK	Bacteria:44	PRK06058, PRK06058, 4-aminobutyrate aminotransferase; Provisional.
CDD:235687	451	PRK	Bacteria:34	PRK06062, PRK06062, hypothetical protein; Provisional.
CDD:235688	389	PRK	Bacteria:52	PRK06064, PRK06064, acetyl-CoA acetyltransferase; Provisional.
CDD:180381	234	PRK	Bacteria:20	PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
CDD:235690	124	PRK	Bacteria:20	PRK06073, PRK06073, NADH dehydrogenase subunit A; Validated.
CDD:235691	189	PRK	Bacteria:159	PRK06074, PRK06074, NADH dehydrogenase subunit C; Provisional.
CDD:180385	392	PRK	Bacteria:340,nodiv:1	PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated.
CDD:235692	322	PRK	Bacteria:449	PRK06076, PRK06076, NADH:ubiquinone oxidoreductase subunit H; Provisional.
CDD:235695	293	PRK	Bacteria:275	PRK06080, PRK06080, 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated.
CDD:235696	268	PRK	Bacteria:110	PRK06092, PRK06092, 4-amino-4-deoxychorismate lyase; Reviewed.
CDD:235697	126	PRK	Bacteria:14	PRK06099, PRK06099, F0F1 ATP synthase subunit I; Validated.
CDD:235698	452	PRK	Bacteria:15,nodiv:1	PRK06102, PRK06102, hypothetical protein; Provisional.
CDD:180401	460	PRK	Bacteria:35	PRK06105, PRK06105, aminotransferase; Provisional.
CDD:180404	382	PRK	Bacteria:42,nodiv:1	PRK06108, PRK06108, aspartate aminotransferase; Provisional.
CDD:235699	322	PRK	Bacteria:31	PRK06110, PRK06110, hypothetical protein; Provisional.
CDD:235701	450	PRK	Bacteria:287,nodiv:1	PRK06116, PRK06116, glutathione reductase; Validated.
CDD:235704	545	PRK	Bacteria:12	PRK06126, PRK06126, hypothetical protein; Provisional.
CDD:235706	308	PRK	Bacteria:14	PRK06129, PRK06129, 3-hydroxyacyl-CoA dehydrogenase; Validated.
CDD:235708	571	PRK	Bacteria:117	PRK06131, PRK06131, dihydroxy-acid dehydratase; Validated.
CDD:235709	359	PRK	Bacteria:36,nodiv:1	PRK06132, PRK06132, hypothetical protein; Provisional.
CDD:235710	410	PRK	Bacteria:25	PRK06133, PRK06133, glutamate carboxypeptidase; Reviewed.
CDD:235711	249	PRK	Bacteria:140	PRK06136, PRK06136, uroporphyrin-III C-methyltransferase; Reviewed.
CDD:180421	314	PRK	Bacteria:33	PRK06141, PRK06141, ornithine cyclodeaminase; Validated.
CDD:235714	272	PRK	Bacteria:47	PRK06142, PRK06142, enoyl-CoA hydratase; Provisional.
CDD:180423	256	PRK	Bacteria:18	PRK06143, PRK06143, enoyl-CoA hydratase; Provisional.
CDD:180424	262	PRK	Bacteria:29	PRK06144, PRK06144, enoyl-CoA hydratase; Provisional.
CDD:235715	348	PRK	Bacteria:14	PRK06147, PRK06147, 3-oxoacyl-(acyl carrier protein) synthase; Validated.
CDD:180426	1013	PRK	Bacteria:22	PRK06148, PRK06148, hypothetical protein; Provisional.
CDD:235716	972	PRK	Bacteria:27	PRK06149, PRK06149, hypothetical protein; Provisional.
CDD:180428	488	PRK	Bacteria:12,nodiv:1	PRK06151, PRK06151, N-ethylammeline chlorohydrolase; Provisional.
CDD:235717	393	PRK	Bacteria:17	PRK06153, PRK06153, hypothetical protein; Provisional.
CDD:235720	520	PRK	Bacteria:35	PRK06156, PRK06156, hypothetical protein; Provisional.
CDD:180433	398	PRK	Bacteria:17	PRK06157, PRK06157, acetyl-CoA acetyltransferase; Validated.
CDD:180434	384	PRK	Bacteria:20	PRK06158, PRK06158, thiolase; Provisional.
CDD:180435	89	PRK	Bacteria:78	PRK06161, PRK06161, putative monovalent cation/H+ antiporter subunit F; Reviewed.
CDD:180437	466	PRK	Bacteria:20	PRK06169, PRK06169, putative amidase; Provisional.
CDD:235723	490	PRK	Bacteria:23	PRK06170, PRK06170, amidase; Provisional.
CDD:180439	266	PRK	Bacteria:44	PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase; Provisional.
CDD:235724	567	PRK	Bacteria:15	PRK06178, PRK06178, acyl-CoA synthetase; Validated.
CDD:235725	270	PRK	Bacteria:43	PRK06179, PRK06179, short chain dehydrogenase; Provisional.
CDD:180446	277	PRK	Bacteria:37	PRK06180, PRK06180, short chain dehydrogenase; Provisional.
CDD:235726	263	PRK	Bacteria:30	PRK06181, PRK06181, short chain dehydrogenase; Provisional.
CDD:180448	273	PRK	Bacteria:21	PRK06182, PRK06182, short chain dehydrogenase; Validated.
CDD:235727	500	PRK	Bacteria:75	PRK06183, mhpA, 3-(3-hydroxyphenyl)propionate hydroxylase; Validated.
CDD:235728	502	PRK	Bacteria:24	PRK06184, PRK06184, hypothetical protein; Provisional.
CDD:235729	407	PRK	Bacteria:54	PRK06185, PRK06185, hypothetical protein; Provisional.
CDD:180452	229	PRK	Bacteria:29	PRK06186, PRK06186, hypothetical protein; Validated.
CDD:235730	521	PRK	Bacteria:124	PRK06187, PRK06187, long-chain-fatty-acid--CoA ligase; Validated.
CDD:235731	524	PRK	Bacteria:35	PRK06188, PRK06188, acyl-CoA synthetase; Validated.
CDD:235733	258	PRK	Bacteria:27	PRK06190, PRK06190, enoyl-CoA hydratase; Provisional.
CDD:235734	206	PRK	Bacteria:9	PRK06193, PRK06193, hypothetical protein; Provisional.
CDD:180458	287	PRK	Bacteria:30	PRK06194, PRK06194, hypothetical protein; Provisional.
CDD:235736	315	PRK	Bacteria:19	PRK06196, PRK06196, oxidoreductase; Provisional.
CDD:235737	306	PRK	Bacteria:26	PRK06197, PRK06197, short chain dehydrogenase; Provisional.
CDD:180462	260	PRK	Bacteria:32	PRK06198, PRK06198, short chain dehydrogenase; Provisional.
CDD:235739	263	PRK	Bacteria:49	PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional.
CDD:180465	221	PRK	Bacteria:26,nodiv:1	PRK06201, PRK06201, hypothetical protein; Validated.
CDD:180466	232	PRK	Bacteria:18	PRK06202, PRK06202, hypothetical protein; Provisional.
CDD:235740	389	PRK	Bacteria:26	PRK06203, aroB, 3-dehydroquinate synthase; Reviewed.
CDD:235741	404	PRK	Bacteria:35	PRK06205, PRK06205, acetyl-CoA acetyltransferase; Provisional.
CDD:235743	274	PRK	Bacteria:46	PRK06208, PRK06208, hypothetical protein; Provisional.
CDD:235744	229	PRK	Bacteria:39	PRK06213, PRK06213, enoyl-CoA hydratase; Provisional.
CDD:235745	530	PRK	Bacteria:22	PRK06214, PRK06214, sulfite reductase; Provisional.
CDD:168472	183	PRK	Bacteria:14	PRK06217, PRK06217, hypothetical protein; Validated.
CDD:235747	281	PRK	Bacteria:123	PRK06222, PRK06222, ferredoxin-NADP(+) reductase subunit alpha; Reviewed.
CDD:180477	307	PRK	Bacteria:251,nodiv:1	PRK06223, PRK06223, malate dehydrogenase; Reviewed.
CDD:235748	263	PRK	Bacteria:41	PRK06224, PRK06224, citrate synthase; Provisional.
CDD:235750	131	PRK	Bacteria:18	PRK06228, PRK06228, F0F1 ATP synthase subunit epsilon; Validated.
CDD:235751	871	PRK	Bacteria:62	PRK06241, PRK06241, phosphoenolpyruvate synthase; Validated.
CDD:180484	150	PRK	Bacteria:24	PRK06242, PRK06242, flavodoxin; Provisional.
CDD:180485	336	PRK	Bacteria:57	PRK06245, cofG, FO synthase subunit 1; Reviewed.
CDD:180486	280	PRK	Bacteria:102	PRK06246, PRK06246, fumarate hydratase; Provisional.
CDD:180487	476	PRK	Bacteria:87	PRK06247, PRK06247, pyruvate kinase; Provisional.
CDD:180488	313	PRK	Bacteria:27	PRK06249, PRK06249, 2-dehydropantoate 2-reductase; Provisional.
CDD:235753	339	PRK	Bacteria:26	PRK06252, PRK06252, methylcobalamin:coenzyme M methyltransferase; Validated.
CDD:235754	529	PRK	Bacteria:32	PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
CDD:235755	336	PRK	Bacteria:156	PRK06256, PRK06256, biotin synthase; Validated.
CDD:235756	486	PRK	Bacteria:21	PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional.
CDD:235757	397	PRK	Bacteria:55	PRK06260, PRK06260, threonine synthase; Validated.
CDD:235758	543	PRK	Bacteria:21	PRK06263, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed.
CDD:235760	199	PRK	Bacteria:69	PRK06265, PRK06265, cobalt transport protein CbiM; Validated.
CDD:235761	178	PRK	Bacteria:19	PRK06266, PRK06266, transcription initiation factor E subunit alpha; Validated.
CDD:235763	341	PRK	Bacteria:43	PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
CDD:235765	197	PRK	Bacteria:16	PRK06274, PRK06274, indolepyruvate oxidoreductase subunit B; Reviewed.
CDD:180505	476	PRK	Bacteria:15	PRK06278, PRK06278, cobyrinic acid a,c-diamide synthase; Validated.
CDD:180509	96	PRK	Bacteria:15	PRK06285, PRK06285, chorismate mutase; Provisional.
CDD:180511	107	PRK	Bacteria:18	PRK06287, PRK06287, cobalt transport protein CbiN; Validated.
CDD:235773	465	PRK	Bacteria:29	PRK06291, PRK06291, aspartate kinase; Provisional.
CDD:235774	460	PRK	Bacteria:180	PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
CDD:235775	565	PRK	Bacteria:549,nodiv:2	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
CDD:235777	155	PRK	Bacteria:290	PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated.
CDD:235779	475	PRK	Bacteria:100	PRK06327, PRK06327, dihydrolipoamide dehydrogenase; Validated.
CDD:235781	424	PRK	Bacteria:42,nodiv:1	PRK06333, PRK06333, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:235783	426	PRK	Bacteria:471,nodiv:1	PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
CDD:235784	590	PRK	Bacteria:82	PRK06354, PRK06354, pyruvate kinase; Provisional.
CDD:180542	354	PRK	Bacteria:17	PRK06358, PRK06358, threonine-phosphate decarboxylase; Provisional.
CDD:180543	212	PRK	Bacteria:35	PRK06361, PRK06361, hypothetical protein; Provisional.
CDD:235786	115	PRK	Bacteria:64	PRK06369, nac, nascent polypeptide-associated complex protein; Reviewed.
CDD:235787	463	PRK	Bacteria:82	PRK06370, PRK06370, mercuric reductase; Validated.
CDD:235793	146	PRK	Bacteria:65	PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
CDD:235795	106	PRK	Bacteria:80	PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
CDD:235797	183	PRK	Bacteria:547,nodiv:1	PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated.
CDD:235798	462	PRK	Bacteria:239	PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
CDD:180559	166	PRK	Bacteria:21	PRK06418, PRK06418, transcription elongation factor NusA-like protein; Validated.
CDD:235799	148	PRK	Bacteria:68	PRK06419, rpl15p, 50S ribosomal protein L15P; Reviewed.
CDD:180561	266	PRK	Bacteria:283	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed.
CDD:180562	88	PRK	Bacteria:16	PRK06433, PRK06433, NADH dehydrogenase subunit J; Provisional.
CDD:235804	155	PRK	Bacteria:58	PRK06455, PRK06455, riboflavin synthase; Provisional.
CDD:235805	490	PRK	Bacteria:76	PRK06458, PRK06458, hydrogenase 4 subunit F; Validated.
CDD:180574	129	PRK	Bacteria:22	PRK06461, PRK06461, single-stranded DNA-binding protein; Reviewed.
CDD:235808	335	PRK	Bacteria:26	PRK06462, PRK06462, asparagine synthetase A; Reviewed.
CDD:235809	795	PRK	Bacteria:401	PRK06464, PRK06464, phosphoenolpyruvate synthase; Validated.
CDD:180579	471	PRK	Bacteria:178	PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed.
CDD:235812	258	PRK	Bacteria:16	PRK06476, PRK06476, pyrroline-5-carboxylate reductase; Reviewed.
CDD:180586	236	PRK	Bacteria:86	PRK06483, PRK06483, dihydromonapterin reductase; Provisional.
CDD:235815	360	PRK	Bacteria:30	PRK06489, PRK06489, hypothetical protein; Provisional.
CDD:180590	239	PRK	Bacteria:31	PRK06490, PRK06490, glutamine amidotransferase; Provisional.
CDD:180592	531	PRK	Bacteria:77	PRK06498, PRK06498, isocitrate lyase; Provisional.
CDD:235816	249	PRK	Bacteria:36,nodiv:1	PRK06500, PRK06500, short chain dehydrogenase; Provisional.
CDD:235817	425	PRK	Bacteria:49	PRK06501, PRK06501, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:235819	398	PRK	Bacteria:48	PRK06519, PRK06519, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:235820	667	PRK	Bacteria:62	PRK06521, PRK06521, hydrogenase 4 subunit B; Validated.
CDD:235821	304	PRK	Bacteria:325	PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
CDD:180604	260	PRK	Bacteria:47	PRK06523, PRK06523, short chain dehydrogenase; Provisional.
CDD:180606	479	PRK	Bacteria:35	PRK06525, PRK06525, hydrogenase 4 subunit D; Validated.
CDD:235823	460	PRK	Bacteria:49	PRK06541, PRK06541, hypothetical protein; Provisional.
CDD:235824	359	PRK	Bacteria:157	PRK06545, PRK06545, prephenate dehydrogenase; Validated.
CDD:180614	578	PRK	Bacteria:29	PRK06546, PRK06546, pyruvate dehydrogenase; Provisional.
CDD:235825	172	PRK	Bacteria:14	PRK06547, PRK06547, hypothetical protein; Provisional.
CDD:180617	235	PRK	Bacteria:59	PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:180618	213	PRK	Bacteria:46	PRK06552, PRK06552, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional.
CDD:235827	308	PRK	Bacteria:47	PRK06553, PRK06553, lipid A biosynthesis lauroyl acyltransferase; Provisional.
CDD:180620	403	PRK	Bacteria:29,nodiv:1	PRK06555, PRK06555, pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Validated.
CDD:235828	953	PRK	Bacteria:41	PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase; Validated.
CDD:235829	221	PRK	Bacteria:41	PRK06557, PRK06557, L-ribulose-5-phosphate 4-epimerase; Validated.
CDD:235830	159	PRK	Bacteria:49	PRK06558, PRK06558, V-type ATP synthase subunit K; Validated.
CDD:180625	255	PRK	Bacteria:28	PRK06563, PRK06563, enoyl-CoA hydratase; Provisional.
CDD:235834	343	PRK	Bacteria:77	PRK06585, holA, DNA polymerase III subunit delta; Reviewed.
CDD:235836	624	PRK	Bacteria:365	PRK06590, PRK06590, NADH:ubiquinone oxidoreductase subunit L; Reviewed.
CDD:235838	284	PRK	Bacteria:370,nodiv:1	PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
CDD:235839	369	PRK	Bacteria:285	PRK06598, PRK06598, aspartate-semialdehyde dehydrogenase; Reviewed.
CDD:235840	675	PRK	Bacteria:107,nodiv:1	PRK06599, PRK06599, DNA topoisomerase I; Validated.
CDD:180638	121	PRK	Bacteria:262	PRK06602, PRK06602, NADH:ubiquinone oxidoreductase subunit A; Validated.
CDD:235841	306	PRK	Bacteria:348	PRK06606, PRK06606, branched-chain amino acid aminotransferase; Validated.
CDD:235843	404	PRK	Bacteria:425,nodiv:1	PRK06635, PRK06635, aspartate kinase; Reviewed.
CDD:235844	198	PRK	Bacteria:356	PRK06638, PRK06638, NADH:ubiquinone oxidoreductase subunit J; Provisional.
CDD:235847	225	PRK	Bacteria:177	PRK06655, flgD, flagellar basal body rod modification protein; Reviewed.
CDD:235849	337	PRK	Bacteria:292	PRK06666, fliM, flagellar motor switch protein FliM; Validated.
CDD:235850	281	PRK	Bacteria:53	PRK06669, fliH, flagellar assembly protein H; Validated.
CDD:235851	390	PRK	Bacteria:158	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
CDD:180656	286	PRK	Bacteria:60,nodiv:1	PRK06680, PRK06680, D-amino acid aminotransferase; Reviewed.
CDD:235852	259	PRK	Bacteria:90	PRK06688, PRK06688, enoyl-CoA hydratase; Provisional.
CDD:180660	223	PRK	Bacteria:29	PRK06696, PRK06696, uridine kinase; Validated.
CDD:235856	229	PRK	Bacteria:50	PRK06732, PRK06732, phosphopantothenate--cysteine ligase; Validated.
CDD:180674	151	PRK	Bacteria:30	PRK06733, PRK06733, hypothetical protein; Provisional.
CDD:180679	208	PRK	Bacteria:37	PRK06754, mtnB, methylthioribulose-1-phosphate dehydratase; Reviewed.
CDD:235858	166	PRK	Bacteria:37	PRK06762, PRK06762, hypothetical protein; Provisional.
CDD:180687	180	PRK	Bacteria:21	PRK06770, PRK06770, hypothetical protein; Provisional.
CDD:180707	189	PRK	Bacteria:36	PRK06811, PRK06811, RNA polymerase factor sigma-70; Validated.
CDD:235865	1140	PRK	Bacteria:37	PRK06814, PRK06814, acylglycerophosphoethanolamine acyltransferase; Provisional.
CDD:235866	378	PRK	Bacteria:29	PRK06816, PRK06816, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed.
CDD:235868	1151	PRK	Bacteria:48	PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
CDD:180714	382	PRK	Bacteria:24	PRK06827, PRK06827, phosphoribosylpyrophosphate synthetase; Provisional.
CDD:235869	443	PRK	Bacteria:45	PRK06830, PRK06830, diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional.
CDD:235870	488	PRK	Bacteria:18	PRK06834, PRK06834, hypothetical protein; Provisional.
CDD:235871	329	PRK	Bacteria:43	PRK06835, PRK06835, DNA replication protein DnaC; Validated.
CDD:180720	394	PRK	Bacteria:81	PRK06836, PRK06836, aspartate aminotransferase; Provisional.
CDD:180721	427	PRK	Bacteria:17	PRK06837, PRK06837, acetylornithine deacetylase; Provisional.
CDD:235872	339	PRK	Bacteria:22	PRK06840, PRK06840, hypothetical protein; Validated.
CDD:180723	255	PRK	Bacteria:50	PRK06841, PRK06841, short chain dehydrogenase; Provisional.
CDD:235873	410	PRK	Bacteria:56	PRK06846, PRK06846, putative deaminase; Validated.
CDD:235874	375	PRK	Bacteria:33	PRK06847, PRK06847, hypothetical protein; Provisional.
CDD:235876	389	PRK	Bacteria:21	PRK06849, PRK06849, hypothetical protein; Provisional.
CDD:235877	507	PRK	Bacteria:36	PRK06850, PRK06850, hypothetical protein; Provisional.
CDD:235878	367	PRK	Bacteria:47	PRK06851, PRK06851, hypothetical protein; Provisional.
CDD:180731	304	PRK	Bacteria:30	PRK06852, PRK06852, aldolase; Validated.
CDD:180732	197	PRK	Bacteria:90	PRK06853, PRK06853, indolepyruvate oxidoreductase subunit beta; Reviewed.
CDD:235879	608	PRK	Bacteria:55	PRK06854, PRK06854, adenylylsulfate reductase subunit alpha; Validated.
CDD:180734	433	PRK	Bacteria:35	PRK06855, PRK06855, aminotransferase; Validated.
CDD:180735	128	PRK	Bacteria:96	PRK06856, PRK06856, DNA polymerase III subunit psi; Validated.
CDD:235880	309	PRK	Bacteria:102	PRK06860, PRK06860, lipid A biosynthesis lauroyl acyltransferase; Provisional.
CDD:235881	76	PRK	Bacteria:688,nodiv:1	PRK06870, secG, preprotein translocase subunit SecG; Reviewed.
CDD:180739	78	PRK	Bacteria:356	PRK06876, PRK06876, F0F1 ATP synthase subunit C; Validated.
CDD:180744	280	PRK	Bacteria:29	PRK06914, PRK06914, short chain dehydrogenase; Provisional.
CDD:180757	170	PRK	Bacteria:15	PRK06930, PRK06930, positive control sigma-like factor; Validated.
CDD:180763	204	PRK	Bacteria:29	PRK06937, PRK06937, type III secretion system protein; Reviewed.
CDD:235893	397	PRK	Bacteria:307,nodiv:1	PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase; Provisional.
CDD:180766	275	PRK	Bacteria:17	PRK06940, PRK06940, short chain dehydrogenase; Provisional.
CDD:235895	651	PRK	Bacteria:42	PRK06945, flgK, flagellar hook-associated protein FlgK; Validated.
CDD:235899	656	PRK	Bacteria:32	PRK06975, PRK06975, bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed.
CDD:235901	236	PRK	Bacteria:207	PRK06986, fliA, flagellar biosynthesis sigma factor; Validated.
CDD:235902	312	PRK	Bacteria:39	PRK06988, PRK06988, putative formyltransferase; Provisional.
CDD:235904	484	PRK	Bacteria:35	PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
CDD:180794	235	PRK	Bacteria:167	PRK07018, flgA, flagellar basal body P-ring biosynthesis protein FlgA; Reviewed.
CDD:235909	162	PRK	Bacteria:126	PRK07021, fliL, flagellar basal body-associated protein FliL; Reviewed.
CDD:180796	243	PRK	Bacteria:38	PRK07023, PRK07023, short chain dehydrogenase; Provisional.
CDD:235910	257	PRK	Bacteria:58	PRK07024, PRK07024, short chain dehydrogenase; Provisional.
CDD:235911	126	PRK	Bacteria:27	PRK07027, PRK07027, cobalamin biosynthesis protein CbiG; Provisional.
CDD:235912	430	PRK	Bacteria:20	PRK07028, PRK07028, bifunctional hexulose-6-phosphate synthase/ribonuclease regulator; Validated.
CDD:180801	427	PRK	Bacteria:35	PRK07033, PRK07033, hypothetical protein; Provisional.
CDD:235914	230	PRK	Bacteria:33	PRK07041, PRK07041, short chain dehydrogenase; Provisional.
CDD:235915	464	PRK	Bacteria:43	PRK07042, PRK07042, amidase; Provisional.
CDD:235916	252	PRK	Bacteria:79	PRK07044, PRK07044, aldolase II superfamily protein; Provisional.
CDD:235917	453	PRK	Bacteria:44	PRK07046, PRK07046, aminotransferase; Validated.
CDD:180811	80	PRK	Bacteria:30	PRK07051, PRK07051, hypothetical protein; Validated.
CDD:235919	234	PRK	Bacteria:51	PRK07053, PRK07053, glutamine amidotransferase; Provisional.
CDD:235921	454	PRK	Bacteria:62	PRK07056, PRK07056, amidase; Provisional.
CDD:180818	265	PRK	Bacteria:42	PRK07062, PRK07062, short chain dehydrogenase; Provisional.
CDD:180820	544	PRK	Bacteria:45	PRK07064, PRK07064, hypothetical protein; Provisional.
CDD:235925	257	PRK	Bacteria:46,nodiv:1	PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
CDD:235926	238	PRK	Bacteria:38	PRK07077, PRK07077, hypothetical protein; Provisional.
CDD:235928	469	PRK	Bacteria:50	PRK07079, PRK07079, hypothetical protein; Provisional.
CDD:235929	317	PRK	Bacteria:50,nodiv:1	PRK07080, PRK07080, hypothetical protein; Validated.
CDD:180828	83	PRK	Bacteria:39	PRK07081, PRK07081, acyl carrier protein; Provisional.
CDD:235930	555	PRK	Bacteria:39	PRK07085, PRK07085, diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional.
CDD:180832	260	PRK	Bacteria:53	PRK07090, PRK07090, class II aldolase/adducin domain protein; Provisional.
CDD:235931	530	PRK	Bacteria:47	PRK07092, PRK07092, benzoylformate decarboxylase; Reviewed.
CDD:235932	323	PRK	Bacteria:36	PRK07093, PRK07093, para-aminobenzoate synthase component I; Validated.
CDD:180835	323	PRK	Bacteria:71	PRK07094, PRK07094, biotin synthase; Provisional.
CDD:235934	187	PRK	Bacteria:25	PRK07101, PRK07101, hypothetical protein; Provisional.
CDD:180838	243	PRK	Bacteria:27	PRK07102, PRK07102, short chain dehydrogenase; Provisional.
CDD:180839	410	PRK	Bacteria:18,nodiv:1	PRK07103, PRK07103, polyketide beta-ketoacyl:acyl carrier protein synthase; Validated.
CDD:180840	284	PRK	Bacteria:48	PRK07105, PRK07105, pyridoxamine kinase; Validated.
CDD:235935	334	PRK	Bacteria:69	PRK07109, PRK07109, short chain dehydrogenase; Provisional.
CDD:235936	249	PRK	Bacteria:30	PRK07110, PRK07110, polyketide biosynthesis enoyl-CoA hydratase; Validated.
CDD:235937	735	PRK	Bacteria:51	PRK07111, PRK07111, anaerobic ribonucleoside triphosphate reductase; Provisional.
CDD:235939	222	PRK	Bacteria:18	PRK07114, PRK07114, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional.
CDD:235940	258	PRK	Bacteria:32	PRK07115, PRK07115, AMP nucleosidase; Provisional.
CDD:180850	160	PRK	Bacteria:11	PRK07116, PRK07116, flavodoxin; Provisional.
CDD:235941	280	PRK	Bacteria:42	PRK07118, PRK07118, ferredoxin; Validated.
CDD:235942	352	PRK	Bacteria:74	PRK07119, PRK07119, 2-ketoisovalerate ferredoxin reductase; Validated.
CDD:180854	492	PRK	Bacteria:41	PRK07121, PRK07121, hypothetical protein; Validated.
CDD:235943	725	PRK	Bacteria:9	PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated.
CDD:235946	279	PRK	Bacteria:12	PRK07143, PRK07143, hypothetical protein; Provisional.
CDD:235947	342	PRK	Bacteria:24	PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase; Validated.
CDD:235951	507	PRK	Bacteria:18	PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
CDD:180866	407	PRK	Bacteria:21	PRK07179, PRK07179, hypothetical protein; Provisional.
CDD:235953	352	PRK	Bacteria:43	PRK07188, PRK07188, nicotinate phosphoribosyltransferase; Provisional.
CDD:235954	301	PRK	Bacteria:93	PRK07189, PRK07189, malonate decarboxylase subunit beta; Reviewed.
CDD:235956	305	PRK	Bacteria:28	PRK07192, flgL, flagellar hook-associated protein FlgL; Reviewed.
CDD:235957	552	PRK	Bacteria:38	PRK07193, fliF, flagellar MS-ring protein; Reviewed.
CDD:235958	334	PRK	Bacteria:35	PRK07194, fliG, flagellar motor switch protein G; Reviewed.
CDD:235960	301	PRK	Bacteria:28	PRK07199, PRK07199, phosphoribosylpyrophosphate synthetase; Provisional.
CDD:235962	657	PRK	Bacteria:36	PRK07201, PRK07201, short chain dehydrogenase; Provisional.
CDD:235963	442	PRK	Bacteria:65	PRK07203, PRK07203, putative chlorohydrolase/aminohydrolase; Validated.
CDD:180883	416	PRK	Bacteria:22	PRK07206, PRK07206, hypothetical protein; Provisional.
CDD:235966	965	PRK	Bacteria:114,nodiv:1	PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit alpha; Validated.
CDD:235967	479	PRK	Bacteria:51	PRK07208, PRK07208, hypothetical protein; Provisional.
CDD:235968	369	PRK	Bacteria:142,nodiv:1	PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit beta; Validated.
CDD:235969	375	PRK	Bacteria:17	PRK07213, PRK07213, chlorohydrolase; Provisional.
CDD:235970	311	PRK	Bacteria:16	PRK07217, PRK07217, replication factor A; Reviewed.
CDD:180890	423	PRK	Bacteria:15	PRK07218, PRK07218, replication factor A; Provisional.
CDD:235971	822	PRK	Bacteria:26	PRK07219, PRK07219, DNA topoisomerase I; Validated.
CDD:235972	605	PRK	Bacteria:43	PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated.
CDD:235973	267	PRK	Bacteria:76	PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional.
CDD:180895	445	PRK	Bacteria:21	PRK07228, PRK07228, N-ethylammeline chlorohydrolase; Provisional.
CDD:235974	646	PRK	Bacteria:136	PRK07229, PRK07229, aconitate hydratase; Validated.
CDD:235975	251	PRK	Bacteria:102	PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:235976	752	PRK	Bacteria:337	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed.
CDD:235977	434	PRK	Bacteria:48	PRK07233, PRK07233, hypothetical protein; Provisional.
CDD:235978	470	PRK	Bacteria:26	PRK07234, PRK07234, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:235979	502	PRK	Bacteria:34	PRK07235, PRK07235, amidase; Provisional.
CDD:235980	386	PRK	Bacteria:30	PRK07236, PRK07236, hypothetical protein; Provisional.
CDD:180903	372	PRK	Bacteria:41	PRK07238, PRK07238, bifunctional RNase H/acid phosphatase; Provisional.
CDD:235981	381	PRK	Bacteria:42	PRK07239, PRK07239, bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated.
CDD:168880	87	PRK	Bacteria:41	PRK07248, PRK07248, hypothetical protein; Provisional.
CDD:235982	301	PRK	Bacteria:198	PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
CDD:180916	290	PRK	Bacteria:48	PRK07276, PRK07276, DNA polymerase III subunit delta'; Validated.
CDD:235986	182	PRK	Bacteria:65	PRK07313, PRK07313, phosphopantothenoylcysteine decarboxylase; Validated.
CDD:235987	411	PRK	Bacteria:376,nodiv:1	PRK07314, PRK07314, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:235988	466	PRK	Bacteria:138	PRK07318, PRK07318, dipeptidase PepV; Reviewed.
CDD:180928	178	PRK	Bacteria:23	PRK07322, PRK07322, adenine phosphoribosyltransferase; Provisional.
CDD:235989	373	PRK	Bacteria:40	PRK07324, PRK07324, transaminase; Validated.
CDD:235990	237	PRK	Bacteria:17	PRK07326, PRK07326, short chain dehydrogenase; Provisional.
CDD:235991	268	PRK	Bacteria:54	PRK07327, PRK07327, enoyl-CoA hydratase; Provisional.
CDD:235992	269	PRK	Bacteria:15	PRK07328, PRK07328, histidinol-phosphatase; Provisional.
CDD:180935	403	PRK	Bacteria:40,nodiv:1	PRK07333, PRK07333, 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional.
CDD:235994	403	PRK	Bacteria:42	PRK07334, PRK07334, threonine dehydratase; Provisional.
CDD:235995	402	PRK	Bacteria:24	PRK07338, PRK07338, hypothetical protein; Provisional.
CDD:235996	304	PRK	Bacteria:38	PRK07340, PRK07340, ornithine cyclodeaminase; Validated.
CDD:180941	174	PRK	Bacteria:35	PRK07352, PRK07352, F0F1 ATP synthase subunit B; Validated.
CDD:235999	140	PRK	Bacteria:34	PRK07353, PRK07353, F0F1 ATP synthase subunit B'; Validated.
CDD:236000	371	PRK	Bacteria:45	PRK07360, PRK07360, FO synthase subunit 2; Reviewed.
CDD:236001	415	PRK	Bacteria:17	PRK07364, PRK07364, 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated.
CDD:236002	418	PRK	Bacteria:20	PRK07369, PRK07369, dihydroorotase; Provisional.
CDD:236004	112	PRK	Bacteria:78	PRK07375, PRK07375, putative monovalent cation/H+ antiporter subunit C; Reviewed.
CDD:236006	184	PRK	Bacteria:18	PRK07377, PRK07377, hypothetical protein; Provisional.
CDD:236007	400	PRK	Bacteria:19	PRK07379, PRK07379, coproporphyrinogen III oxidase; Provisional.
CDD:236008	613	PRK	Bacteria:25	PRK07390, PRK07390, NAD(P)H-quinone oxidoreductase subunit F; Validated.
CDD:236009	360	PRK	Bacteria:12	PRK07392, PRK07392, threonine-phosphate decarboxylase; Validated.
CDD:168934	342	PRK	Bacteria:29	PRK07394, PRK07394, hypothetical protein; Provisional.
CDD:236010	553	PRK	Bacteria:18	PRK07395, PRK07395, L-aspartate oxidase; Provisional.
CDD:180958	273	PRK	Bacteria:274	PRK07396, PRK07396, dihydroxynaphthoic acid synthetase; Validated.
CDD:236011	314	PRK	Bacteria:34	PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
CDD:180965	256	PRK	Bacteria:18	PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed.
CDD:236013	353	PRK	Bacteria:170	PRK07409, PRK07409, threonine synthase; Validated.
CDD:180970	279	PRK	Bacteria:30	PRK07417, PRK07417, arogenate dehydrogenase; Reviewed.
CDD:236015	304	PRK	Bacteria:38	PRK07419, PRK07419, 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional.
CDD:180975	327	PRK	Bacteria:22	PRK07429, PRK07429, phosphoribulokinase; Provisional.
CDD:236018	587	PRK	Bacteria:39	PRK07431, PRK07431, aspartate kinase; Provisional.
CDD:236019	452	PRK	Bacteria:18	PRK07445, PRK07445, O-succinylbenzoic acid--CoA ligase; Reviewed.
CDD:236020	568	PRK	Bacteria:231	PRK07449, PRK07449, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated.
CDD:180982	326	PRK	Bacteria:36	PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
CDD:180983	322	PRK	Bacteria:38	PRK07453, PRK07453, protochlorophyllide oxidoreductase; Validated.
CDD:180984	241	PRK	Bacteria:32	PRK07454, PRK07454, short chain dehydrogenase; Provisional.
CDD:180988	528	PRK	Bacteria:17	PRK07470, PRK07470, acyl-CoA synthetase; Validated.
CDD:236022	365	PRK	Bacteria:29	PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
CDD:236023	154	PRK	Bacteria:22	PRK07474, PRK07474, sulfur oxidation protein SoxY; Provisional.
CDD:236024	245	PRK	Bacteria:26	PRK07475, PRK07475, hypothetical protein; Provisional.
CDD:236025	322	PRK	Bacteria:27,nodiv:1	PRK07476, eutB, threonine dehydratase; Provisional.
CDD:180993	254	PRK	Bacteria:40	PRK07478, PRK07478, short chain dehydrogenase; Provisional.
CDD:180994	456	PRK	Bacteria:79,nodiv:1	PRK07480, PRK07480, putative aminotransferase; Validated.
CDD:236027	443	PRK	Bacteria:61	PRK07483, PRK07483, hypothetical protein; Provisional.
CDD:236028	484	PRK	Bacteria:44	PRK07486, PRK07486, amidase; Provisional.
CDD:236029	469	PRK	Bacteria:29	PRK07487, PRK07487, amidase; Provisional.
CDD:236030	472	PRK	Bacteria:25	PRK07488, PRK07488, indole acetimide hydrolase; Validated.
CDD:181000	435	PRK	Bacteria:89,nodiv:1	PRK07492, PRK07492, adenylosuccinate lyase; Provisional.
CDD:181001	388	PRK	Bacteria:48	PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional.
CDD:236033	289	PRK	Bacteria:45	PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
CDD:236034	307	PRK	Bacteria:59,nodiv:1	PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
CDD:181006	402	PRK	Bacteria:20,nodiv:1	PRK07505, PRK07505, hypothetical protein; Provisional.
CDD:236035	378	PRK	Bacteria:34,nodiv:1	PRK07508, PRK07508, aminodeoxychorismate synthase; Provisional.
CDD:181008	262	PRK	Bacteria:59	PRK07509, PRK07509, enoyl-CoA hydratase; Provisional.
CDD:181009	260	PRK	Bacteria:42	PRK07511, PRK07511, enoyl-CoA hydratase; Provisional.
CDD:236036	513	PRK	Bacteria:43,nodiv:1	PRK07512, PRK07512, L-aspartate oxidase; Provisional.
CDD:181011	504	PRK	Bacteria:72	PRK07514, PRK07514, malonyl-CoA synthase; Validated.
CDD:236037	372	PRK	Bacteria:84	PRK07515, PRK07515, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed.
CDD:181013	389	PRK	Bacteria:39	PRK07516, PRK07516, acetyl-CoA acetyltransferase; Provisional.
CDD:236038	483	PRK	Bacteria:47	PRK07521, flgK, flagellar hook-associated protein FlgK; Validated.
CDD:236039	385	PRK	Bacteria:102	PRK07522, PRK07522, acetylornithine deacetylase; Provisional.
CDD:236041	535	PRK	Bacteria:21	PRK07524, PRK07524, hypothetical protein; Provisional.
CDD:236042	588	PRK	Bacteria:40	PRK07525, PRK07525, sulfoacetaldehyde acetyltransferase; Validated.
CDD:236043	632	PRK	Bacteria:45	PRK07529, PRK07529, AMP-binding domain protein; Validated.
CDD:181020	258	PRK	Bacteria:58	PRK07533, PRK07533, enoyl-(acyl carrier protein) reductase; Provisional.
CDD:181022	261	PRK	Bacteria:29	PRK07535, PRK07535, methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated.
CDD:236046	413	PRK	Bacteria:46	PRK07538, PRK07538, hypothetical protein; Provisional.
CDD:181024	154	PRK	Bacteria:315	PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated.
CDD:181025	292	PRK	Bacteria:41	PRK07544, PRK07544, branched-chain amino acid aminotransferase; Validated.
CDD:169002	209	PRK	Bacteria:34,nodiv:1	PRK07546, PRK07546, hypothetical protein; Provisional.
CDD:181026	386	PRK	Bacteria:29	PRK07550, PRK07550, hypothetical protein; Provisional.
CDD:181027	74	PRK	Bacteria:81	PRK07558, PRK07558, F0F1 ATP synthase subunit C; Validated.
CDD:181028	365	PRK	Bacteria:75	PRK07559, PRK07559, 2'-deoxycytidine 5'-triphosphate deaminase; Provisional.
CDD:236047	731	PRK	Bacteria:80	PRK07560, PRK07560, elongation factor EF-2; Reviewed.
CDD:236048	859	PRK	Bacteria:375	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
CDD:236049	1220	PRK	Bacteria:77	PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit alpha; Validated.
CDD:236050	543	PRK	Bacteria:405,nodiv:1	PRK07564, PRK07564, phosphoglucomutase; Validated.
CDD:236051	334	PRK	Bacteria:47	PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
CDD:236052	314	PRK	Bacteria:82	PRK07566, PRK07566, bacteriochlorophyll/chlorophyll a synthase; Reviewed.
CDD:181035	242	PRK	Bacteria:26	PRK07567, PRK07567, glutamine amidotransferase; Provisional.
CDD:181036	397	PRK	Bacteria:65	PRK07568, PRK07568, aspartate aminotransferase; Provisional.
CDD:181037	234	PRK	Bacteria:25	PRK07569, PRK07569, bidirectional hydrogenase complex protein HoxU; Validated.
CDD:181038	250	PRK	Bacteria:120	PRK07570, PRK07570, succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated.
CDD:181039	426	PRK	Bacteria:47	PRK07572, PRK07572, cytosine deaminase; Validated.
CDD:236054	640	PRK	Bacteria:120	PRK07573, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed.
CDD:181041	385	PRK	Bacteria:50	PRK07574, PRK07574, formate dehydrogenase; Provisional.
CDD:236056	264	PRK	Bacteria:35	PRK07576, PRK07576, short chain dehydrogenase; Provisional.
CDD:236057	199	PRK	Bacteria:82	PRK07578, PRK07578, short chain dehydrogenase; Provisional.
CDD:236059	230	PRK	Bacteria:83	PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase; Validated.
CDD:236060	339	PRK	Bacteria:35	PRK07581, PRK07581, hypothetical protein; Validated.
CDD:236061	366	PRK	Bacteria:27	PRK07582, PRK07582, cystathionine gamma-lyase; Validated.
CDD:236062	438	PRK	Bacteria:27	PRK07583, PRK07583, cytosine deaminase-like protein; Validated.
CDD:236063	514	PRK	Bacteria:69	PRK07586, PRK07586, hypothetical protein; Validated.
CDD:236064	346	PRK	Bacteria:82,nodiv:2	PRK07589, PRK07589, ornithine cyclodeaminase; Validated.
CDD:181053	409	PRK	Bacteria:97	PRK07590, PRK07590, L,L-diaminopimelate aminotransferase; Validated.
CDD:236065	421	PRK	Bacteria:52	PRK07591, PRK07591, threonine synthase; Validated.
CDD:236066	64	PRK	Bacteria:416,nodiv:1	PRK07597, secE, preprotein translocase subunit SecE; Reviewed.
CDD:181057	388	PRK	Bacteria:48	PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family protein; Provisional.
CDD:181058	339	PRK	Bacteria:112	PRK07609, PRK07609, CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated.
CDD:236068	312	PRK	Bacteria:43	PRK07630, PRK07630, CobD/CbiB family protein; Provisional.
CDD:181067	283	PRK	Bacteria:32	PRK07650, PRK07650, 4-amino-4-deoxychorismate lyase; Provisional.
CDD:236072	513	PRK	Bacteria:66	PRK07656, PRK07656, long-chain-fatty-acid--CoA ligase; Validated.
CDD:181070	257	PRK	Bacteria:34	PRK07658, PRK07658, enoyl-CoA hydratase; Provisional.
CDD:236073	260	PRK	Bacteria:33	PRK07659, PRK07659, enoyl-CoA hydratase; Provisional.
CDD:181074	254	PRK	Bacteria:23	PRK07668, PRK07668, hypothetical protein; Validated.
CDD:181078	451	PRK	Bacteria:37	PRK07678, PRK07678, aminotransferase; Validated.
CDD:181080	273	PRK	Bacteria:36	PRK07680, PRK07680, late competence protein ComER; Validated.
CDD:181084	339	PRK	Bacteria:35	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated.
CDD:181085	496	PRK	Bacteria:40	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:181086	201	PRK	Bacteria:31	PRK07695, PRK07695, transcriptional regulator TenI; Provisional.
CDD:181087	298	PRK	Bacteria:25	PRK07701, flgL, flagellar hook-associated protein FlgL; Validated.
CDD:181088	219	PRK	Bacteria:35	PRK07708, PRK07708, hypothetical protein; Validated.
CDD:181090	142	PRK	Bacteria:14	PRK07718, fliL, flagellar basal body-associated protein FliL; Reviewed.
CDD:181091	146	PRK	Bacteria:12	PRK07720, fliJ, flagellar biosynthesis chaperone; Validated.
CDD:236078	658	PRK	Bacteria:284	PRK07726, PRK07726, DNA topoisomerase III; Provisional.
CDD:236083	117	PRK	Bacteria:10	PRK07738, PRK07738, flagellar protein FlaG; Provisional.
CDD:236084	507	PRK	Bacteria:28	PRK07739, flgK, flagellar hook-associated protein FlgK; Validated.
CDD:236085	244	PRK	Bacteria:11	PRK07740, PRK07740, hypothetical protein; Provisional.
CDD:236088	152	PRK	Bacteria:86	PRK07757, PRK07757, acetyltransferase; Provisional.
CDD:236089	376	PRK	Bacteria:86	PRK07761, PRK07761, DNA polymerase III subunit beta; Validated.
CDD:236090	824	PRK	Bacteria:46	PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated.
CDD:236091	545	PRK	Bacteria:30	PRK07768, PRK07768, long-chain-fatty-acid--CoA ligase; Validated.
CDD:236092	186	PRK	Bacteria:58	PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional.
CDD:181115	235	PRK	Bacteria:60	PRK07785, PRK07785, NADH dehydrogenase subunit C; Provisional.
CDD:236096	471	PRK	Bacteria:41	PRK07787, PRK07787, acyl-CoA synthetase; Validated.
CDD:236097	549	PRK	Bacteria:32	PRK07788, PRK07788, acyl-CoA synthetase; Validated.
CDD:236098	612	PRK	Bacteria:78	PRK07789, PRK07789, acetolactate synthase 1 catalytic subunit; Validated.
CDD:236099	286	PRK	Bacteria:34	PRK07791, PRK07791, short chain dehydrogenase; Provisional.
CDD:236100	533	PRK	Bacteria:40	PRK07798, PRK07798, acyl-CoA synthetase; Validated.
CDD:236101	626	PRK	Bacteria:46	PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed.
CDD:236102	541	PRK	Bacteria:44	PRK07804, PRK07804, L-aspartate oxidase; Provisional.
CDD:181126	248	PRK	Bacteria:20	PRK07806, PRK07806, short chain dehydrogenase; Provisional.
CDD:181127	479	PRK	Bacteria:74	PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase; Validated.
CDD:181133	286	PRK	Bacteria:36	PRK07819, PRK07819, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
CDD:181136	273	PRK	Bacteria:24	PRK07825, PRK07825, short chain dehydrogenase; Provisional.
CDD:236109	260	PRK	Bacteria:30	PRK07827, PRK07827, enoyl-CoA hydratase; Provisional.
CDD:236110	262	PRK	Bacteria:46	PRK07831, PRK07831, short chain dehydrogenase; Provisional.
CDD:236112	466	PRK	Bacteria:78	PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed.
CDD:181142	451	PRK	Bacteria:41	PRK07846, PRK07846, mycothione reductase; Reviewed.
CDD:236113	510	PRK	Bacteria:75	PRK07847, PRK07847, amidophosphoribosyltransferase; Provisional.
CDD:236114	292	PRK	Bacteria:44	PRK07849, PRK07849, 4-amino-4-deoxychorismate lyase; Provisional.
CDD:236115	243	PRK	Bacteria:30	PRK07854, PRK07854, enoyl-CoA hydratase; Provisional.
CDD:181147	386	PRK	Bacteria:40	PRK07855, PRK07855, lipid-transfer protein; Provisional.
CDD:236116	252	PRK	Bacteria:45	PRK07856, PRK07856, short chain dehydrogenase; Provisional.
CDD:236117	106	PRK	Bacteria:34	PRK07857, PRK07857, hypothetical protein; Provisional.
CDD:236118	797	PRK	Bacteria:54	PRK07860, PRK07860, NADH dehydrogenase subunit G; Validated.
CDD:236119	364	PRK	Bacteria:70	PRK07865, PRK07865, N-succinyldiaminopimelate aminotransferase; Reviewed.
CDD:236120	529	PRK	Bacteria:28	PRK07867, PRK07867, acyl-CoA synthetase; Validated.
CDD:181154	468	PRK	Bacteria:30	PRK07869, PRK07869, amidase; Provisional.
CDD:236122	722	PRK	Bacteria:28	PRK07877, PRK07877, hypothetical protein; Provisional.
CDD:236123	557	PRK	Bacteria:60	PRK07883, PRK07883, hypothetical protein; Validated.
CDD:236124	256	PRK	Bacteria:62	PRK07889, PRK07889, enoyl-(acyl carrier protein) reductase; Provisional.
CDD:181159	258	PRK	Bacteria:38	PRK07890, PRK07890, short chain dehydrogenase; Provisional.
CDD:181163	426	PRK	Bacteria:70	PRK07906, PRK07906, hypothetical protein; Provisional.
CDD:236127	449	PRK	Bacteria:61	PRK07907, PRK07907, hypothetical protein; Provisional.
CDD:236128	349	PRK	Bacteria:34	PRK07908, PRK07908, hypothetical protein; Provisional.
CDD:236131	298	PRK	Bacteria:60	PRK07920, PRK07920, lipid A biosynthesis lauroyl acyltransferase; Provisional.
CDD:236132	169	PRK	Bacteria:60	PRK07922, PRK07922, N-acetylglutamate synthase; Validated.
CDD:236133	213	PRK	Bacteria:41	PRK07933, PRK07933, thymidylate kinase; Validated.
CDD:181173	352	PRK	Bacteria:33	PRK07937, PRK07937, lipid-transfer protein; Provisional.
CDD:181174	249	PRK	Bacteria:44	PRK07938, PRK07938, enoyl-CoA hydratase; Provisional.
CDD:236134	394	PRK	Bacteria:67	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
CDD:181176	232	PRK	Bacteria:28	PRK07942, PRK07942, DNA polymerase III subunit epsilon; Provisional.
CDD:236135	335	PRK	Bacteria:43	PRK07945, PRK07945, hypothetical protein; Provisional.
CDD:236136	163	PRK	Bacteria:23	PRK07946, PRK07946, putative monovalent cation/H+ antiporter subunit C; Reviewed.
CDD:236137	665	PRK	Bacteria:417	PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
CDD:236138	647	PRK	Bacteria:163	PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated.
CDD:181199	391	PRK	Bacteria:94	PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed.
CDD:236140	529	PRK	Bacteria:35	PRK08026, PRK08026, flagellin; Validated.
CDD:236141	462	PRK	Bacteria:77	PRK08032, fliD, flagellar capping protein; Reviewed.
CDD:236142	232	PRK	Bacteria:141	PRK08051, fre, FMN reductase; Validated.
CDD:181210	66	PRK	Bacteria:66	PRK08053, PRK08053, sulfur carrier protein ThiS; Provisional.
CDD:236143	181	PRK	Bacteria:46	PRK08055, PRK08055, chorismate mutase; Provisional.
CDD:236144	248	PRK	Bacteria:169,nodiv:1	PRK08057, PRK08057, cobalt-precorrin-6x reductase; Reviewed.
CDD:181214	329	PRK	Bacteria:51	PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
CDD:181216	61	PRK	Bacteria:321	PRK08061, rpsN, 30S ribosomal protein S14; Reviewed.
CDD:181219	389	PRK	Bacteria:59	PRK08068, PRK08068, transaminase; Reviewed.
CDD:236147	510	PRK	Bacteria:38	PRK08071, PRK08071, L-aspartate oxidase; Provisional.
CDD:236148	928	PRK	Bacteria:42	PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated.
CDD:236150	562	PRK	Bacteria:99	PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed.
CDD:236151	399	PRK	Bacteria:110	PRK08099, PRK08099, bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional.
CDD:181230	149	PRK	Bacteria:118	PRK08105, PRK08105, flavodoxin; Provisional.
CDD:236153	268	PRK	Bacteria:30	PRK08116, PRK08116, hypothetical protein; Validated.
CDD:181235	167	PRK	Bacteria:27	PRK08118, PRK08118, topology modulation protein; Reviewed.
CDD:236154	382	PRK	Bacteria:50	PRK08119, PRK08119, flagellar motor switch protein; Validated.
CDD:236155	270	PRK	Bacteria:39	PRK08123, PRK08123, histidinol-phosphatase; Reviewed.
CDD:181238	263	PRK	Bacteria:56	PRK08124, PRK08124, flagellar motor protein MotA; Validated.
CDD:236156	660	PRK	Bacteria:99	PRK08125, PRK08125, bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated.
CDD:181241	213	PRK	Bacteria:150	PRK08130, PRK08130, putative aldolase; Validated.
CDD:236158	547	PRK	Bacteria:66	PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
CDD:181244	390	PRK	Bacteria:77	PRK08133, PRK08133, O-succinylhomoserine sulfhydrylase; Validated.
CDD:236160	317	PRK	Bacteria:135	PRK08136, PRK08136, glycosyl transferase family protein; Provisional.
CDD:181249	266	PRK	Bacteria:61	PRK08139, PRK08139, enoyl-CoA hydratase; Validated.
CDD:236163	262	PRK	Bacteria:80	PRK08140, PRK08140, enoyl-CoA hydratase; Provisional.
CDD:236165	547	PRK	Bacteria:81	PRK08147, flgK, flagellar hook-associated protein FlgK; Validated.
CDD:236166	428	PRK	Bacteria:40	PRK08149, PRK08149, ATP synthase SpaL; Validated.
CDD:181254	255	PRK	Bacteria:21	PRK08150, PRK08150, enoyl-CoA hydratase; Provisional.
CDD:181255	369	PRK	Bacteria:32,nodiv:1	PRK08153, PRK08153, histidinol-phosphate aminotransferase; Provisional.
CDD:236167	309	PRK	Bacteria:41	PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional regulator; Reviewed.
CDD:236168	361	PRK	Bacteria:39	PRK08156, PRK08156, type III secretion system protein SpaS; Validated.
CDD:236169	545	PRK	Bacteria:71	PRK08162, PRK08162, acyl-CoA synthetase; Validated.
CDD:181262	396	PRK	Bacteria:40	PRK08163, PRK08163, salicylate hydroxylase; Provisional.
CDD:236170	791	PRK	Bacteria:160	PRK08166, PRK08166, NADH dehydrogenase subunit G; Validated.
CDD:236171	516	PRK	Bacteria:16	PRK08168, PRK08168, NADH dehydrogenase subunit L; Provisional.
CDD:236172	862	PRK	Bacteria:56	PRK08173, PRK08173, DNA topoisomerase III; Validated.
CDD:181269	281	PRK	Bacteria:67	PRK08176, pdxK, pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed.
CDD:236174	96	PRK	Bacteria:88	PRK08178, PRK08178, acetolactate synthase 1 regulatory subunit; Reviewed.
CDD:181271	200	PRK	Bacteria:57	PRK08179, prfH, peptide chain release factor-like protein; Reviewed.
CDD:236175	614	PRK	Bacteria:66,nodiv:1	PRK08180, PRK08180, feruloyl-CoA synthase; Reviewed.
CDD:169261	148	PRK	Bacteria:30	PRK08182, PRK08182, single-stranded DNA-binding protein; Provisional.
CDD:236176	133	PRK	Bacteria:64,nodiv:1	PRK08183, PRK08183, NADH dehydrogenase; Validated.
CDD:181274	550	PRK	Bacteria:35	PRK08184, PRK08184, benzoyl-CoA-dihydrodiol lyase; Provisional.
CDD:236177	600	PRK	Bacteria:79	PRK08186, PRK08186, allophanate hydrolase; Provisional.
CDD:236178	493	PRK	Bacteria:22	PRK08187, PRK08187, pyruvate kinase; Validated.
CDD:236180	466	PRK	Bacteria:60	PRK08190, PRK08190, bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated.
CDD:236181	231	PRK	Bacteria:173	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase; Reviewed.
CDD:181282	337	PRK	Bacteria:129	PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated.
CDD:181283	394	PRK	Bacteria:23	PRK08197, PRK08197, threonine synthase; Validated.
CDD:236182	404	PRK	Bacteria:116	PRK08198, PRK08198, threonine dehydratase; Provisional.
CDD:181285	557	PRK	Bacteria:86,nodiv:1	PRK08199, PRK08199, thiamine pyrophosphate protein; Validated.
CDD:236183	272	PRK	Bacteria:286,nodiv:1	PRK08202, PRK08202, purine nucleoside phosphorylase; Provisional.
CDD:236184	451	PRK	Bacteria:104	PRK08203, PRK08203, hydroxydechloroatrazine ethylaminohydrolase; Reviewed.
CDD:181288	449	PRK	Bacteria:13	PRK08204, PRK08204, hypothetical protein; Provisional.
CDD:236186	399	PRK	Bacteria:122	PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional.
CDD:236187	488	PRK	Bacteria:84	PRK08207, PRK08207, coproporphyrinogen III oxidase; Provisional.
CDD:181292	430	PRK	Bacteria:22	PRK08208, PRK08208, coproporphyrinogen III oxidase; Validated.
CDD:236188	403	PRK	Bacteria:86	PRK08210, PRK08210, aspartate kinase I; Reviewed.
CDD:181295	259	PRK	Bacteria:37	PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional.
CDD:181296	258	PRK	Bacteria:93	PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed.
CDD:181297	253	PRK	Bacteria:55	PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:181298	227	PRK	Bacteria:37	PRK08219, PRK08219, short chain dehydrogenase; Provisional.
CDD:236190	252	PRK	Bacteria:122	PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated.
CDD:181300	263	PRK	Bacteria:47	PRK08221, PRK08221, anaerobic sulfite reductase subunit B; Provisional.
CDD:236191	350	PRK	Bacteria:64	PRK08224, ligC, ATP-dependent DNA ligase; Reviewed.
CDD:236193	341	PRK	Bacteria:28	PRK08229, PRK08229, 2-dehydropantoate 2-reductase; Provisional.
CDD:236194	212	PRK	Bacteria:15	PRK08236, PRK08236, hypothetical protein; Provisional.
CDD:236195	479	PRK	Bacteria:54	PRK08238, PRK08238, hypothetical protein; Validated.
CDD:236196	339	PRK	Bacteria:50	PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated.
CDD:236197	402	PRK	Bacteria:125	PRK08242, PRK08242, acetyl-CoA acetyltransferase; Validated.
CDD:236198	392	PRK	Bacteria:146,nodiv:1	PRK08243, PRK08243, 4-hydroxybenzoate 3-monooxygenase; Validated.
CDD:236200	240	PRK	Bacteria:47	PRK08245, PRK08245, hypothetical protein; Validated.
CDD:181319	310	PRK	Bacteria:23	PRK08246, PRK08246, threonine dehydratase; Provisional.
CDD:181323	235	PRK	Bacteria:44	PRK08250, PRK08250, glutamine amidotransferase; Provisional.
CDD:181324	248	PRK	Bacteria:46	PRK08251, PRK08251, short chain dehydrogenase; Provisional.
CDD:181325	254	PRK	Bacteria:34	PRK08252, PRK08252, enoyl-CoA hydratase; Provisional.
CDD:236203	765	PRK	Bacteria:49	PRK08255, PRK08255, salicylyl-CoA 5-hydroxylase; Reviewed.
CDD:181327	391	PRK	Bacteria:50	PRK08256, PRK08256, lipid-transfer protein; Provisional.
CDD:236204	498	PRK	Bacteria:43	PRK08257, PRK08257, acetyl-CoA acetyltransferase; Validated.
CDD:181329	277	PRK	Bacteria:50	PRK08258, PRK08258, enoyl-CoA hydratase; Provisional.
CDD:236205	254	PRK	Bacteria:65	PRK08259, PRK08259, enoyl-CoA hydratase; Provisional.
CDD:236206	296	PRK	Bacteria:29	PRK08260, PRK08260, enoyl-CoA hydratase; Provisional.
CDD:236207	450	PRK	Bacteria:97	PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:236208	486	PRK	Bacteria:34	PRK08262, PRK08262, hypothetical protein; Provisional.
CDD:181334	275	PRK	Bacteria:18	PRK08263, PRK08263, short chain dehydrogenase; Provisional.
CDD:181335	238	PRK	Bacteria:65	PRK08264, PRK08264, short chain dehydrogenase; Validated.
CDD:236209	261	PRK	Bacteria:29	PRK08265, PRK08265, short chain dehydrogenase; Provisional.
CDD:181337	542	PRK	Bacteria:21	PRK08266, PRK08266, hypothetical protein; Provisional.
CDD:236210	260	PRK	Bacteria:45	PRK08267, PRK08267, short chain dehydrogenase; Provisional.
CDD:236211	507	PRK	Bacteria:90	PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
CDD:236212	656	PRK	Bacteria:124	PRK08270, PRK08270, anaerobic ribonucleoside triphosphate reductase; Provisional.
CDD:181342	623	PRK	Bacteria:23	PRK08271, PRK08271, anaerobic ribonucleoside triphosphate reductase; Provisional.
CDD:236213	302	PRK	Bacteria:31	PRK08272, PRK08272, enoyl-CoA hydratase; Provisional.
CDD:181344	597	PRK	Bacteria:61	PRK08273, PRK08273, thiamine pyrophosphate protein; Provisional.
CDD:236214	466	PRK	Bacteria:79	PRK08274, PRK08274, tricarballylate dehydrogenase; Validated.
CDD:236215	502	PRK	Bacteria:55	PRK08276, PRK08276, long-chain-fatty-acid--CoA ligase; Validated.
CDD:236216	278	PRK	Bacteria:49	PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
CDD:181349	273	PRK	Bacteria:71	PRK08278, PRK08278, short chain dehydrogenase; Provisional.
CDD:236217	600	PRK	Bacteria:69	PRK08279, PRK08279, long-chain-acyl-CoA synthetase; Validated.
CDD:236218	253	PRK	Bacteria:91	PRK08284, PRK08284, precorrin 6A synthase; Provisional.
CDD:181352	208	PRK	Bacteria:117	PRK08285, cobH, precorrin-8X methylmutase; Reviewed.
CDD:181354	187	PRK	Bacteria:44	PRK08287, PRK08287, cobalt-precorrin-6Y C(15)-methyltransferase; Validated.
CDD:236219	477	PRK	Bacteria:110	PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase; Reviewed.
CDD:236220	288	PRK	Bacteria:50	PRK08290, PRK08290, enoyl-CoA hydratase; Provisional.
CDD:236221	330	PRK	Bacteria:31	PRK08291, PRK08291, ectoine utilization protein EutC; Validated.
CDD:236222	489	PRK	Bacteria:222,nodiv:1	PRK08292, PRK08292, AMP nucleosidase; Provisional.
CDD:181359	287	PRK	Bacteria:26	PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
CDD:236223	634	PRK	Bacteria:23	PRK08294, PRK08294, phenol 2-monooxygenase; Provisional.
CDD:181361	208	PRK	Bacteria:112	PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
CDD:181362	603	PRK	Bacteria:15	PRK08296, PRK08296, hypothetical protein; Provisional.
CDD:236224	443	PRK	Bacteria:41	PRK08297, PRK08297, L-lysine aminotransferase; Provisional.
CDD:236226	402	PRK	Bacteria:184,nodiv:1	PRK08299, PRK08299, isocitrate dehydrogenase; Validated.
CDD:236227	302	PRK	Bacteria:145	PRK08300, PRK08300, acetaldehyde dehydrogenase; Validated.
CDD:236228	234	PRK	Bacteria:99	PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed.
CDD:236229	305	PRK	Bacteria:29	PRK08303, PRK08303, short chain dehydrogenase; Provisional.
CDD:236230	337	PRK	Bacteria:92	PRK08304, PRK08304, stage V sporulation protein AD; Validated.
CDD:181370	196	PRK	Bacteria:69	PRK08305, spoVFB, dipicolinate synthase subunit B; Reviewed.
CDD:181371	296	PRK	Bacteria:63	PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
CDD:181372	171	PRK	Bacteria:72	PRK08307, PRK08307, stage III sporulation protein SpoAB; Provisional.
CDD:236231	414	PRK	Bacteria:24	PRK08308, PRK08308, acyl-CoA synthetase; Validated.
CDD:181375	395	PRK	Bacteria:25	PRK08310, PRK08310, amidase; Provisional.
CDD:236233	237	PRK	Bacteria:57	PRK08311, PRK08311, putative RNA polymerase sigma factor SigI; Reviewed.
CDD:236234	510	PRK	Bacteria:16	PRK08312, PRK08312, putative indolepyruvate oxidoreductase subunit B; Reviewed.
CDD:236235	546	PRK	Bacteria:36	PRK08314, PRK08314, long-chain-fatty-acid--CoA ligase; Validated.
CDD:236236	559	PRK	Bacteria:169	PRK08315, PRK08315, AMP-binding domain protein; Validated.
CDD:181381	523	PRK	Bacteria:34	PRK08316, PRK08316, acyl-CoA synthetase; Validated.
CDD:181382	241	PRK	Bacteria:17	PRK08317, PRK08317, hypothetical protein; Provisional.
CDD:236237	420	PRK	Bacteria:141	PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B; Validated.
CDD:181384	224	PRK	Bacteria:120	PRK08319, PRK08319, cobalt transport protein CbiM; Validated.
CDD:236238	288	PRK	Bacteria:81	PRK08320, PRK08320, branched-chain amino acid aminotransferase; Reviewed.
CDD:181386	302	PRK	Bacteria:77	PRK08321, PRK08321, naphthoate synthase; Validated.
CDD:236239	547	PRK	Bacteria:83	PRK08322, PRK08322, acetolactate synthase; Reviewed.
CDD:236240	459	PRK	Bacteria:163,nodiv:1	PRK08323, PRK08323, phenylhydantoinase; Validated.
CDD:236241	681	PRK	Bacteria:111,nodiv:1	PRK08324, PRK08324, short chain dehydrogenase; Validated.
CDD:236242	311	PRK	Bacteria:40	PRK08326, PRK08326, ribonucleotide-diphosphate reductase subunit beta; Validated.
CDD:236243	569	PRK	Bacteria:25	PRK08327, PRK08327, acetolactate synthase catalytic subunit; Validated.
CDD:236245	417	PRK	Bacteria:42	PRK08343, secD, preprotein translocase subunit SecD; Reviewed.
CDD:236251	487	PRK	Bacteria:46	PRK08375, PRK08375, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:181413	140	PRK	Bacteria:48	PRK08406, PRK08406, transcription elongation factor NusA-like protein; Validated.
CDD:181414	311	PRK	Bacteria:27	PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
CDD:181419	408	PRK	Bacteria:27	PRK08418, PRK08418, chlorohydrolase; Provisional.
CDD:181420	298	PRK	Bacteria:20	PRK08419, PRK08419, lipid A biosynthesis lauroyl acyltransferase; Reviewed.
CDD:236263	731	PRK	Bacteria:23	PRK08425, flgE, flagellar hook protein FlgE; Validated.
CDD:236264	283	PRK	Bacteria:22	PRK08432, PRK08432, flagellar motor switch protein FliY; Validated.
CDD:181428	350	PRK	Bacteria:26	PRK08446, PRK08446, coproporphyrinogen III oxidase; Provisional.
CDD:236267	535	PRK	Bacteria:20	PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated.
CDD:236268	124	PRK	Bacteria:18	PRK08452, PRK08452, flagellar protein FlaG; Provisional.
CDD:181435	257	PRK	Bacteria:21	PRK08457, motB, flagellar motor protein MotB; Reviewed.
CDD:236270	613	PRK	Bacteria:21	PRK08471, flgK, flagellar hook-associated protein FlgK; Validated.
CDD:236271	176	PRK	Bacteria:18	PRK08474, PRK08474, F0F1 ATP synthase subunit delta; Validated.
CDD:236272	167	PRK	Bacteria:24	PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
CDD:181442	141	PRK	Bacteria:20	PRK08476, PRK08476, F0F1 ATP synthase subunit B'; Validated.
CDD:236273	211	PRK	Bacteria:27	PRK08477, PRK08477, biotin--protein ligase; Provisional.
CDD:236274	206	PRK	Bacteria:20	PRK08485, PRK08485, DNA polymerase III subunit delta'; Validated.
CDD:236276	328	PRK	Bacteria:29	PRK08487, PRK08487, DNA polymerase III subunit delta; Validated.
CDD:181449	263	PRK	Bacteria:22	PRK08491, PRK08491, NADH dehydrogenase subunit C; Provisional.
CDD:236277	819	PRK	Bacteria:22	PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
CDD:236278	472	PRK	Bacteria:26	PRK08506, PRK08506, replicative DNA helicase; Provisional.
CDD:181452	275	PRK	Bacteria:37	PRK08507, PRK08507, prephenate dehydrogenase; Validated.
CDD:236279	279	PRK	Bacteria:28	PRK08508, PRK08508, biotin synthase; Provisional.
CDD:236280	222	PRK	Bacteria:20	PRK08515, flgA, flagellar basal body P-ring biosynthesis protein FlgA; Reviewed.
CDD:236281	257	PRK	Bacteria:23	PRK08517, PRK08517, DNA polymerase III subunit epsilon; Provisional.
CDD:236282	310	PRK	Bacteria:41	PRK08535, PRK08535, translation initiation factor IF-2B subunit delta; Provisional.
CDD:236283	449	PRK	Bacteria:40	PRK08540, PRK08540, adenylosuccinate lyase; Reviewed.
CDD:236284	211	PRK	Bacteria:18	PRK08541, PRK08541, flagellin; Validated.
CDD:181466	238	PRK	Bacteria:19	PRK08558, PRK08558, adenine phosphoribosyltransferase; Provisional.
CDD:181467	153	PRK	Bacteria:59	PRK08559, nusG, transcription antitermination protein NusG; Validated.
CDD:236286	329	PRK	Bacteria:77	PRK08560, PRK08560, tyrosyl-tRNA synthetase; Validated.
CDD:236287	151	PRK	Bacteria:79	PRK08561, rps15p, 30S ribosomal protein S15P; Reviewed.
CDD:236288	125	PRK	Bacteria:57	PRK08562, rpl32e, 50S ribosomal protein L32e; Validated.
CDD:236289	187	PRK	Bacteria:74	PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional.
CDD:236291	1103	PRK	Bacteria:33	PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional.
CDD:236292	882	PRK	Bacteria:73	PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated.
CDD:236293	462	PRK	Bacteria:74	PRK08568, PRK08568, preprotein translocase subunit SecY; Reviewed.
CDD:236294	193	PRK	Bacteria:82	PRK08569, rpl18p, 50S ribosomal protein L18P; Reviewed.
CDD:236295	150	PRK	Bacteria:80	PRK08570, rpl19e, 50S ribosomal protein L19e; Reviewed.
CDD:181478	132	PRK	Bacteria:77	PRK08571, rpl14p, 50S ribosomal protein L14P; Reviewed.
CDD:236296	108	PRK	Bacteria:68	PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed.
CDD:236300	438	PRK	Bacteria:9	PRK08576, PRK08576, hypothetical protein; Provisional.
CDD:236301	136	PRK	Bacteria:12	PRK08577, PRK08577, hypothetical protein; Provisional.
CDD:236302	292	PRK	Bacteria:42	PRK08578, PRK08578, preprotein translocase subunit SecF; Reviewed.
CDD:236304	619	PRK	Bacteria:23	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
CDD:181490	377	PRK	Bacteria:40	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed.
CDD:236307	451	PRK	Bacteria:426	PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase subunit; Validated.
CDD:236309	377	PRK	Bacteria:120	PRK08599, PRK08599, coproporphyrinogen III oxidase; Provisional.
CDD:181497	113	PRK	Bacteria:47	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed.
CDD:236310	509	PRK	Bacteria:46	PRK08601, PRK08601, NADH dehydrogenase subunit 5; Validated.
CDD:236311	570	PRK	Bacteria:67	PRK08609, PRK08609, hypothetical protein; Provisional.
CDD:181502	576	PRK	Bacteria:47	PRK08611, PRK08611, pyruvate oxidase; Provisional.
CDD:236312	552	PRK	Bacteria:120	PRK08617, PRK08617, acetolactate synthase; Reviewed.
CDD:181507	657	PRK	Bacteria:61	PRK08626, PRK08626, fumarate reductase flavoprotein subunit; Provisional.
CDD:181508	258	PRK	Bacteria:38	PRK08628, PRK08628, short chain dehydrogenase; Provisional.
CDD:236315	1146	PRK	Bacteria:29	PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated.
CDD:181512	388	PRK	Bacteria:38	PRK08637, PRK08637, hypothetical protein; Provisional.
CDD:236318	420	PRK	Bacteria:169,nodiv:1	PRK08639, PRK08639, threonine dehydratase; Validated.
CDD:181515	249	PRK	Bacteria:88	PRK08640, sdhB, succinate dehydrogenase iron-sulfur subunit; Reviewed.
CDD:236319	589	PRK	Bacteria:87	PRK08641, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed.
CDD:236320	212	PRK	Bacteria:47	PRK08644, PRK08644, thiamine biosynthesis protein ThiF; Provisional.
CDD:236321	612	PRK	Bacteria:107	PRK08645, PRK08645, bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed.
CDD:236322	368	PRK	Bacteria:128	PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase; Validated.
CDD:236323	394	PRK	Bacteria:34	PRK08651, PRK08651, succinyl-diaminopimelate desuccinylase; Reviewed.
CDD:236325	499	PRK	Bacteria:36	PRK08654, PRK08654, pyruvate carboxylase subunit A; Validated.
CDD:236326	437	PRK	Bacteria:24	PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
CDD:181526	376	PRK	Bacteria:72	PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated.
CDD:181527	181	PRK	Bacteria:22	PRK08660, PRK08660, L-fuculose phosphate aldolase; Provisional.
CDD:236327	477	PRK	Bacteria:239	PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
CDD:236328	343	PRK	Bacteria:60	PRK08662, PRK08662, nicotinate phosphoribosyltransferase; Reviewed.
CDD:236329	349	PRK	Bacteria:108	PRK08664, PRK08664, aspartate-semialdehyde dehydrogenase; Reviewed.
CDD:236330	752	PRK	Bacteria:40	PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit alpha; Validated.
CDD:236332	610	PRK	Bacteria:13	PRK08668, PRK08668, NADH dehydrogenase subunit M; Validated.
CDD:181534	291	PRK	Bacteria:82	PRK08671, PRK08671, methionine aminopeptidase; Provisional.
CDD:181535	335	PRK	Bacteria:94	PRK08673, PRK08673, 3-deoxy-7-phosphoheptulonate synthase; Reviewed.
CDD:181536	337	PRK	Bacteria:39	PRK08674, PRK08674, bifunctional phosphoglucose/phosphomannose isomerase; Validated.
CDD:236337	376	PRK	Bacteria:25	PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB; Validated.
CDD:236338	287	PRK	Bacteria:45	PRK08788, PRK08788, enoyl-CoA hydratase; Validated.
CDD:236344	376	PRK	Bacteria:43	PRK08869, PRK08869, flagellin; Reviewed.
CDD:236345	404	PRK	Bacteria:89	PRK08870, flgL, flagellar hook-associated protein FlgL; Reviewed.
CDD:181574	101	PRK	Bacteria:613	PRK08881, rpsN, 30S ribosomal protein S14; Reviewed.
CDD:236346	394	PRK	Bacteria:56	PRK08898, PRK08898, coproporphyrinogen III oxidase; Provisional.
CDD:236347	227	PRK	Bacteria:52	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
CDD:236348	289	PRK	Bacteria:26	PRK08905, PRK08905, lipid A biosynthesis lauroyl acyltransferase; Validated.
CDD:181580	387	PRK	Bacteria:37	PRK08912, PRK08912, hypothetical protein; Provisional.
CDD:236351	442	PRK	Bacteria:35	PRK08927, fliI, flagellum-specific ATP synthase; Validated.
CDD:236352	216	PRK	Bacteria:310	PRK08937, PRK08937, adenylosuccinate lyase; Provisional.
CDD:236353	306	PRK	Bacteria:125	PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
CDD:236354	181	PRK	Bacteria:217,nodiv:1	PRK08942, PRK08942, D,D-heptose 1,7-bisphosphate phosphatase; Validated.
CDD:236355	314	PRK	Bacteria:150	PRK08943, PRK08943, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase; Validated.
CDD:236356	302	PRK	Bacteria:50	PRK08944, motB, flagellar motor protein MotB; Reviewed.
CDD:236357	247	PRK	Bacteria:154	PRK08945, PRK08945, putative oxoacyl-(acyl carrier protein) reductase; Provisional.
CDD:181592	387	PRK	Bacteria:170	PRK08947, fadA, 3-ketoacyl-CoA thiolase; Reviewed.
CDD:181593	190	PRK	Bacteria:32	PRK08951, PRK08951, malate synthase; Provisional.
CDD:181597	428	PRK	Bacteria:142	PRK08963, fadI, 3-ketoacyl-CoA thiolase; Reviewed.
CDD:181598	162	PRK	Bacteria:139,nodiv:1	PRK08965, PRK08965, putative monovalent cation/H+ antiporter subunit E; Reviewed.
CDD:181601	548	PRK	Bacteria:149	PRK08978, PRK08978, acetolactate synthase 2 catalytic subunit; Reviewed.
CDD:236361	312	PRK	Bacteria:59	PRK08999, PRK08999, hypothetical protein; Provisional.
CDD:181608	146	PRK	Bacteria:138	PRK09004, PRK09004, FMN-binding protein MioC; Provisional.
CDD:181611	162	PRK	Bacteria:114	PRK09014, rfaH, transcriptional activator RfaH; Provisional.
CDD:181613	108	PRK	Bacteria:127	PRK09019, PRK09019, translation initiation factor Sui1; Validated.
CDD:181614	295	PRK	Bacteria:148	PRK09027, PRK09027, cytidine deaminase; Provisional.
CDD:236363	458	PRK	Bacteria:117	PRK09029, PRK09029, O-succinylbenzoic acid--CoA ligase; Provisional.
CDD:236364	454	PRK	Bacteria:128	PRK09034, PRK09034, aspartate kinase; Reviewed.
CDD:181618	281	PRK	Bacteria:43	PRK09038, PRK09038, flagellar motor protein MotD; Reviewed.
CDD:181619	343	PRK	Bacteria:48	PRK09039, PRK09039, hypothetical protein; Validated.
CDD:181620	214	PRK	Bacteria:51	PRK09040, PRK09040, hypothetical protein; Provisional.
CDD:236365	317	PRK	Bacteria:141	PRK09041, motB, flagellar motor protein MotB; Validated.
CDD:236366	443	PRK	Bacteria:58,nodiv:1	PRK09045, PRK09045, N-ethylammeline chlorohydrolase; Provisional.
CDD:236367	161	PRK	Bacteria:73	PRK09047, PRK09047, RNA polymerase factor sigma-70; Validated.
CDD:181624	401	PRK	Bacteria:127,nodiv:1	PRK09050, PRK09050, beta-ketoadipyl CoA thiolase; Validated.
CDD:181625	394	PRK	Bacteria:74	PRK09051, PRK09051, beta-ketothiolase; Provisional.
CDD:181626	399	PRK	Bacteria:86	PRK09052, PRK09052, acetyl-CoA acetyltransferase; Provisional.
CDD:181627	452	PRK	Bacteria:55	PRK09053, PRK09053, 3-carboxy-cis,cis-muconate cycloisomerase; Provisional.
CDD:181628	603	PRK	Bacteria:319	PRK09054, PRK09054, phosphogluconate dehydratase; Validated.
CDD:181629	380	PRK	Bacteria:62,nodiv:1	PRK09057, PRK09057, coproporphyrinogen III oxidase; Provisional.
CDD:236368	449	PRK	Bacteria:61	PRK09058, PRK09058, coproporphyrinogen III oxidase; Provisional.
CDD:181632	444	PRK	Bacteria:69	PRK09060, PRK09060, dihydroorotase; Validated.
CDD:236369	509	PRK	Bacteria:12	PRK09061, PRK09061, D-glutamate deacylase; Validated.
CDD:236370	407	PRK	Bacteria:117,nodiv:1	PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
CDD:181635	237	PRK	Bacteria:35	PRK09065, PRK09065, glutamine amidotransferase; Provisional.
CDD:181637	323	PRK	Bacteria:44	PRK09071, PRK09071, hypothetical protein; Validated.
CDD:236372	263	PRK	Bacteria:28	PRK09072, PRK09072, short chain dehydrogenase; Provisional.
CDD:236373	258	PRK	Bacteria:79	PRK09076, PRK09076, enoyl-CoA hydratase; Provisional.
CDD:236374	536	PRK	Bacteria:189	PRK09077, PRK09077, L-aspartate oxidase; Provisional.
CDD:236375	598	PRK	Bacteria:128	PRK09078, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed.
CDD:181642	386	PRK	Bacteria:164	PRK09082, PRK09082, methionine aminotransferase; Validated.
CDD:236376	448	PRK	Bacteria:155	PRK09084, PRK09084, aspartate kinase III; Validated.
CDD:236377	114	PRK	Bacteria:114	PRK09094, PRK09094, putative monovalent cation/H+ antiporter subunit C; Reviewed.
CDD:181647	376	PRK	Bacteria:180	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed.
CDD:236378	601	PRK	Bacteria:82	PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit alpha; Validated.
CDD:181649	758	PRK	Bacteria:177	PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit alpha; Validated.
CDD:236379	464	PRK	Bacteria:66,nodiv:1	PRK09104, PRK09104, hypothetical protein; Validated.
CDD:181651	370	PRK	Bacteria:19	PRK09105, PRK09105, putative aminotransferase; Provisional.
CDD:181654	246	PRK	Bacteria:45	PRK09109, motC, flagellar motor protein; Reviewed.
CDD:181655	283	PRK	Bacteria:223,nodiv:1	PRK09110, PRK09110, flagellar motor protein MotA; Validated.
CDD:236382	598	PRK	Bacteria:83	PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated.
CDD:169667	351	PRK	Bacteria:25,nodiv:1	PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
CDD:181657	405	PRK	Bacteria:79	PRK09116, PRK09116, 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed.
CDD:236383	275	PRK	Bacteria:62	PRK09120, PRK09120, p-hydroxycinnamoyl CoA hydratase/lyase; Validated.
CDD:236384	479	PRK	Bacteria:96	PRK09123, PRK09123, amidophosphoribosyltransferase; Provisional.
CDD:181661	574	PRK	Bacteria:130	PRK09124, PRK09124, pyruvate dehydrogenase; Provisional.
CDD:181662	282	PRK	Bacteria:91	PRK09125, PRK09125, DNA ligase; Provisional.
CDD:236385	392	PRK	Bacteria:27	PRK09126, PRK09126, hypothetical protein; Provisional.
CDD:236386	776	PRK	Bacteria:108,nodiv:1	PRK09129, PRK09129, NADH dehydrogenase subunit G; Validated.
CDD:236387	687	PRK	Bacteria:117,nodiv:1	PRK09130, PRK09130, NADH dehydrogenase subunit G; Validated.
CDD:236388	472	PRK	Bacteria:20	PRK09133, PRK09133, hypothetical protein; Provisional.
CDD:236389	258	PRK	Bacteria:54,nodiv:1	PRK09134, PRK09134, short chain dehydrogenase; Provisional.
CDD:181668	249	PRK	Bacteria:40	PRK09135, PRK09135, pteridine reductase; Provisional.
CDD:236390	245	PRK	Bacteria:38	PRK09136, PRK09136, 5'-methylthioadenosine phosphorylase; Validated.
CDD:181670	206	PRK	Bacteria:130	PRK09140, PRK09140, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed.
CDD:236391	202	PRK	Bacteria:40	PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated.
CDD:236392	239	PRK	Bacteria:28	PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated.
CDD:236393	396	PRK	Bacteria:108	PRK09147, PRK09147, succinyldiaminopimelate transaminase; Provisional.
CDD:181675	181	PRK	Bacteria:101,nodiv:1	PRK09162, PRK09162, hypoxanthine-guanine phosphoribosyltransferase; Provisional.
CDD:181676	497	PRK	Bacteria:93	PRK09165, PRK09165, replicative DNA helicase; Provisional.
CDD:236394	2316	PRK	Bacteria:5	PRK09169, PRK09169, hypothetical protein; Validated.
CDD:236395	156	PRK	Bacteria:198,nodiv:1	PRK09177, PRK09177, xanthine-guanine phosphoribosyltransferase; Validated.
CDD:236396	475	PRK	Bacteria:35	PRK09181, PRK09181, aspartate kinase; Validated.
CDD:236397	294	PRK	Bacteria:30	PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated.
CDD:236398	392	PRK	Bacteria:111	PRK09185, PRK09185, 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed.
CDD:236399	256	PRK	Bacteria:17	PRK09186, PRK09186, flagellin modification protein A; Provisional.
CDD:169701	240	PRK	Bacteria:20	PRK09189, PRK09189, uroporphyrinogen-III synthase; Validated.
CDD:236401	220	PRK	Bacteria:58	PRK09190, PRK09190, hypothetical protein; Provisional.
CDD:236402	261	PRK	Bacteria:84,nodiv:1	PRK09191, PRK09191, two-component response regulator; Provisional.
CDD:236403	579	PRK	Bacteria:37	PRK09192, PRK09192, acyl-CoA synthetase; Validated.
CDD:236404	1165	PRK	Bacteria:132	PRK09193, PRK09193, indolepyruvate ferredoxin oxidoreductase; Validated.
CDD:236405	565	PRK	Bacteria:713,nodiv:1	PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
CDD:181691	347	PRK	Bacteria:227,nodiv:1	PRK09196, PRK09196, fructose-1,6-bisphosphate aldolase; Reviewed.
CDD:236406	350	PRK	Bacteria:288	PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional.
CDD:236407	463	PRK	Bacteria:83	PRK09198, PRK09198, putative nicotinate phosphoribosyltransferase; Provisional.
CDD:236408	790	PRK	Bacteria:59	PRK09200, PRK09200, preprotein translocase subunit SecA; Reviewed.
CDD:236409	465	PRK	Bacteria:62	PRK09201, PRK09201, amidase; Provisional.
CDD:236410	470	PRK	Bacteria:578,nodiv:1	PRK09202, nusA, transcription elongation factor NusA; Validated.
CDD:236411	138	PRK	Bacteria:961,nodiv:1	PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
CDD:236412	426	PRK	Bacteria:868,nodiv:2	PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
CDD:236413	367	PRK	Bacteria:173	PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated.
CDD:236414	271	PRK	Bacteria:188	PRK09213, PRK09213, pur operon repressor; Provisional.
CDD:181703	144	PRK	Bacteria:940,nodiv:2	PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
CDD:181704	136	PRK	Bacteria:68	PRK09218, PRK09218, peptide deformylase; Validated.
CDD:181705	189	PRK	Bacteria:177	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated.
CDD:236415	204	PRK	Bacteria:59	PRK09220, PRK09220, methylthioribulose-1-phosphate dehydratase; Provisional.
CDD:181707	445	PRK	Bacteria:164	PRK09221, PRK09221, beta alanine--pyruvate transaminase; Provisional.
CDD:236416	482	PRK	Bacteria:53	PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
CDD:236417	504	PRK	Bacteria:288	PRK09224, PRK09224, threonine dehydratase; Reviewed.
CDD:236418	462	PRK	Bacteria:533,nodiv:1	PRK09225, PRK09225, threonine synthase; Validated.
CDD:236419	433	PRK	Bacteria:159	PRK09228, PRK09228, guanine deaminase; Provisional.
CDD:236420	456	PRK	Bacteria:152,nodiv:1	PRK09229, PRK09229, N-formimino-L-glutamate deiminase; Validated.
CDD:236422	843	PRK	Bacteria:52	PRK09234, fbiC, FO synthase; Reviewed.
CDD:181716	444	PRK	Bacteria:65	PRK09236, PRK09236, dihydroorotase; Reviewed.
CDD:236423	380	PRK	Bacteria:102,nodiv:1	PRK09237, PRK09237, dihydroorotase; Provisional.
CDD:236424	835	PRK	Bacteria:372,nodiv:1	PRK09238, PRK09238, bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated.
CDD:181719	104	PRK	Bacteria:54	PRK09239, PRK09239, chorismate mutase; Provisional.
CDD:236425	371	PRK	Bacteria:182	PRK09240, thiH, thiamine biosynthesis protein ThiH; Reviewed.
CDD:236426	464	PRK	Bacteria:315,nodiv:1	PRK09243, PRK09243, nicotinate phosphoribosyltransferase; Validated.
CDD:181723	266	PRK	Bacteria:29	PRK09245, PRK09245, enoyl-CoA hydratase; Provisional.
CDD:236427	501	PRK	Bacteria:333,nodiv:1	PRK09246, PRK09246, amidophosphoribosyltransferase; Provisional.
CDD:236428	539	PRK	Bacteria:90,nodiv:1	PRK09247, PRK09247, ATP-dependent DNA ligase; Validated.
CDD:236429	246	PRK	Bacteria:159	PRK09248, PRK09248, putative hydrolase; Validated.
CDD:236430	453	PRK	Bacteria:386,nodiv:1	PRK09249, PRK09249, coproporphyrinogen III oxidase; Provisional.
CDD:236431	348	PRK	Bacteria:156	PRK09250, PRK09250, fructose-bisphosphate aldolase; Provisional.
CDD:236432	531	PRK	Bacteria:226	PRK09255, PRK09255, malate synthase; Validated.
CDD:181730	138	PRK	Bacteria:270,nodiv:2	PRK09256, PRK09256, hypothetical protein; Provisional.
CDD:181731	396	PRK	Bacteria:329	PRK09257, PRK09257, aromatic amino acid aminotransferase; Provisional.
CDD:181732	338	PRK	Bacteria:68	PRK09258, PRK09258, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed.
CDD:236433	569	PRK	Bacteria:83	PRK09259, PRK09259, putative oxalyl-CoA decarboxylase; Validated.
CDD:236435	349	PRK	Bacteria:514,nodiv:1	PRK09261, PRK09261, phospho-2-dehydro-3-deoxyheptonate aldolase; Validated.
CDD:181735	225	PRK	Bacteria:64	PRK09262, PRK09262, hypothetical protein; Provisional.
CDD:236436	711	PRK	Bacteria:264	PRK09263, PRK09263, anaerobic ribonucleoside triphosphate reductase; Provisional.
CDD:236437	425	PRK	Bacteria:102	PRK09264, PRK09264, diaminobutyrate--2-oxoglutarate aminotransferase; Validated.
CDD:181738	404	PRK	Bacteria:352	PRK09265, PRK09265, aminotransferase AlaT; Validated.
CDD:236438	266	PRK	Bacteria:29	PRK09266, PRK09266, hypothetical protein; Provisional.
CDD:236439	169	PRK	Bacteria:216	PRK09267, PRK09267, flavodoxin FldA; Validated.
CDD:236440	427	PRK	Bacteria:109	PRK09268, PRK09268, acetyl-CoA acetyltransferase; Provisional.
CDD:236441	193	PRK	Bacteria:64	PRK09269, PRK09269, chorismate mutase; Provisional.
CDD:236442	229	PRK	Bacteria:87,nodiv:1	PRK09270, PRK09270, nucleoside triphosphate hydrolase domain-containing protein; Reviewed.
CDD:181745	109	PRK	Bacteria:79	PRK09272, PRK09272, hypothetical protein; Provisional.
CDD:181746	211	PRK	Bacteria:111	PRK09273, PRK09273, hypothetical protein; Provisional.
CDD:236443	552	PRK	Bacteria:60	PRK09274, PRK09274, peptide synthase; Provisional.
CDD:236444	527	PRK	Bacteria:62	PRK09275, PRK09275, aspartate aminotransferase; Provisional.
CDD:181749	385	PRK	Bacteria:38	PRK09276, PRK09276, LL-diaminopimelate aminotransferase; Provisional.
CDD:236445	888	PRK	Bacteria:519,nodiv:1	PRK09277, PRK09277, aconitate hydratase; Validated.
CDD:236446	879	PRK	Bacteria:362,nodiv:1	PRK09279, PRK09279, pyruvate phosphate dikinase; Provisional.
CDD:236447	463	PRK	Bacteria:915,nodiv:2	PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
CDD:236448	502	PRK	Bacteria:878,nodiv:1	PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
CDD:236449	592	PRK	Bacteria:92	PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
CDD:236450	323	PRK	Bacteria:913,nodiv:2	PRK09283, PRK09283, delta-aminolevulinic acid dehydratase; Validated.
CDD:236451	607	PRK	Bacteria:456,nodiv:2	PRK09284, PRK09284, thiamine biosynthesis protein ThiC; Provisional.
CDD:236452	456	PRK	Bacteria:393,nodiv:1	PRK09285, PRK09285, adenylosuccinate lyase; Provisional.
CDD:236453	459	PRK	Bacteria:476	PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
CDD:236454	395	PRK	Bacteria:354	PRK09288, purT, phosphoribosylglycinamide formyltransferase 2; Validated.
CDD:236455	194	PRK	Bacteria:757,nodiv:2	PRK09289, PRK09289, riboflavin synthase subunit alpha; Provisional.
CDD:236456	413	PRK	Bacteria:287,nodiv:1	PRK09290, PRK09290, allantoate amidohydrolase; Reviewed.
CDD:181762	257	PRK	Bacteria:30	PRK09291, PRK09291, short chain dehydrogenase; Provisional.
CDD:236457	209	PRK	Bacteria:139	PRK09292, PRK09292, Na(+)-translocating NADH-quinone reductase subunit D; Validated.
CDD:236458	327	PRK	Bacteria:393	PRK09293, PRK09293, fructose-1,6-bisphosphatase; Provisional.
CDD:181765	416	PRK	Bacteria:21	PRK09294, PRK09294, acyltransferase PapA5; Provisional.
CDD:181767	138	PRK	Bacteria:86	PRK09296, PRK09296, cysteine desufuration protein SufE; Provisional.
CDD:236459	169	PRK	Bacteria:40	PRK09297, PRK09297, tRNA-splicing endonuclease subunit alpha; Reviewed.
CDD:236460	330	PRK	Bacteria:27	PRK09300, PRK09300, tRNA splicing endonuclease; Reviewed.
CDD:236461	509	PRK	Bacteria:68	PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
CDD:236462	380	PRK	Bacteria:36	PRK09303, PRK09303, adaptive-response sensory kinase; Validated.
CDD:181774	402	PRK	Bacteria:94	PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional.
CDD:181775	339	PRK	Bacteria:29	PRK09314, PRK09314, bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional.
CDD:236465	555	PRK	Bacteria:34	PRK09319, PRK09319, bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II/unknown domain fusion protein; Provisional.
CDD:236466	282	PRK	Bacteria:26	PRK09325, PRK09325, coenzyme F420-reducing hydrogenase subunit beta; Validated.
CDD:236467	275	PRK	Bacteria:792,nodiv:1	PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional.
CDD:236468	384	PRK	Bacteria:800,nodiv:1	PRK09330, PRK09330, cell division protein FtsZ; Validated.
CDD:236469	387	PRK	Bacteria:32	PRK09331, PRK09331, Sep-tRNA:Cys-tRNA synthetase; Provisional.
CDD:236470	150	PRK	Bacteria:81	PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional.
CDD:181784	86	PRK	Bacteria:24	PRK09334, PRK09334, 30S ribosomal protein S25e; Provisional.
CDD:236471	526	PRK	Bacteria:434,nodiv:2	PRK09344, PRK09344, phosphoenolpyruvate carboxykinase; Provisional.
CDD:236472	188	PRK	Bacteria:570,nodiv:1	PRK09347, folE, GTP cyclohydrolase I; Provisional.
CDD:236473	283	PRK	Bacteria:713,nodiv:2	PRK09348, glyQ, glycyl-tRNA synthetase subunit alpha; Validated.
CDD:236474	306	PRK	Bacteria:137	PRK09350, PRK09350, poxB regulator PoxA; Provisional.
CDD:236475	319	PRK	Bacteria:593,nodiv:1	PRK09352, PRK09352, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed.
CDD:236476	349	PRK	Bacteria:863,nodiv:2	PRK09354, recA, recombinase A; Provisional.
CDD:236477	263	PRK	Bacteria:237	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated.
CDD:236478	406	PRK	Bacteria:324,nodiv:1	PRK09356, PRK09356, imidazolonepropionase; Validated.
CDD:236479	423	PRK	Bacteria:262	PRK09357, pyrC, dihydroorotase; Validated.
CDD:236480	340	PRK	Bacteria:339,nodiv:1	PRK09358, PRK09358, adenosine deaminase; Provisional.
CDD:236481	415	PRK	Bacteria:106	PRK09360, lamB, maltoporin; Provisional.
CDD:236482	225	PRK	Bacteria:47	PRK09361, radB, DNA repair and recombination protein RadB; Provisional.
CDD:181800	238	PRK	Bacteria:560,nodiv:2	PRK09362, PRK09362, phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed.
CDD:236483	159	PRK	Bacteria:348	PRK09364, moaC, molybdenum cofactor biosynthesis protein MoaC; Provisional.
CDD:236484	500	PRK	Bacteria:355	PRK09367, PRK09367, histidine ammonia-lyase; Provisional.
CDD:236486	417	PRK	Bacteria:867,nodiv:2	PRK09369, PRK09369, UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated.
CDD:236487	159	PRK	Bacteria:293	PRK09372, PRK09372, ribonuclease activity regulator protein RraA; Provisional.
CDD:236488	276	PRK	Bacteria:1039,nodiv:1	PRK09374, rplB, 50S ribosomal protein L2; Validated.
CDD:236489	319	PRK	Bacteria:679,nodiv:2	PRK09375, PRK09375, quinolinate synthetase; Provisional.
CDD:236490	416	PRK	Bacteria:693,nodiv:1	PRK09376, rho, transcription termination factor Rho; Provisional.
CDD:236491	290	PRK	Bacteria:822,nodiv:2	PRK09377, tsf, elongation factor Ts; Provisional.
CDD:236492	378	PRK	Bacteria:64,nodiv:1	PRK09382, ispDF, bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional.
CDD:236493	488	PRK	Bacteria:36	PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
CDD:181815	202	PRK	Bacteria:20	PRK09390, fixJ, response regulator FixJ; Provisional.
CDD:236494	230	PRK	Bacteria:17	PRK09391, fixK, transcriptional regulator FixK; Provisional.
CDD:181817	236	PRK	Bacteria:19	PRK09392, ftrB, transcriptional activator FtrB; Provisional.
CDD:181818	322	PRK	Bacteria:50	PRK09393, ftrA, transcriptional activator FtrA; Provisional.
CDD:236495	551	PRK	Bacteria:165	PRK09395, actP, acetate permease; Provisional.
CDD:236497	61	PRK	Bacteria:57	PRK09400, secE, preprotein translocase subunit SecE; Reviewed.
CDD:236498	1176	PRK	Bacteria:40	PRK09401, PRK09401, reverse gyrase; Reviewed.
CDD:236499	924	PRK	Bacteria:543,nodiv:2	PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component; Reviewed.
CDD:236500	891	PRK	Bacteria:436,nodiv:1	PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
CDD:236501	524	PRK	Bacteria:45	PRK09407, gabD2, succinic semialdehyde dehydrogenase; Reviewed.
CDD:236502	452	PRK	Bacteria:231	PRK09410, ulaA, PTS system ascorbate-specific transporter subunit IIC; Reviewed.
CDD:236503	433	PRK	Bacteria:190	PRK09412, PRK09412, anaerobic C4-dicarboxylate transporter; Reviewed.
CDD:181834	445	PRK	Bacteria:405	PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
CDD:181837	193	PRK	Bacteria:213	PRK09417, mogA, molybdenum cofactor biosynthesis protein MogA; Provisional.
CDD:236506	649	PRK	Bacteria:142	PRK09420, cpdB, bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed.
CDD:181841	229	PRK	Bacteria:157,nodiv:1	PRK09421, modB, molybdate ABC transporter permease protein; Reviewed.
CDD:181843	366	PRK	Bacteria:172	PRK09423, gldA, glycerol dehydrogenase; Provisional.
CDD:236507	509	PRK	Bacteria:215	PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
CDD:181845	480	PRK	Bacteria:167,nodiv:1	PRK09425, prpD, 2-methylcitrate dehydratase; Provisional.
CDD:236508	714	PRK	Bacteria:216	PRK09426, PRK09426, methylmalonyl-CoA mutase; Reviewed.
CDD:236509	454	PRK	Bacteria:185	PRK09427, PRK09427, bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional.
CDD:236510	451	PRK	Bacteria:167	PRK09428, pssA, phosphatidylserine synthase; Provisional.
CDD:236511	275	PRK	Bacteria:188,nodiv:1	PRK09429, mepA, penicillin-insensitive murein endopeptidase; Reviewed.
CDD:236512	267	PRK	Bacteria:164,nodiv:1	PRK09430, djlA, Dna-J like membrane chaperone protein; Provisional.
CDD:236513	554	PRK	Bacteria:182	PRK09431, asnB, asparagine synthetase B; Provisional.
CDD:181853	525	PRK	Bacteria:146	PRK09433, thiP, thiamine transporter membrane protein; Reviewed.
CDD:236514	304	PRK	Bacteria:58	PRK09434, PRK09434, aminoimidazole riboside kinase; Provisional.
CDD:236515	332	PRK	Bacteria:170	PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
CDD:181856	819	PRK	Bacteria:201	PRK09436, thrA, bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional.
CDD:181857	154	PRK	Bacteria:141	PRK09437, bcp, thioredoxin-dependent thiol peroxidase; Reviewed.
CDD:236516	148	PRK	Bacteria:148	PRK09438, nudB, dihydroneopterin triphosphate pyrophosphatase; Provisional.
CDD:181859	169	PRK	Bacteria:156	PRK09439, PRK09439, PTS system glucose-specific transporter subunit; Provisional.
CDD:236517	416	PRK	Bacteria:156	PRK09440, avtA, valine--pyruvate transaminase; Provisional.
CDD:236518	479	PRK	Bacteria:147,nodiv:1	PRK09441, PRK09441, cytoplasmic alpha-amylase; Reviewed.
CDD:236519	483	PRK	Bacteria:165	PRK09442, panF, sodium/panthothenate symporter; Provisional.
CDD:236521	162	PRK	Bacteria:121	PRK09448, PRK09448, DNA starvation/stationary phase protection protein Dps; Provisional.
CDD:181865	224	PRK	Bacteria:125	PRK09449, PRK09449, dUMP phosphatase; Provisional.
CDD:236522	830	PRK	Bacteria:175	PRK09450, cyaA, adenylate cyclase; Provisional.
CDD:236523	375	PRK	Bacteria:114	PRK09452, potA, putrescine/spermidine ABC transporter ATPase protein; Reviewed.
CDD:181869	182	PRK	Bacteria:129	PRK09453, PRK09453, phosphodiesterase; Provisional.
CDD:236524	249	PRK	Bacteria:128	PRK09454, ugpQ, cytoplasmic glycerophosphodiester phosphodiesterase; Provisional.
CDD:236525	319	PRK	Bacteria:118	PRK09455, rseB, anti-sigma E factor; Provisional.
CDD:181873	487	PRK	Bacteria:142	PRK09457, astD, succinylglutamic semialdehyde dehydrogenase; Reviewed.
CDD:236526	75	PRK	Bacteria:136	PRK09458, pspB, phage shock protein B; Provisional.
CDD:181875	76	PRK	Bacteria:90	PRK09459, pspG, phage shock protein G; Reviewed.
CDD:181876	335	PRK	Bacteria:134	PRK09461, ansA, cytoplasmic asparaginase I; Provisional.
CDD:236528	777	PRK	Bacteria:224,nodiv:1	PRK09463, fadE, acyl-CoA dehydrogenase; Reviewed.
CDD:181879	254	PRK	Bacteria:136	PRK09464, pdhR, transcriptional regulator PdhR; Reviewed.
CDD:236529	446	PRK	Bacteria:134	PRK09465, tolC, outer membrane channel protein; Reviewed.
CDD:236530	810	PRK	Bacteria:134	PRK09466, metL, bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional.
CDD:236531	435	PRK	Bacteria:132	PRK09467, envZ, osmolarity sensor protein; Provisional.
CDD:181883	239	PRK	Bacteria:216	PRK09468, ompR, osmolarity response regulator; Provisional.
CDD:236532	461	PRK	Bacteria:117	PRK09470, cpxA, two-component sensor protein; Provisional.
CDD:236533	396	PRK	Bacteria:111	PRK09474, malE, maltose ABC transporter periplasmic protein; Reviewed.
CDD:236534	254	PRK	Bacteria:109	PRK09476, napG, quinol dehydrogenase periplasmic component; Provisional.
CDD:236535	271	PRK	Bacteria:107	PRK09477, napH, quinol dehydrogenase membrane component; Provisional.
CDD:236536	319	PRK	Bacteria:453	PRK09479, glpX, fructose 1,6-bisphosphatase II; Reviewed.
CDD:181894	194	PRK	Bacteria:220	PRK09480, slmA, division inhibitor protein; Provisional.
CDD:181896	256	PRK	Bacteria:114	PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
CDD:181898	183	PRK	Bacteria:129	PRK09484, PRK09484, 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; Provisional.
CDD:181899	304	PRK	Bacteria:103	PRK09485, mmuM, homocysteine methyltransferase; Provisional.
CDD:181902	342	PRK	Bacteria:108	PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase; Provisional.
CDD:236539	1229	PRK	Bacteria:286,nodiv:1	PRK09490, metH, B12-dependent methionine synthase; Provisional.
CDD:181904	146	PRK	Bacteria:102	PRK09491, rimI, ribosomal-protein-alanine N-acetyltransferase; Provisional.
CDD:181905	315	PRK	Bacteria:96	PRK09492, treR, trehalose repressor; Provisional.
CDD:236541	453	PRK	Bacteria:364	PRK09496, trkA, potassium transporter peripheral membrane component; Reviewed.
CDD:236542	256	PRK	Bacteria:110	PRK09500, potC, spermidine/putrescine ABC transporter membrane protein; Reviewed.
CDD:236543	683	PRK	Bacteria:90	PRK09505, malS, alpha-amylase; Reviewed.
CDD:181918	314	PRK	Bacteria:92	PRK09508, leuO, leucine transcriptional activator; Reviewed.
CDD:181921	108	PRK	Bacteria:96	PRK09511, nirD, nitrite reductase small subunit; Provisional.
CDD:181924	140	PRK	Bacteria:121	PRK09514, zntR, zinc-responsive transcriptional regulator; Provisional.
CDD:236547	189	PRK	Bacteria:21	PRK09521, PRK09521, exosome complex RNA-binding protein Csl4; Provisional.
CDD:236548	1027	PRK	Bacteria:82	PRK09525, lacZ, beta-D-galactosidase; Reviewed.
CDD:181929	342	PRK	Bacteria:62	PRK09526, lacI, lac repressor; Reviewed.
CDD:236549	420	PRK	Bacteria:82	PRK09528, lacY, galactoside permease; Reviewed.
CDD:236550	711	PRK	Bacteria:35	PRK09529, PRK09529, bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta; Reviewed.
CDD:236551	948	PRK	Bacteria:32	PRK09533, PRK09533, bifunctional transaldolase/phosoglucose isomerase; Validated.
CDD:236557	445	PRK	Bacteria:48	PRK09542, manB, phosphomannomutase/phosphoglucomutase; Reviewed.
CDD:236558	311	PRK	Bacteria:108	PRK09545, znuA, high-affinity zinc transporter periplasmic component; Reviewed.
CDD:181941	324	PRK	Bacteria:98	PRK09546, zntB, zinc transporter; Reviewed.
CDD:181942	513	PRK	Bacteria:156	PRK09547, nhaB, sodium/proton antiporter; Reviewed.
CDD:236560	407	PRK	Bacteria:39	PRK09549, mtnW, 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed.
CDD:236561	401	PRK	Bacteria:107	PRK09550, mtnK, methylthioribose kinase; Reviewed.
CDD:236562	219	PRK	Bacteria:37	PRK09552, mtnX, 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed.
CDD:236566	551	PRK	Bacteria:138	PRK09558, ushA, bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed.
CDD:236568	389	PRK	Bacteria:63	PRK09560, nhaA, pH-dependent sodium/proton antiporter; Reviewed.
CDD:181955	388	PRK	Bacteria:127	PRK09561, nhaA, pH-dependent sodium/proton antiporter; Reviewed.
CDD:236569	262	PRK	Bacteria:302,nodiv:1	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed.
CDD:236570	287	PRK	Bacteria:237	PRK09563, rbgA, GTPase YlqF; Reviewed.
CDD:236572	513	PRK	Bacteria:26	PRK09566, nirA, ferredoxin-nitrite reductase; Reviewed.
CDD:236573	593	PRK	Bacteria:25	PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
CDD:236575	79	PRK	Bacteria:74	PRK09570, rpoH, DNA-directed RNA polymerase subunit H; Reviewed.
CDD:181963	279	PRK	Bacteria:24	PRK09573, PRK09573, (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase; Reviewed.
CDD:236576	453	PRK	Bacteria:19	PRK09575, vmrA, multidrug efflux pump VmrA; Reviewed.
CDD:236577	457	PRK	Bacteria:64	PRK09581, pleD, response regulator PleD; Reviewed.
CDD:236578	241	PRK	Bacteria:24	PRK09583, PRK09583, mycothiol-dependent maleylpyruvate isomerase; Reviewed.
CDD:236579	365	PRK	Bacteria:479,nodiv:2	PRK09585, anmK, anhydro-N-acetylmuramic acid kinase; Reviewed.
CDD:181972	376	PRK	Bacteria:59	PRK09588, PRK09588, hypothetical protein; Reviewed.
CDD:236582	301	PRK	Bacteria:241,nodiv:1	PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein; Reviewed.
CDD:236583	364	PRK	Bacteria:937,nodiv:2	PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
CDD:236584	396	PRK	Bacteria:74	PRK09602, PRK09602, translation-associated GTPase; Reviewed.
CDD:236585	332	PRK	Bacteria:854,nodiv:2	PRK09604, PRK09604, UGMP family protein; Validated.
CDD:236586	535	PRK	Bacteria:37	PRK09605, PRK09605, bifunctional UGMP family protein/serine/threonine protein kinase; Validated.
CDD:236587	494	PRK	Bacteria:44	PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated.
CDD:236588	132	PRK	Bacteria:79	PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
CDD:181988	312	PRK	Bacteria:17	PRK09609, PRK09609, hypothetical protein; Provisional.
CDD:236589	238	PRK	Bacteria:80	PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
CDD:236590	469	PRK	Bacteria:94	PRK09613, thiH, thiamine biosynthesis protein ThiH; Reviewed.
CDD:236591	324	PRK	Bacteria:415,nodiv:1	PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta; Reviewed.
CDD:236592	552	PRK	Bacteria:94	PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta; Reviewed.
CDD:236594	142	PRK	Bacteria:23	PRK09618, flgD, flagellar basal body rod modification protein; Provisional.
CDD:236599	764	PRK	Bacteria:35	PRK09632, PRK09632, ATP-dependent DNA ligase; Reviewed.
CDD:182006	610	PRK	Bacteria:7	PRK09633, ligD, ATP-dependent DNA ligase; Reviewed.
CDD:182007	207	PRK	Bacteria:38	PRK09634, nusB, transcription antitermination protein NusB; Provisional.
CDD:236600	293	PRK	Bacteria:70	PRK09636, PRK09636, RNA polymerase sigma factor SigJ; Provisional.
CDD:236601	181	PRK	Bacteria:14	PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional.
CDD:182010	176	PRK	Bacteria:13	PRK09638, PRK09638, RNA polymerase sigma factor SigY; Reviewed.
CDD:236602	166	PRK	Bacteria:41	PRK09639, PRK09639, RNA polymerase sigma factor SigX; Provisional.
CDD:236604	192	PRK	Bacteria:25	PRK09643, PRK09643, RNA polymerase sigma factor SigM; Reviewed.
CDD:236605	173	PRK	Bacteria:27	PRK09645, PRK09645, RNA polymerase sigma factor SigL; Provisional.
CDD:182015	194	PRK	Bacteria:27	PRK09646, PRK09646, RNA polymerase sigma factor SigK; Reviewed.
CDD:236607	189	PRK	Bacteria:38	PRK09648, PRK09648, RNA polymerase sigma factor SigD; Reviewed.
CDD:236608	182	PRK	Bacteria:335	PRK09652, PRK09652, RNA polymerase sigma factor RpoE; Provisional.
CDD:236609	324	PRK	Bacteria:227	PRK09653, eutD, phosphotransacetylase; Reviewed.
CDD:236611	305	PRK	Bacteria:7	PRK09672, PRK09672, phage exclusion protein Lit; Provisional.
CDD:236612	302	PRK	Bacteria:29	PRK09685, PRK09685, DNA-binding transcriptional activator FeaR; Provisional.
CDD:182034	302	PRK	Bacteria:28	PRK09698, PRK09698, D-allose kinase; Provisional.
CDD:236616	229	PRK	Bacteria:39	PRK09722, PRK09722, allulose-6-phosphate 3-epimerase; Provisional.
CDD:236618	352	PRK	Bacteria:27	PRK09736, PRK09736, 5-methylcytosine-specific restriction enzyme subunit McrC; Provisional.
CDD:236623	442	PRK	Bacteria:35	PRK09775, PRK09775, putative DNA-binding transcriptional regulator; Provisional.
CDD:236626	333	PRK	Bacteria:33	PRK09814, PRK09814, beta-1,6-galactofuranosyltransferase; Provisional.
CDD:182093	875	PRK	Bacteria:38	PRK09819, PRK09819, alpha-mannosidase; Provisional.
CDD:182100	263	PRK	Bacteria:41	PRK09834, PRK09834, DNA-binding transcriptional activator MhpR; Provisional.
CDD:236628	266	PRK	Bacteria:24	PRK09846, recT, recombination and repair protein RecT; Reviewed.
CDD:236629	702	PRK	Bacteria:44	PRK09849, PRK09849, putative oxidoreductase; Provisional.
CDD:236630	1019	PRK	Bacteria:55	PRK09853, PRK09853, putative selenate reductase subunit YgfK; Provisional.
CDD:182133	296	PRK	Bacteria:38	PRK09894, PRK09894, diguanylate cyclase; Provisional.
CDD:236632	230	PRK	Bacteria:33	PRK09918, PRK09918, putative fimbrial chaperone protein; Provisional.
CDD:236633	114	PRK	Bacteria:32	PRK09919, PRK09919, anti-adapter protein IraM; Provisional.
CDD:236638	111	PRK	Bacteria:38	PRK09974, PRK09974, putative regulator PrlF; Provisional.
CDD:236647	183	PRK	Bacteria:43	PRK10069, PRK10069, 3-phenylpropionate dioxygenase subunit beta; Provisional.
CDD:182223	328	PRK	Bacteria:60	PRK10073, PRK10073, putative glycosyl transferase; Provisional.
CDD:182231	311	PRK	Bacteria:55	PRK10086, PRK10086, DNA-binding transcriptional regulator DsdC; Provisional.
CDD:182232	112	PRK	Bacteria:151	PRK10089, PRK10089, tRNA-binding protein; Provisional.
CDD:236655	196	PRK	Bacteria:112	PRK10147, phnH, carbon-phosphorus lyase complex subunit; Validated.
CDD:236657	604	PRK	Bacteria:58	PRK10150, PRK10150, beta-D-glucuronidase; Provisional.
CDD:236658	517	PRK	Bacteria:60	PRK10153, PRK10153, DNA-binding transcriptional activator CadC; Provisional.
CDD:236662	184	PRK	Bacteria:54	PRK10178, PRK10178, D-alanyl-D-alanine dipeptidase; Provisional.
CDD:236666	88	PRK	Bacteria:71	PRK10244, PRK10244, anti-RssB factor; Provisional.
CDD:236668	1296	PRK	Bacteria:70	PRK10252, entF, enterobactin synthase subunit F; Provisional.
CDD:236670	412	PRK	Bacteria:67	PRK10307, PRK10307, putative glycosyl transferase; Provisional.
CDD:236676	290	PRK	Bacteria:64,nodiv:1	PRK10376, PRK10376, putative oxidoreductase; Provisional.
CDD:182422	377	PRK	Bacteria:66	PRK10381, PRK10381, LPS O-antigen length regulator; Provisional.
CDD:236679	210	PRK	Bacteria:106	PRK10387, PRK10387, glutaredoxin 2; Provisional.
CDD:236683	100	PRK	Bacteria:123	PRK10410, PRK10410, hypothetical protein; Provisional.
CDD:236686	318	PRK	Bacteria:773,nodiv:1	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional.
CDD:236691	635	PRK	Bacteria:54	PRK10426, PRK10426, alpha-glucosidase; Provisional.
CDD:236693	228	PRK	Bacteria:77	PRK10433, PRK10433, putative RNA methyltransferase; Provisional.
CDD:236694	462	PRK	Bacteria:84	PRK10436, PRK10436, hypothetical protein; Provisional.
CDD:236695	411	PRK	Bacteria:71	PRK10439, PRK10439, enterobactin/ferric enterobactin esterase; Provisional.
CDD:182467	263	PRK	Bacteria:75	PRK10445, PRK10445, endonuclease VIII; Provisional.
CDD:236697	492	PRK	Bacteria:58	PRK10459, PRK10459, colanic acid exporter; Provisional.
CDD:182480	159	PRK	Bacteria:70	PRK10465, PRK10465, hydrogenase 2-specific chaperone; Provisional.
CDD:182488	346	PRK	Bacteria:68	PRK10476, PRK10476, multidrug resistance protein MdtN; Provisional.
CDD:182491	224	PRK	Bacteria:77	PRK10481, PRK10481, hypothetical protein; Provisional.
CDD:236699	523	PRK	Bacteria:60	PRK10484, PRK10484, putative transporter; Provisional.
CDD:236700	417	PRK	Bacteria:74	PRK10489, PRK10489, enterobactin exporter EntS; Provisional.
CDD:236702	259	PRK	Bacteria:84	PRK10494, PRK10494, hypothetical protein; Provisional.
CDD:236703	182	PRK	Bacteria:75	PRK10502, PRK10502, putative acyl transferase; Provisional.
CDD:236704	162	PRK	Bacteria:76	PRK10506, PRK10506, hypothetical protein; Provisional.
CDD:182510	145	PRK	Bacteria:67,nodiv:1	PRK10514, PRK10514, putative acetyltransferase; Provisional.
CDD:236706	476	PRK	Bacteria:85	PRK10518, PRK10518, alkaline phosphatase; Provisional.
CDD:182513	151	PRK	Bacteria:79	PRK10519, PRK10519, hypothetical protein; Provisional.
CDD:236707	547	PRK	Bacteria:83	PRK10522, PRK10522, multidrug transporter membrane component/ATP-binding component; Provisional.
CDD:236708	234	PRK	Bacteria:85	PRK10523, PRK10523, lipoprotein involved with copper homeostasis and adhesion; Provisional.
CDD:182517	629	PRK	Bacteria:91	PRK10524, prpE, propionyl-CoA synthetase; Provisional.
CDD:182523	272	PRK	Bacteria:90	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional.
CDD:236711	393	PRK	Bacteria:65	PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
CDD:182538	121	PRK	Bacteria:80	PRK10548, PRK10548, flagellar biosynthesis protein FliT; Provisional.
CDD:182539	466	PRK	Bacteria:87	PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional.
CDD:182541	518	PRK	Bacteria:80	PRK10551, PRK10551, phage resistance protein; Provisional.
CDD:236714	192	PRK	Bacteria:80	PRK10557, PRK10557, hypothetical protein; Provisional.
CDD:236715	145	PRK	Bacteria:76	PRK10562, PRK10562, putative acetyltransferase; Provisional.
CDD:236716	303	PRK	Bacteria:91	PRK10564, PRK10564, maltose regulon periplasmic protein; Provisional.
CDD:182555	249	PRK	Bacteria:87	PRK10566, PRK10566, esterase; Provisional.
CDD:182557	191	PRK	Bacteria:79	PRK10569, PRK10569, NAD(P)H-dependent FMN reductase; Provisional.
CDD:236717	290	PRK	Bacteria:94	PRK10572, PRK10572, DNA-binding transcriptional regulator AraC; Provisional.
CDD:182559	399	PRK	Bacteria:89	PRK10573, PRK10573, type IV pilin biogenesis protein; Provisional.
CDD:236718	146	PRK	Bacteria:86	PRK10574, PRK10574, putative major pilin subunit; Provisional.
CDD:236719	292	PRK	Bacteria:83	PRK10576, PRK10576, iron-hydroxamate transporter substrate-binding subunit; Provisional.
CDD:236720	668	PRK	Bacteria:192	PRK10577, PRK10577, iron-hydroxamate transporter permease subunit; Provisional.
CDD:182573	92	PRK	Bacteria:78	PRK10591, PRK10591, hypothetical protein; Provisional.
CDD:236723	608	PRK	Bacteria:87	PRK10594, PRK10594, murein L,D-transpeptidase; Provisional.
CDD:182577	164	PRK	Bacteria:95	PRK10595, PRK10595, SOS cell division inhibitor; Provisional.
CDD:182579	186	PRK	Bacteria:96	PRK10598, PRK10598, lipoprotein; Provisional.
CDD:182581	569	PRK	Bacteria:81	PRK10600, PRK10600, nitrate/nitrite sensor protein NarX; Provisional.
CDD:182582	237	PRK	Bacteria:87	PRK10602, PRK10602, murein peptide amidase A; Provisional.
CDD:236724	433	PRK	Bacteria:90	PRK10604, PRK10604, sensor protein RstB; Provisional.
CDD:236726	894	PRK	Bacteria:84	PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional.
CDD:182595	382	PRK	Bacteria:90	PRK10624, PRK10624, L-1,2-propanediol oxidoreductase; Provisional.
CDD:182597	239	PRK	Bacteria:89	PRK10626, PRK10626, hypothetical protein; Provisional.
CDD:236728	127	PRK	Bacteria:91	PRK10629, PRK10629, EnvZ/OmpR regulon moderator; Provisional.
CDD:236730	614	PRK	Bacteria:89	PRK10641, btuB, vitamin B12/cobalamin outer membrane transporter; Provisional.
CDD:182616	262	PRK	Bacteria:80	PRK10647, PRK10647, ferric iron reductase involved in ferric hydroximate transport; Provisional.
CDD:182623	388	PRK	Bacteria:113	PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional.
CDD:236731	665	PRK	Bacteria:94	PRK10658, PRK10658, putative alpha-glucosidase; Provisional.
CDD:182626	436	PRK	Bacteria:75	PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
CDD:236732	378	PRK	Bacteria:94	PRK10662, PRK10662, beta-lactam binding protein AmpH; Provisional.
CDD:182631	122	PRK	Bacteria:92	PRK10667, PRK10667, Hha toxicity attenuator; Provisional.
CDD:182632	215	PRK	Bacteria:90	PRK10668, PRK10668, DNA-binding transcriptional repressor AcrR; Provisional.
CDD:236733	361	PRK	Bacteria:96	PRK10672, PRK10672, rare lipoprotein A; Provisional.
CDD:236734	472	PRK	Bacteria:87	PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional.
CDD:182640	263	PRK	Bacteria:94	PRK10676, PRK10676, DNA-binding transcriptional regulator ModE; Provisional.
CDD:182651	92	PRK	Bacteria:95	PRK10692, PRK10692, hypothetical protein; Provisional.
CDD:182652	303	PRK	Bacteria:94	PRK10693, PRK10693, response regulator of RpoS; Provisional.
CDD:182654	859	PRK	Bacteria:101	PRK10695, PRK10695, hypothetical protein; Provisional.
CDD:236737	258	PRK	Bacteria:326,nodiv:2	PRK10696, PRK10696, tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional.
CDD:182656	118	PRK	Bacteria:96	PRK10697, PRK10697, DNA-binding transcriptional activator PspC; Provisional.
CDD:182658	244	PRK	Bacteria:88	PRK10699, PRK10699, phosphatidylglycerophosphatase B; Provisional.
CDD:182663	190	PRK	Bacteria:92	PRK10707, PRK10707, putative NUDIX hydrolase; Provisional.
CDD:182670	335	PRK	Bacteria:89	PRK10715, flk, flagella biosynthesis regulator; Provisional.
CDD:182672	330	PRK	Bacteria:184	PRK10717, PRK10717, cysteine synthase A; Provisional.
CDD:236742	191	PRK	Bacteria:93	PRK10718, PRK10718, RpoE-regulated lipoprotein; Provisional.
CDD:236743	475	PRK	Bacteria:92	PRK10719, eutA, reactivating factor for ethanolamine ammonia lyase; Provisional.
CDD:236745	247	PRK	Bacteria:96	PRK10722, PRK10722, hypothetical protein; Provisional.
CDD:182677	243	PRK	Bacteria:88	PRK10723, PRK10723, hypothetical protein; Provisional.
CDD:236746	105	PRK	Bacteria:92	PRK10726, PRK10726, hypothetical protein; Provisional.
CDD:236747	374	PRK	Bacteria:80	PRK10736, PRK10736, hypothetical protein; Provisional.
CDD:182697	330	PRK	Bacteria:93	PRK10749, PRK10749, lysophospholipase L2; Provisional.
CDD:236751	356	PRK	Bacteria:88	PRK10755, PRK10755, sensor protein BasS/PmrB; Provisional.
CDD:236755	501	PRK	Bacteria:104	PRK10762, PRK10762, D-ribose transporter ATP binding protein; Provisional.
CDD:236756	324	PRK	Bacteria:83	PRK10764, PRK10764, potassium-tellurite ethidium and proflavin transporter; Provisional.
CDD:182710	240	PRK	Bacteria:91	PRK10765, PRK10765, nitroreductase A; Provisional.
CDD:236757	371	PRK	Bacteria:391,nodiv:2	PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
CDD:182713	304	PRK	Bacteria:81	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional.
CDD:182716	232	PRK	Bacteria:97	PRK10771, thiQ, thiamine transporter ATP-binding subunit; Provisional.
CDD:182721	129	PRK	Bacteria:86	PRK10776, PRK10776, nucleoside triphosphate pyrophosphohydrolase; Provisional.
CDD:182725	133	PRK	Bacteria:86	PRK10781, rcsF, outer membrane lipoprotein; Reviewed.
CDD:236759	598	PRK	Bacteria:79	PRK10785, PRK10785, maltodextrin glucosidase; Provisional.
CDD:182731	623	PRK	Bacteria:95	PRK10788, PRK10788, periplasmic folding chaperone; Provisional.
CDD:236760	285	PRK	Bacteria:202,nodiv:1	PRK10792, PRK10792, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional.
CDD:236765	98	PRK	Bacteria:82	PRK10810, PRK10810, anti-sigma28 factor FlgM; Provisional.
CDD:236766	1068	PRK	Bacteria:89	PRK10811, rne, ribonuclease E; Reviewed.
CDD:182754	485	PRK	Bacteria:95	PRK10815, PRK10815, sensor protein PhoQ; Provisional.
CDD:236768	246	PRK	Bacteria:93	PRK10819, PRK10819, transport protein TonB; Provisional.
CDD:236770	222	PRK	Bacteria:107	PRK10826, PRK10826, 2-deoxyglucose-6-phosphatase; Provisional.
CDD:236771	373	PRK	Bacteria:95	PRK10829, PRK10829, ribonuclease D; Provisional.
CDD:236772	617	PRK	Bacteria:96	PRK10833, PRK10833, putative assembly protein; Provisional.
CDD:182766	373	PRK	Bacteria:90	PRK10835, PRK10835, hypothetical protein; Provisional.
CDD:182772	924	PRK	Bacteria:97	PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional.
CDD:236776	331	PRK	Bacteria:90	PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional.
CDD:236778	482	PRK	Bacteria:181	PRK10859, PRK10859, membrane-bound lytic transglycosylase F; Provisional.
CDD:182788	154	PRK	Bacteria:93	PRK10862, PRK10862, SoxR reducing system protein RseC; Provisional.
CDD:182789	216	PRK	Bacteria:94	PRK10863, PRK10863, anti-RNA polymerase sigma factor SigE; Provisional.
CDD:236779	346	PRK	Bacteria:94	PRK10864, PRK10864, putative methyltransferase; Provisional.
CDD:236780	433	PRK	Bacteria:870,nodiv:2	PRK10867, PRK10867, signal recognition particle protein; Provisional.
CDD:236781	553	PRK	Bacteria:130	PRK10869, PRK10869, recombination and repair protein; Provisional.
CDD:236783	615	PRK	Bacteria:93	PRK10875, recD, exonuclease V subunit alpha; Provisional.
CDD:236784	1181	PRK	Bacteria:92	PRK10876, recB, exonuclease V subunit beta; Provisional.
CDD:236785	394	PRK	Bacteria:85	PRK10881, PRK10881, putative hydrogenase 2 b cytochrome subunit; Provisional.
CDD:236786	328	PRK	Bacteria:86	PRK10882, PRK10882, hydrogenase 2 protein HybA; Provisional.
CDD:182810	409	PRK	Bacteria:194	PRK10885, cca, multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed.
CDD:236787	443	PRK	Bacteria:285,nodiv:1	PRK10887, glmM, phosphoglucosamine mutase; Provisional.
CDD:236788	192	PRK	Bacteria:96	PRK10893, PRK10893, lipopolysaccharide exporter periplasmic protein; Provisional.
CDD:182820	353	PRK	Bacteria:96	PRK10898, PRK10898, serine endoprotease; Provisional.
CDD:236789	1022	PRK	Bacteria:97	PRK10899, PRK10899, hypothetical protein; Provisional.
CDD:236790	427	PRK	Bacteria:259,nodiv:1	PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
CDD:182828	276	PRK	Bacteria:92	PRK10907, PRK10907, intramembrane serine protease GlpG; Provisional.
CDD:236794	681	PRK	Bacteria:692,nodiv:2	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
CDD:236795	390	PRK	Bacteria:93	PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional.
CDD:236800	565	PRK	Bacteria:103	PRK10935, PRK10935, nitrate/nitrite sensor protein NarQ; Provisional.
CDD:236801	343	PRK	Bacteria:91	PRK10936, PRK10936, TMAO reductase system periplasmic protein TorT; Provisional.
CDD:182852	490	PRK	Bacteria:96	PRK10938, PRK10938, putative molybdenum transport ATP-binding protein ModF; Provisional.
CDD:182853	520	PRK	Bacteria:83	PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
CDD:236803	536	PRK	Bacteria:95	PRK10946, entE, enterobactin synthase subunit E; Provisional.
CDD:236804	424	PRK	Bacteria:81	PRK10948, PRK10948, cysteine desulfurase activator complex subunit SufD; Provisional.
CDD:236806	317	PRK	Bacteria:109	PRK10957, PRK10957, iron-enterobactin transporter periplasmic binding protein; Provisional.
CDD:236807	212	PRK	Bacteria:110	PRK10958, PRK10958, leucine export protein LeuE; Provisional.
CDD:182867	212	PRK	Bacteria:112	PRK10959, PRK10959, outer membrane protein W; Provisional.
CDD:236808	223	PRK	Bacteria:96	PRK10963, PRK10963, hypothetical protein; Provisional.
CDD:236809	322	PRK	Bacteria:102	PRK10964, PRK10964, ADP-heptose:LPS heptosyl transferase I; Provisional.
CDD:236810	523	PRK	Bacteria:102	PRK10965, PRK10965, multicopper oxidase; Provisional.
CDD:182871	407	PRK	Bacteria:97	PRK10966, PRK10966, exonuclease subunit SbcD; Provisional.
CDD:182877	194	PRK	Bacteria:98	PRK10975, PRK10975, TDP-fucosamine acetyltransferase; Provisional.
CDD:182879	509	PRK	Bacteria:99	PRK10977, PRK10977, hypothetical protein; Provisional.
CDD:182882	127	PRK	Bacteria:103	PRK10984, PRK10984, DNA-binding transcriptional regulator Crl; Provisional.
CDD:182883	324	PRK	Bacteria:102	PRK10985, PRK10985, putative hydrolase; Provisional.
CDD:236811	284	PRK	Bacteria:120	PRK10987, PRK10987, regulatory protein AmpE; Provisional.
CDD:182885	588	PRK	Bacteria:99	PRK10991, fucI, L-fucose isomerase; Provisional.
CDD:236812	220	PRK	Bacteria:98	PRK10992, PRK10992, iron-sulfur cluster repair di-iron protein; Provisional.
CDD:236813	314	PRK	Bacteria:81	PRK10993, PRK10993, outer membrane protease; Reviewed.
CDD:236814	221	PRK	Bacteria:98	PRK10995, PRK10995, inner membrane protein; Provisional.
CDD:236815	487	PRK	Bacteria:110	PRK10997, yieM, hypothetical protein; Provisional.
CDD:236816	520	PRK	Bacteria:105	PRK10999, malF, maltose transporter membrane protein; Provisional.
CDD:236817	171	PRK	Bacteria:109	PRK11001, mtlR, mannitol repressor protein; Provisional.
CDD:236818	237	PRK	Bacteria:93	PRK11009, aphA, acid phosphatase/phosphotransferase; Provisional.
CDD:236819	309	PRK	Bacteria:107	PRK11013, PRK11013, DNA-binding transcriptional regulator LysR; Provisional.
CDD:236821	404	PRK	Bacteria:100	PRK11017, codB, cytosine permease; Provisional.
CDD:236822	78	PRK	Bacteria:106	PRK11018, PRK11018, hypothetical protein; Provisional.
CDD:182903	88	PRK	Bacteria:119	PRK11019, PRK11019, hypothetical protein; Provisional.
CDD:182904	118	PRK	Bacteria:119	PRK11020, PRK11020, hypothetical protein; Provisional.
CDD:236823	410	PRK	Bacteria:110	PRK11021, PRK11021, putative transporter; Provisional.
CDD:182907	191	PRK	Bacteria:112	PRK11023, PRK11023, outer membrane lipoprotein; Provisional.
CDD:182910	309	PRK	Bacteria:110	PRK11026, ftsX, cell division ABC transporter subunit FtsX; Provisional.
CDD:236825	112	PRK	Bacteria:151	PRK11027, PRK11027, hypothetical protein; Provisional.
CDD:182912	330	PRK	Bacteria:92	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional.
CDD:236826	496	PRK	Bacteria:102	PRK11031, PRK11031, guanosine pentaphosphate phosphohydrolase; Provisional.
CDD:182915	160	PRK	Bacteria:106	PRK11032, PRK11032, hypothetical protein; Provisional.
CDD:236827	741	PRK	Bacteria:106	PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase; Provisional.
CDD:182918	255	PRK	Bacteria:106	PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional.
CDD:182919	83	PRK	Bacteria:104	PRK11037, PRK11037, hypothetical protein; Provisional.
CDD:182920	47	PRK	Bacteria:90	PRK11038, PRK11038, hypothetical protein; Provisional.
CDD:182924	401	PRK	Bacteria:120	PRK11043, PRK11043, putative transporter; Provisional.
CDD:236829	184	PRK	Bacteria:97	PRK11045, pagP, phospholipid:lipid A palmitoyltransferase; Provisional.
CDD:182927	152	PRK	Bacteria:100	PRK11050, PRK11050, manganese transport regulator MntR; Provisional.
CDD:236831	695	PRK	Bacteria:119	PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
CDD:182929	217	PRK	Bacteria:110	PRK11053, PRK11053, dihydropteridine reductase; Provisional.
CDD:182930	684	PRK	Bacteria:107	PRK11054, helD, DNA helicase IV; Provisional.
CDD:182931	342	PRK	Bacteria:99	PRK11055, galM, galactose-1-epimerase; Provisional.
CDD:236832	120	PRK	Bacteria:109	PRK11056, PRK11056, hypothetical protein; Provisional.
CDD:236833	640	PRK	Bacteria:124	PRK11059, PRK11059, regulatory protein CsrD; Provisional.
CDD:182937	748	PRK	Bacteria:111	PRK11061, PRK11061, fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional.
CDD:182938	296	PRK	Bacteria:124	PRK11062, nhaR, transcriptional activator NhaR; Provisional.
CDD:182940	415	PRK	Bacteria:112	PRK11064, wecC, UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional.
CDD:236835	1122	PRK	Bacteria:106	PRK11069, recC, exonuclease V subunit gamma; Provisional.
CDD:182945	190	PRK	Bacteria:111	PRK11071, PRK11071, esterase YqiA; Provisional.
CDD:236836	943	PRK	Bacteria:215	PRK11072, PRK11072, bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed.
CDD:182948	300	PRK	Bacteria:123	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional.
CDD:236837	229	PRK	Bacteria:115	PRK11081, PRK11081, tRNA guanosine-2'-O-methyltransferase; Provisional.
CDD:236838	228	PRK	Bacteria:101	PRK11083, PRK11083, DNA-binding response regulator CreB; Provisional.
CDD:236839	542	PRK	Bacteria:94	PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional.
CDD:236840	231	PRK	Bacteria:128	PRK11087, PRK11087, oxidative stress defense protein; Provisional.
CDD:236841	272	PRK	Bacteria:102	PRK11088, rrmA, 23S rRNA methyltransferase A; Provisional.
CDD:236842	779	PRK	Bacteria:116	PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional.
CDD:236844	376	PRK	Bacteria:117	PRK11097, PRK11097, endo-1,4-D-glucanase; Provisional.
CDD:182960	409	PRK	Bacteria:104,nodiv:1	PRK11098, PRK11098, microcin B17 transporter; Reviewed.
CDD:236845	399	PRK	Bacteria:107	PRK11099, PRK11099, putative inner membrane protein; Provisional.
CDD:236846	475	PRK	Bacteria:122	PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
CDD:236847	546	PRK	Bacteria:106	PRK11101, glpA, sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional.
CDD:182964	377	PRK	Bacteria:115	PRK11102, PRK11102, bicyclomycin/multidrug efflux system; Provisional.
CDD:182966	177	PRK	Bacteria:108	PRK11104, hemG, protoporphyrinogen oxidase; Provisional.
CDD:236848	919	PRK	Bacteria:127	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional.
CDD:236849	375	PRK	Bacteria:108	PRK11109, PRK11109, bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional.
CDD:236850	214	PRK	Bacteria:128	PRK11111, PRK11111, hypothetical protein; Provisional.
CDD:182971	257	PRK	Bacteria:114	PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
CDD:182972	477	PRK	Bacteria:117	PRK11113, PRK11113, D-alanyl-D-alanine carboxypeptidase/endopeptidase; Provisional.
CDD:236851	756	PRK	Bacteria:120	PRK11114, PRK11114, cellulose synthase regulator protein; Provisional.
CDD:182975	100	PRK	Bacteria:98	PRK11118, PRK11118, putative monooxygenase; Provisional.
CDD:236852	331	PRK	Bacteria:124	PRK11119, proX, glycine betaine transporter periplasmic subunit; Provisional.
CDD:236853	154	PRK	Bacteria:119	PRK11121, nrdG, anaerobic ribonucleotide reductase-activating protein; Provisional.
CDD:182978	222	PRK	Bacteria:125	PRK11122, artM, arginine transporter permease subunit ArtM; Provisional.
CDD:236854	480	PRK	Bacteria:110	PRK11125, nrfA, cytochrome c nitrite reductase subunit c552; Provisional.
CDD:236855	242	PRK	Bacteria:111	PRK11126, PRK11126, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; Provisional.
CDD:236856	382	PRK	Bacteria:117	PRK11128, PRK11128, putative 3-phenylpropionic acid transporter; Provisional.
CDD:182985	81	PRK	Bacteria:101	PRK11130, moaD, molybdopterin synthase small subunit; Provisional.
CDD:182988	322	PRK	Bacteria:118	PRK11133, serB, phosphoserine phosphatase; Provisional.
CDD:236857	394	PRK	Bacteria:134	PRK11138, PRK11138, outer membrane biogenesis protein BamB; Provisional.
CDD:182990	297	PRK	Bacteria:190	PRK11139, PRK11139, DNA-binding transcriptional activator GcvA; Provisional.
CDD:236858	306	PRK	Bacteria:136	PRK11142, PRK11142, ribokinase; Provisional.
CDD:236859	355	PRK	Bacteria:115	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional.
CDD:182993	352	PRK	Bacteria:124	PRK11144, modC, molybdate transporter ATP-binding protein; Provisional.
CDD:236860	412	PRK	Bacteria:121	PRK11146, PRK11146, outer membrane-specific lipoprotein transporter subunit LolE; Provisional.
CDD:236861	635	PRK	Bacteria:141	PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
CDD:182997	275	PRK	Bacteria:109	PRK11148, PRK11148, cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional.
CDD:182999	305	PRK	Bacteria:125	PRK11151, PRK11151, DNA-binding transcriptional regulator OxyR; Provisional.
CDD:236862	76	PRK	Bacteria:129	PRK11152, ilvM, acetolactate synthase 2 regulatory subunit; Provisional.
CDD:236863	343	PRK	Bacteria:221	PRK11153, metN, DL-methionine transporter ATP-binding subunit; Provisional.
CDD:236864	708	PRK	Bacteria:132	PRK11154, fadJ, multifunctional fatty acid oxidation complex subunit alpha; Reviewed.
CDD:236865	574	PRK	Bacteria:154	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed.
CDD:236866	355	PRK	Bacteria:125	PRK11162, mltA, murein transglycosylase A; Provisional.
CDD:236867	420	PRK	Bacteria:131	PRK11165, PRK11165, diaminopimelate decarboxylase; Provisional.
CDD:236868	214	PRK	Bacteria:138	PRK11166, PRK11166, chemotaxis regulator CheZ; Provisional.
CDD:236869	396	PRK	Bacteria:134	PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional.
CDD:183010	382	PRK	Bacteria:123	PRK11170, nagA, N-acetylglucosamine-6-phosphate deacetylase; Provisional.
CDD:183011	266	PRK	Bacteria:143,nodiv:1	PRK11171, PRK11171, hypothetical protein; Provisional.
CDD:183012	267	PRK	Bacteria:123	PRK11172, dkgB, 2,5-diketo-D-gluconate reductase B; Provisional.
CDD:236870	588	PRK	Bacteria:154	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed.
CDD:236871	305	PRK	Bacteria:146	PRK11175, PRK11175, universal stress protein UspE; Provisional.
CDD:183017	575	PRK	Bacteria:134	PRK11177, PRK11177, phosphoenolpyruvate-protein phosphotransferase; Provisional.
CDD:183021	244	PRK	Bacteria:149	PRK11181, PRK11181, 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional.
CDD:236872	564	PRK	Bacteria:159	PRK11183, PRK11183, D-lactate dehydrogenase; Provisional.
CDD:236873	667	PRK	Bacteria:152	PRK11186, PRK11186, carboxy-terminal protease; Provisional.
CDD:236874	182	PRK	Bacteria:140	PRK11187, PRK11187, replication initiation regulator SeqA; Provisional.
CDD:236875	296	PRK	Bacteria:153	PRK11189, PRK11189, lipoprotein NlpI; Provisional.
CDD:236876	138	PRK	Bacteria:156	PRK11191, PRK11191, RNase E inhibitor protein; Provisional.
CDD:236877	434	PRK	Bacteria:148	PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
CDD:236878	172	PRK	Bacteria:150	PRK11193, PRK11193, hypothetical protein; Provisional.
CDD:236879	393	PRK	Bacteria:166	PRK11195, PRK11195, lysophospholipid transporter LplT; Provisional.
CDD:236880	147	PRK	Bacteria:128	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional.
CDD:183035	374	PRK	Bacteria:155	PRK11199, tyrA, bifunctional chorismate mutase/prephenate dehydrogenase; Provisional.
CDD:183036	85	PRK	Bacteria:137	PRK11200, grxA, glutaredoxin 1; Provisional.
CDD:236881	203	PRK	Bacteria:142	PRK11202, PRK11202, DNA-binding transcriptional repressor FabR; Provisional.
CDD:236882	420	PRK	Bacteria:97	PRK11204, PRK11204, N-glycosyltransferase; Provisional.
CDD:236883	330	PRK	Bacteria:115,nodiv:1	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional.
CDD:183041	210	PRK	Bacteria:171	PRK11212, PRK11212, hypothetical protein; Provisional.
CDD:183051	296	PRK	Bacteria:57	PRK11242, PRK11242, DNA-binding transcriptional regulator CynR; Provisional.
CDD:183052	250	PRK	Bacteria:67	PRK11244, phnP, carbon-phosphorus lyase complex accessory protein; Provisional.
CDD:183053	120	PRK	Bacteria:88	PRK11245, folX, D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional.
CDD:236886	752	PRK	Bacteria:88	PRK11249, katE, hydroperoxidase II; Provisional.
CDD:183058	109	PRK	Bacteria:91	PRK11251, PRK11251, DNA-binding transcriptional activator OsmE; Provisional.
CDD:183059	305	PRK	Bacteria:94	PRK11253, ldcA, L,D-carboxypeptidase A; Provisional.
CDD:236887	376	PRK	Bacteria:123	PRK11259, solA, N-methyltryptophan oxidase; Provisional.
CDD:236888	411	PRK	Bacteria:99	PRK11263, PRK11263, cardiolipin synthase 2; Provisional.
CDD:183066	591	PRK	Bacteria:135	PRK11269, PRK11269, glyoxylate carboligase; Provisional.
CDD:183067	292	PRK	Bacteria:100	PRK11272, PRK11272, putative DMT superfamily transporter inner membrane protein; Provisional.
CDD:236890	407	PRK	Bacteria:108	PRK11274, glcF, glycolate oxidase iron-sulfur subunit; Provisional.
CDD:183072	170	PRK	Bacteria:118	PRK11280, PRK11280, hypothetical protein; Provisional.
CDD:236892	1113	PRK	Bacteria:114	PRK11281, PRK11281, hypothetical protein; Provisional.
CDD:236893	352	PRK	Bacteria:100	PRK11282, glcE, glycolate oxidase FAD binding subunit; Provisional.
CDD:183076	333	PRK	Bacteria:114	PRK11285, araH, L-arabinose transporter permease protein; Provisional.
CDD:183077	501	PRK	Bacteria:116	PRK11288, araG, L-arabinose transporter ATP-binding protein; Provisional.
CDD:236894	384	PRK	Bacteria:134,nodiv:1	PRK11289, ampC, beta-lactamase/D-alanine carboxypeptidase; Provisional.
CDD:236895	113	PRK	Bacteria:127	PRK11295, PRK11295, hypothetical protein; Provisional.
CDD:236896	419	PRK	Bacteria:140	PRK11301, livM, leucine/isoleucine/valine transporter permease subunit; Provisional.
CDD:183082	284	PRK	Bacteria:151	PRK11302, PRK11302, DNA-binding transcriptional regulator HexR; Provisional.
CDD:236897	328	PRK	Bacteria:135	PRK11303, PRK11303, DNA-binding transcriptional regulator FruR; Provisional.
CDD:236898	327	PRK	Bacteria:158	PRK11308, dppF, dipeptide transporter ATP-binding subunit; Provisional.
CDD:183085	473	PRK	Bacteria:180,nodiv:1	PRK11316, PRK11316, bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional.
CDD:183086	292	PRK	Bacteria:205,nodiv:1	PRK11320, prpB, 2-methylisocitrate lyase; Provisional.
CDD:183087	127	PRK	Bacteria:256	PRK11325, PRK11325, scaffold protein; Provisional.
CDD:236901	607	PRK	Bacteria:30	PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional.
CDD:183103	99	PRK	Bacteria:153	PRK11370, PRK11370, YciI-like protein; Reviewed.
CDD:183114	638	PRK	Bacteria:43	PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR; Provisional.
CDD:236906	145	PRK	Bacteria:25	PRK11408, PRK11408, hypothetical protein; Provisional.
CDD:236907	561	PRK	Bacteria:45	PRK11410, PRK11410, hypothetical protein; Provisional.
CDD:183123	303	PRK	Bacteria:32	PRK11411, fecB, iron-dicitrate transporter substrate-binding subunit; Provisional.
CDD:183125	751	PRK	Bacteria:50	PRK11413, PRK11413, putative hydratase; Provisional.
CDD:183140	1157	PRK	Bacteria:60	PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
CDD:236912	1123	PRK	Bacteria:43	PRK11448, hsdR, type I restriction enzyme EcoKI subunit R; Provisional.
CDD:183144	232	PRK	Bacteria:63	PRK11460, PRK11460, putative hydrolase; Provisional.
CDD:236913	148	PRK	Bacteria:197	PRK11463, fxsA, phage T7 F exclusion suppressor FxsA; Reviewed.
CDD:236916	216	PRK	Bacteria:49	PRK11492, hyfE, hydrogenase 4 membrane subunit; Provisional.
CDD:236918	852	PRK	Bacteria:68	PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional.
CDD:236919	647	PRK	Bacteria:46	PRK11504, tynA, tyramine oxidase; Provisional.
CDD:183178	279	PRK	Bacteria:59	PRK11525, dinD, DNA-damage-inducible protein D; Provisional.
CDD:236923	183	PRK	Bacteria:73	PRK11530, PRK11530, hypothetical protein; Provisional.
CDD:236924	755	PRK	Bacteria:67	PRK11539, PRK11539, ComEC family competence protein; Provisional.
CDD:236925	156	PRK	Bacteria:78	PRK11544, hycI, hydrogenase 3 maturation protease; Provisional.
CDD:236927	406	PRK	Bacteria:67	PRK11551, PRK11551, putative 3-hydroxyphenylpropionic transporter MhpT; Provisional.
CDD:236928	225	PRK	Bacteria:77	PRK11552, PRK11552, putative DNA-binding transcriptional regulator; Provisional.
CDD:236931	675	PRK	Bacteria:89	PRK11563, PRK11563, bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase; Provisional.
CDD:236932	426	PRK	Bacteria:81	PRK11564, PRK11564, stationary phase inducible protein CsiE; Provisional.
CDD:183205	204	PRK	Bacteria:88	PRK11568, PRK11568, hypothetical protein; Provisional.
CDD:183208	248	PRK	Bacteria:88	PRK11572, PRK11572, copper homeostasis protein CutC; Provisional.
CDD:183213	169	PRK	Bacteria:84	PRK11582, PRK11582, flagella biosynthesis protein FliZ; Provisional.
CDD:183215	218	PRK	Bacteria:93	PRK11587, PRK11587, putative phosphatase; Provisional.
CDD:236934	506	PRK	Bacteria:77	PRK11588, PRK11588, hypothetical protein; Provisional.
CDD:183222	255	PRK	Bacteria:84	PRK11596, PRK11596, cyclic-di-GMP phosphodiesterase; Provisional.
CDD:183228	212	PRK	Bacteria:93	PRK11609, PRK11609, nicotinamidase/pyrazinamidase; Provisional.
CDD:236937	224	PRK	Bacteria:118	PRK11617, PRK11617, endonuclease V; Provisional.
CDD:183235	317	PRK	Bacteria:99	PRK11618, PRK11618, inner membrane ABC transporter permease protein YjfF; Provisional.
CDD:183236	644	PRK	Bacteria:96	PRK11619, PRK11619, lytic murein transglycosylase; Provisional.
CDD:236938	204	PRK	Bacteria:82	PRK11621, PRK11621, twin-argninine leader-binding protein DmsD; Provisional.
CDD:183238	401	PRK	Bacteria:97	PRK11622, PRK11622, hypothetical protein; Provisional.
CDD:236940	226	PRK	Bacteria:91	PRK11633, PRK11633, cell division protein DedD; Provisional.
CDD:236942	428	PRK	Bacteria:93	PRK11637, PRK11637, AmiB activator; Provisional.
CDD:236943	342	PRK	Bacteria:96	PRK11638, PRK11638, lipopolysaccharide biosynthesis protein WzzE; Provisional.
CDD:183252	191	PRK	Bacteria:92	PRK11640, PRK11640, putative transcriptional regulator; Provisional.
CDD:236945	495	PRK	Bacteria:84	PRK11644, PRK11644, sensory histidine kinase UhpB; Provisional.
CDD:183256	195	PRK	Bacteria:97	PRK11648, PRK11648, inner membrane protein; Provisional.
CDD:236947	356	PRK	Bacteria:166,nodiv:1	PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding subunit; Provisional.
CDD:183259	394	PRK	Bacteria:103	PRK11652, emrD, multidrug resistance protein D; Provisional.
CDD:236948	225	PRK	Bacteria:102	PRK11653, PRK11653, hypothetical protein; Provisional.
CDD:236949	169	PRK	Bacteria:87	PRK11655, ubiC, chorismate pyruvate lyase; Provisional.
CDD:183262	251	PRK	Bacteria:83	PRK11657, dsbG, disulfide isomerase/thiol-disulfide oxidase; Provisional.
CDD:183264	183	PRK	Bacteria:80	PRK11659, PRK11659, cytochrome c nitrite reductase pentaheme subunit; Provisional.
CDD:183265	568	PRK	Bacteria:118	PRK11660, PRK11660, putative transporter; Provisional.
CDD:236950	812	PRK	Bacteria:104	PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
CDD:236951	163	PRK	Bacteria:92	PRK11667, PRK11667, hypothetical protein; Provisional.
CDD:236952	306	PRK	Bacteria:113	PRK11669, pbpG, D-alanyl-D-alanine endopeptidase; Provisional.
CDD:183272	90	PRK	Bacteria:132	PRK11675, PRK11675, LexA regulated protein; Provisional.
CDD:236953	134	PRK	Bacteria:107	PRK11677, PRK11677, hypothetical protein; Provisional.
CDD:236954	450	PRK	Bacteria:126	PRK11678, PRK11678, putative chaperone; Provisional.
CDD:236955	346	PRK	Bacteria:110	PRK11679, PRK11679, lipoprotein; Provisional.
CDD:183276	154	PRK	Bacteria:135	PRK11688, PRK11688, hypothetical protein; Provisional.
CDD:183277	295	PRK	Bacteria:136	PRK11689, PRK11689, aromatic amino acid exporter; Provisional.
CDD:236956	238	PRK	Bacteria:134	PRK11697, PRK11697, putative two-component response-regulatory protein YehT; Provisional.
CDD:236957	187	PRK	Bacteria:140	PRK11700, PRK11700, hypothetical protein; Provisional.
CDD:183280	258	PRK	Bacteria:132,nodiv:1	PRK11701, phnK, phosphonate C-P lyase system protein PhnK; Provisional.
CDD:183281	108	PRK	Bacteria:152	PRK11702, PRK11702, hypothetical protein; Provisional.
CDD:183282	383	PRK	Bacteria:139	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase; Provisional.
CDD:183283	375	PRK	Bacteria:142	PRK11706, PRK11706, TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional.
CDD:236958	355	PRK	Bacteria:134	PRK11709, PRK11709, putative L-ascorbate 6-phosphate lactonase; Provisional.
CDD:236959	234	PRK	Bacteria:722,nodiv:1	PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional.
CDD:236960	436	PRK	Bacteria:148,nodiv:1	PRK11715, PRK11715, inner membrane protein; Provisional.
CDD:236961	269	PRK	Bacteria:159	PRK11716, PRK11716, DNA-binding transcriptional regulator IlvY; Provisional.
CDD:236962	161	PRK	Bacteria:155	PRK11718, PRK11718, anti-RNA polymerase sigma 70 factor; Provisional.
CDD:236963	346	PRK	Bacteria:151	PRK11720, PRK11720, galactose-1-phosphate uridylyltransferase; Provisional.
CDD:236964	321	PRK	Bacteria:161	PRK11727, PRK11727, 23S rRNA mA1618 methyltransferase; Provisional.
CDD:183292	393	PRK	Bacteria:123	PRK11728, PRK11728, hydroxyglutarate oxidase; Provisional.
CDD:183293	715	PRK	Bacteria:173	PRK11730, fadB, multifunctional fatty acid oxidation complex subunit alpha; Reviewed.
CDD:236965	575	PRK	Bacteria:161	PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional.
CDD:236966	697	PRK	Bacteria:185	PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
CDD:236967	457	PRK	Bacteria:221	PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A; Provisional.
CDD:236968	1485	PRK	Bacteria:175	PRK11750, gltB, glutamate synthase subunit alpha; Provisional.
CDD:183298	264	PRK	Bacteria:148,nodiv:1	PRK11752, PRK11752, putative S-transferase; Provisional.
CDD:236969	211	PRK	Bacteria:201	PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp; Provisional.
CDD:236970	268	PRK	Bacteria:165	PRK11756, PRK11756, exonuclease III; Provisional.
CDD:236971	357	PRK	Bacteria:199	PRK11760, PRK11760, putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional.
CDD:236972	296	PRK	Bacteria:211	PRK11761, cysM, cysteine synthase B; Provisional.
CDD:183303	185	PRK	Bacteria:200,nodiv:1	PRK11762, nudE, adenosine nucleotide hydrolase NudE; Provisional.
CDD:236973	498	PRK	Bacteria:249	PRK11767, PRK11767, SpoVR family protein; Provisional.
CDD:236974	325	PRK	Bacteria:231	PRK11768, PRK11768, serine/threonine protein kinase; Provisional.
CDD:236975	135	PRK	Bacteria:236	PRK11770, PRK11770, hypothetical protein; Provisional.
CDD:236976	721	PRK	Bacteria:197,nodiv:1	PRK11773, uvrD, DNA-dependent helicase II; Provisional.
CDD:236977	460	PRK	Bacteria:209	PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
CDD:236978	330	PRK	Bacteria:236,nodiv:1	PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
CDD:236979	476	PRK	Bacteria:217	PRK11779, sbcB, exonuclease I; Provisional.
CDD:236980	217	PRK	Bacteria:211	PRK11780, PRK11780, isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional.
CDD:236981	702	PRK	Bacteria:227	PRK11783, rlmL, 23S rRNA m(2)G2445 methyltransferase; Provisional.
CDD:236982	345	PRK	Bacteria:242	PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
CDD:236983	389	PRK	Bacteria:268,nodiv:1	PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
CDD:236984	185	PRK	Bacteria:288	PRK11789, PRK11789, N-acetyl-anhydromuranmyl-L-alanine amidase; Provisional.
CDD:236985	409	PRK	Bacteria:282	PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase; Provisional.
CDD:236986	273	PRK	Bacteria:289,nodiv:1	PRK11792, queF, 7-cyano-7-deazaguanine reductase; Provisional.
CDD:183318	139	PRK	Bacteria:229	PRK11797, PRK11797, D-ribose pyranase; Provisional.
CDD:236987	138	PRK	Bacteria:270,nodiv:1	PRK11798, PRK11798, ClpXP protease specificity-enhancing factor; Provisional.
CDD:236988	307	PRK	Bacteria:306	PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional.
CDD:236989	1318	PRK	Bacteria:139	PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed.
CDD:236990	486	PRK	Bacteria:308,nodiv:2	PRK11814, PRK11814, cysteine desulfurase activator complex subunit SufB; Provisional.
CDD:236991	333	PRK	Bacteria:385,nodiv:1	PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
CDD:236992	556	PRK	Bacteria:571,nodiv:1	PRK11819, PRK11819, putative ABC transporter ATP-binding protein; Reviewed.
CDD:236993	288	PRK	Bacteria:501,nodiv:1	PRK11820, PRK11820, hypothetical protein; Provisional.
CDD:236994	446	PRK	Bacteria:962,nodiv:1	PRK11823, PRK11823, DNA repair protein RadA; Provisional.
CDD:236995	693	PRK	Bacteria:896,nodiv:1	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional.
CDD:236996	272	PRK	Bacteria:407,nodiv:2	PRK11830, dapD, 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional.
CDD:183333	114	PRK	Bacteria:95	PRK11835, PRK11835, hypothetical protein; Provisional.
CDD:183335	202	PRK	Bacteria:78	PRK11837, PRK11837, undecaprenyl pyrophosphate phosphatase; Provisional.
CDD:236999	633	PRK	Bacteria:107	PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated.
CDD:237000	547	PRK	Bacteria:173	PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed.
CDD:237001	411	PRK	Bacteria:385,nodiv:2	PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed.
CDD:183341	378	PRK	Bacteria:99	PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
CDD:237004	313	PRK	Bacteria:151,nodiv:1	PRK11863, PRK11863, N-acetyl-gamma-glutamyl-phosphate reductase; Provisional.
CDD:237006	286	PRK	Bacteria:170	PRK11867, PRK11867, 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed.
CDD:237007	272	PRK	Bacteria:30	PRK11873, arsM, arsenite S-adenosylmethyltransferase; Reviewed.
CDD:237008	267	PRK	Bacteria:384,nodiv:1	PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed.
CDD:237009	451	PRK	Bacteria:105	PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
CDD:237010	319	PRK	Bacteria:215	PRK11886, PRK11886, bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional.
CDD:183361	312	PRK	Bacteria:35	PRK11890, PRK11890, phosphate acetyltransferase; Provisional.
CDD:237011	464	PRK	Bacteria:91	PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional.
CDD:237012	511	PRK	Bacteria:197	PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
CDD:183365	161	PRK	Bacteria:586	PRK11895, ilvH, acetolactate synthase 3 regulatory subunit; Reviewed.
CDD:237013	283	PRK	Bacteria:122	PRK11898, PRK11898, prephenate dehydratase; Provisional.
CDD:237014	279	PRK	Bacteria:71	PRK11899, PRK11899, prephenate dehydratase; Provisional.
CDD:237015	327	PRK	Bacteria:34	PRK11901, PRK11901, hypothetical protein; Reviewed.
CDD:237017	1038	PRK	Bacteria:120,nodiv:1	PRK11904, PRK11904, bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed.
CDD:237018	1208	PRK	Bacteria:79	PRK11905, PRK11905, bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed.
CDD:237020	275	PRK	Bacteria:159	PRK11913, phhA, phenylalanine 4-monooxygenase; Reviewed.
CDD:237024	231	PRK	Bacteria:37	PRK11922, PRK11922, RNA polymerase sigma factor; Provisional.
CDD:183384	179	PRK	Bacteria:28,nodiv:1	PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
CDD:237025	958	PRK	Bacteria:11	PRK11929, PRK11929, putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional.
CDD:237026	822	PRK	Bacteria:19	PRK11930, PRK11930, putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional.
CDD:183387	470	PRK	Bacteria:110	PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed.
CDD:237027	508	PRK	Bacteria:267,nodiv:1	PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
CDD:237028	648	PRK	Bacteria:235	PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
CDD:237029	556	PRK	Bacteria:150,nodiv:1	PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
CDD:237030	1228	PRK	Bacteria:90	PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
CDD:183392	102	PRK	Bacteria:78	PRK12271, rps10p, 30S ribosomal protein S10P; Reviewed.
CDD:237031	472	PRK	Bacteria:362	PRK12273, aspA, aspartate ammonia-lyase; Provisional.
CDD:183395	116	PRK	Bacteria:63	PRK12275, PRK12275, hypothetical protein; Reviewed.
CDD:237033	248	PRK	Bacteria:76	PRK12276, PRK12276, putative heme peroxidase; Provisional.
CDD:237035	158	PRK	Bacteria:14	PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
CDD:183400	333	PRK	Bacteria:166	PRK12282, PRK12282, tryptophanyl-tRNA synthetase II; Reviewed.
CDD:183401	398	PRK	Bacteria:73	PRK12283, PRK12283, tryptophanyl-tRNA synthetase; Reviewed.
CDD:237036	431	PRK	Bacteria:49	PRK12284, PRK12284, tryptophanyl-tRNA synthetase; Reviewed.
CDD:237037	368	PRK	Bacteria:79	PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
CDD:237038	57	PRK	Bacteria:280	PRK12286, rpmF, 50S ribosomal protein L32; Reviewed.
CDD:237039	347	PRK	Bacteria:176	PRK12288, PRK12288, GTPase RsgA; Reviewed.
CDD:237040	352	PRK	Bacteria:17	PRK12289, PRK12289, GTPase RsgA; Reviewed.
CDD:237042	418	PRK	Bacteria:26	PRK12291, PRK12291, apolipoprotein N-acyltransferase; Reviewed.
CDD:237043	391	PRK	Bacteria:181	PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional.
CDD:183411	281	PRK	Bacteria:14	PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional.
CDD:183413	373	PRK	Bacteria:62	PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional.
CDD:237045	500	PRK	Bacteria:95	PRK12296, obgE, GTPase CgtA; Reviewed.
CDD:237046	424	PRK	Bacteria:260	PRK12297, obgE, GTPase CgtA; Reviewed.
CDD:237047	390	PRK	Bacteria:207	PRK12298, obgE, GTPase CgtA; Reviewed.
CDD:237048	335	PRK	Bacteria:386,nodiv:2	PRK12299, obgE, GTPase CgtA; Reviewed.
CDD:237049	897	PRK	Bacteria:67	PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
CDD:237050	575	PRK	Bacteria:181	PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
CDD:183427	433	PRK	Bacteria:59	PRK12310, PRK12310, hydroxylamine reductase; Provisional.
CDD:237052	633	PRK	Bacteria:57	PRK12313, PRK12313, glycogen branching enzyme; Provisional.
CDD:183430	266	PRK	Bacteria:83	PRK12314, PRK12314, gamma-glutamyl kinase; Provisional.
CDD:237053	581	PRK	Bacteria:20	PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional.
CDD:237055	425	PRK	Bacteria:83	PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
CDD:237056	1100	PRK	Bacteria:27	PRK12321, cobN, cobaltochelatase subunit CobN; Reviewed.
CDD:237058	295	PRK	Bacteria:88	PRK12324, PRK12324, phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional.
CDD:237059	439	PRK	Bacteria:114,nodiv:1	PRK12325, PRK12325, prolyl-tRNA synthetase; Provisional.
CDD:237060	764	PRK	Bacteria:44	PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed.
CDD:237061	362	PRK	Bacteria:205	PRK12327, nusA, transcription elongation factor NusA; Provisional.
CDD:237062	374	PRK	Bacteria:29	PRK12328, nusA, transcription elongation factor NusA; Provisional.
CDD:183447	198	PRK	Bacteria:111	PRK12332, tsf, elongation factor Ts; Reviewed.
CDD:237065	277	PRK	Bacteria:44	PRK12334, PRK12334, nucleoside triphosphate pyrophosphohydrolase; Reviewed.
CDD:183450	287	PRK	Bacteria:69	PRK12335, PRK12335, tellurite resistance protein TehB; Provisional.
CDD:183451	201	PRK	Bacteria:26	PRK12336, PRK12336, translation initiation factor IF-2 subunit beta; Provisional.
CDD:237067	151	PRK	Bacteria:44	PRK12343, PRK12343, putative molybdenum cofactor biosynthesis protein MoaC; Reviewed.
CDD:237068	524	PRK	Bacteria:250	PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional.
CDD:237070	353	PRK	Bacteria:65,nodiv:1	PRK12350, PRK12350, citrate synthase 2; Provisional.
CDD:183463	378	PRK	Bacteria:173	PRK12351, PRK12351, methylcitrate synthase; Provisional.
CDD:237071	314	PRK	Bacteria:206	PRK12353, PRK12353, putative amino acid kinase; Reviewed.
CDD:183466	307	PRK	Bacteria:97	PRK12354, PRK12354, carbamate kinase; Reviewed.
CDD:237072	558	PRK	Bacteria:50	PRK12355, PRK12355, conjugal transfer mating pair stabilization protein TraN; Reviewed.
CDD:237073	319	PRK	Bacteria:72	PRK12356, PRK12356, glutaminase; Reviewed.
CDD:183471	172	PRK	Bacteria:122	PRK12359, PRK12359, flavodoxin FldB; Provisional.
CDD:183473	547	PRK	Bacteria:19	PRK12361, PRK12361, hypothetical protein; Provisional.
CDD:237076	318	PRK	Bacteria:60	PRK12362, PRK12362, germination protease; Provisional.
CDD:237078	637	PRK	Bacteria:15	PRK12366, PRK12366, replication factor A; Reviewed.
CDD:237079	245	PRK	Bacteria:18	PRK12367, PRK12367, short chain dehydrogenase; Provisional.
CDD:183481	236	PRK	Bacteria:62,nodiv:1	PRK12376, PRK12376, putative translaldolase; Provisional.
CDD:237084	235	PRK	Bacteria:309	PRK12378, PRK12378, hypothetical protein; Provisional.
CDD:237085	406	PRK	Bacteria:45	PRK12383, PRK12383, putative mutase; Provisional.
CDD:183492	180	PRK	Bacteria:71	PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur subunit; Provisional.
CDD:237087	427	PRK	Bacteria:190	PRK12391, PRK12391, tryptophan synthase subunit beta; Reviewed.
CDD:237090	337	PRK	Bacteria:20	PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
CDD:183504	334	PRK	Bacteria:47	PRK12404, PRK12404, stage V sporulation protein AD; Provisional.
CDD:237091	231	PRK	Bacteria:248	PRK12405, PRK12405, electron transport complex RsxE subunit; Provisional.
CDD:237093	410	PRK	Bacteria:26	PRK12409, PRK12409, D-amino acid dehydrogenase small subunit; Provisional.
CDD:237094	433	PRK	Bacteria:28	PRK12410, PRK12410, glutamylglutaminyl-tRNA synthetase; Provisional.
CDD:237095	404	PRK	Bacteria:29	PRK12417, secY, preprotein translocase subunit SecY; Reviewed.
CDD:183518	384	PRK	Bacteria:59	PRK12418, PRK12418, cysteinyl-tRNA synthetase; Provisional.
CDD:237096	158	PRK	Bacteria:47	PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional.
CDD:237098	392	PRK	Bacteria:24	PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory subunit; Provisional.
CDD:237099	241	PRK	Bacteria:34	PRK12428, PRK12428, 3-alpha-hydroxysteroid dehydrogenase; Provisional.
CDD:237100	258	PRK	Bacteria:142	PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
CDD:183526	311	PRK	Bacteria:73	PRK12435, PRK12435, ferrochelatase; Provisional.
CDD:183527	269	PRK	Bacteria:55	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed.
CDD:237103	426	PRK	Bacteria:42	PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
CDD:237104	615	PRK	Bacteria:353,nodiv:1	PRK12448, PRK12448, dihydroxy-acid dehydratase; Provisional.
CDD:183535	313	PRK	Bacteria:21	PRK12454, PRK12454, carbamate kinase-like carbamoyl phosphate synthetase; Reviewed.
CDD:183536	338	PRK	Bacteria:17,nodiv:1	PRK12458, PRK12458, glutathione synthetase; Provisional.
CDD:237106	386	PRK	Bacteria:27	PRK12459, PRK12459, S-adenosylmethionine synthetase; Provisional.
CDD:183538	312	PRK	Bacteria:29	PRK12460, PRK12460, 2-keto-3-deoxygluconate permease; Provisional.
CDD:183543	471	PRK	Bacteria:43	PRK12466, PRK12466, isopropylmalate isomerase large subunit; Provisional.
CDD:183553	163	PRK	Bacteria:31	PRK12487, PRK12487, ribonuclease activity regulator protein RraA; Reviewed.
CDD:237115	443	PRK	Bacteria:137	PRK12489, PRK12489, anaerobic C4-dicarboxylate transporter; Reviewed.
CDD:237117	1310	PRK	Bacteria:53	PRK12493, PRK12493, magnesium chelatase subunit H; Provisional.
CDD:183557	172	PRK	Bacteria:39	PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional.
CDD:237118	164	PRK	Bacteria:24	PRK12496, PRK12496, hypothetical protein; Provisional.
CDD:237119	119	PRK	Bacteria:367	PRK12497, PRK12497, hypothetical protein; Reviewed.
CDD:183561	178	PRK	Bacteria:19	PRK12504, PRK12504, putative monovalent cation/H+ antiporter subunit B; Reviewed.
CDD:183566	194	PRK	Bacteria:21	PRK12513, PRK12513, RNA polymerase sigma factor; Provisional.
CDD:183569	188	PRK	Bacteria:38	PRK12517, PRK12517, RNA polymerase sigma factor; Provisional.
CDD:183586	284	PRK	Bacteria:60	PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
CDD:183587	272	PRK	Bacteria:67	PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
CDD:237133	207	PRK	Bacteria:106,nodiv:1	PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit; Reviewed.
CDD:237134	276	PRK	Bacteria:97,nodiv:1	PRK12554, PRK12554, undecaprenyl pyrophosphate phosphatase; Reviewed.
CDD:237135	337	PRK	Bacteria:63	PRK12555, PRK12555, chemotaxis-specific methylesterase; Provisional.
CDD:183594	445	PRK	Bacteria:84	PRK12558, PRK12558, glutamyl-tRNA synthetase; Provisional.
CDD:237139	360	PRK	Bacteria:796,nodiv:2	PRK12564, PRK12564, carbamoyl phosphate synthase small subunit; Reviewed.
CDD:237140	218	PRK	Bacteria:34	PRK12567, PRK12567, putative monovalent cation/H+ antiporter subunit B; Reviewed.
CDD:237141	245	PRK	Bacteria:45	PRK12569, PRK12569, hypothetical protein; Provisional.
CDD:183602	140	PRK	Bacteria:48,nodiv:1	PRK12573, PRK12573, putative monovalent cation/H+ antiporter subunit B; Reviewed.
CDD:237144	624	PRK	Bacteria:16	PRK12582, PRK12582, acyl-CoA synthetase; Provisional.
CDD:183614	360	PRK	Bacteria:79	PRK12595, PRK12595, bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed.
CDD:183615	461	PRK	Bacteria:65	PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
CDD:237148	91	PRK	Bacteria:43	PRK12599, PRK12599, putative monovalent cation/H+ antiporter subunit F; Reviewed.
CDD:183621	313	PRK	Bacteria:56	PRK12607, PRK12607, phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional.
CDD:237151	87	PRK	Bacteria:24	PRK12612, PRK12612, putative monovalent cation/H+ antiporter subunit F; Reviewed.
CDD:183642	246	PRK	Bacteria:181	PRK12640, flgF, flagellar basal body rod protein FlgF; Reviewed.
CDD:237154	965	PRK	Bacteria:36	PRK12644, PRK12644, putative monovalent cation/H+ antiporter subunit A; Reviewed.
CDD:237155	800	PRK	Bacteria:44	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed.
CDD:237156	761	PRK	Bacteria:29,nodiv:1	PRK12647, PRK12647, putative monovalent cation/H+ antiporter subunit A; Reviewed.
CDD:237157	948	PRK	Bacteria:125	PRK12648, PRK12648, putative monovalent cation/H+ antiporter subunit A; Reviewed.
CDD:237159	158	PRK	Bacteria:73	PRK12651, PRK12651, putative monovalent cation/H+ antiporter subunit E; Reviewed.
CDD:237163	497	PRK	Bacteria:33	PRK12663, PRK12663, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:237165	521	PRK	Bacteria:33	PRK12665, PRK12665, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:237166	528	PRK	Bacteria:117,nodiv:1	PRK12666, PRK12666, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:237167	520	PRK	Bacteria:9	PRK12667, PRK12667, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:237168	581	PRK	Bacteria:36	PRK12668, PRK12668, putative monovalent cation/H+ antiporter subunit D; Reviewed.
CDD:183670	120	PRK	Bacteria:32	PRK12671, PRK12671, putative monovalent cation/H+ antiporter subunit G; Reviewed.
CDD:237169	99	PRK	Bacteria:141	PRK12674, PRK12674, putative monovalent cation/H+ antiporter subunit G; Reviewed.
CDD:183673	263	PRK	Bacteria:23	PRK12676, PRK12676, bifunctional inositol-1 monophosphatase/fructose-1,6-bisphosphatase; Reviewed.
CDD:237170	384	PRK	Bacteria:47	PRK12677, PRK12677, xylose isomerase; Provisional.
CDD:237171	672	PRK	Bacteria:75	PRK12678, PRK12678, transcription termination factor Rho; Provisional.
CDD:183678	324	PRK	Bacteria:175	PRK12681, cysB, transcriptional regulator CysB; Reviewed.
CDD:183679	309	PRK	Bacteria:37	PRK12682, PRK12682, transcriptional regulator CysB-like protein; Reviewed.
CDD:237173	313	PRK	Bacteria:53	PRK12684, PRK12684, transcriptional regulator CysB-like protein; Reviewed.
CDD:183686	262	PRK	Bacteria:67,nodiv:1	PRK12691, flgG, flagellar basal body rod protein FlgG; Reviewed.
CDD:183687	261	PRK	Bacteria:198	PRK12693, flgG, flagellar basal body rod protein FlgG; Provisional.
CDD:237177	520	PRK	Bacteria:258	PRK12704, PRK12704, phosphodiesterase; Provisional.
CDD:237178	508	PRK	Bacteria:18	PRK12705, PRK12705, hypothetical protein; Provisional.
CDD:237181	187	PRK	Bacteria:153	PRK12722, PRK12722, transcriptional activator FlhC; Provisional.
CDD:237183	102	PRK	Bacteria:36	PRK12728, fliE, flagellar hook-basal body protein FliE; Provisional.
CDD:183708	396	PRK	Bacteria:493,nodiv:1	PRK12735, PRK12735, elongation factor Tu; Reviewed.
CDD:237184	394	PRK	Bacteria:141	PRK12736, PRK12736, elongation factor Tu; Reviewed.
CDD:237185	691	PRK	Bacteria:209	PRK12739, PRK12739, elongation factor G; Reviewed.
CDD:237186	668	PRK	Bacteria:329	PRK12740, PRK12740, elongation factor G; Reviewed.
CDD:237187	256	PRK	Bacteria:62	PRK12743, PRK12743, oxidoreductase; Provisional.
CDD:237188	256	PRK	Bacteria:47	PRK12745, PRK12745, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:237189	256	PRK	Bacteria:25	PRK12748, PRK12748, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:237190	353	PRK	Bacteria:260	PRK12755, PRK12755, phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional.
CDD:183726	348	PRK	Bacteria:127	PRK12756, PRK12756, phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional.
CDD:237191	256	PRK	Bacteria:44	PRK12757, PRK12757, cell division protein FtsN; Provisional.
CDD:237192	869	PRK	Bacteria:24	PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
CDD:237195	326	PRK	Bacteria:37	PRK12767, PRK12767, carbamoyl phosphate synthase-like protein; Provisional.
CDD:237196	240	PRK	Bacteria:36	PRK12768, PRK12768, CysZ-like protein; Reviewed.
CDD:237197	352	PRK	Bacteria:20	PRK12770, PRK12770, putative glutamate synthase subunit beta; Provisional.
CDD:237198	564	PRK	Bacteria:56	PRK12771, PRK12771, putative glutamate synthase (NADPH) small subunit; Provisional.
CDD:237201	338	PRK	Bacteria:19	PRK12786, flgA, flagellar basal body P-ring biosynthesis protein FlgA; Reviewed.
CDD:183745	138	PRK	Bacteria:23	PRK12787, fliX, flagellar assembly regulator FliX; Reviewed.
CDD:237206	115	PRK	Bacteria:37,nodiv:1	PRK12793, flaF, flagellar biosynthesis regulatory protein FlaF; Reviewed.
CDD:237207	122	PRK	Bacteria:33	PRK12794, flaF, flagellar biosynthesis regulatory protein FlaF; Reviewed.
CDD:237208	388	PRK	Bacteria:35	PRK12795, fliM, flagellar motor switch protein FliM; Reviewed.
CDD:237209	221	PRK	Bacteria:52	PRK12796, spaP, type III secretion system protein SpaP; Provisional.
CDD:237210	213	PRK	Bacteria:123	PRK12797, PRK12797, type III secretion system protein YscR; Provisional.
CDD:237211	421	PRK	Bacteria:32,nodiv:1	PRK12798, PRK12798, chemotaxis protein; Reviewed.
CDD:237213	471	PRK	Bacteria:424	PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
CDD:237214	223	PRK	Bacteria:11	PRK12813, flgD, flagellar basal body rod modification protein; Reviewed.
CDD:237215	1068	PRK	Bacteria:30	PRK12815, carB, carbamoyl phosphate synthase large subunit; Reviewed.
CDD:183772	260	PRK	Bacteria:70	PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional.
CDD:237218	249	PRK	Bacteria:95	PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
CDD:183775	251	PRK	Bacteria:60	PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed.
CDD:183778	264	PRK	Bacteria:33	PRK12829, PRK12829, short chain dehydrogenase; Provisional.
CDD:183779	417	PRK	Bacteria:145	PRK12830, PRK12830, UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Reviewed.
CDD:183780	464	PRK	Bacteria:37	PRK12831, PRK12831, putative oxidoreductase; Provisional.
CDD:183782	549	PRK	Bacteria:67,nodiv:1	PRK12834, PRK12834, putative FAD-binding dehydrogenase; Reviewed.
CDD:183784	354	PRK	Bacteria:37	PRK12838, PRK12838, carbamoyl phosphate synthase small subunit; Reviewed.
CDD:237227	165	PRK	Bacteria:170	PRK12846, PRK12846, peptide deformylase; Reviewed.
CDD:237228	285	PRK	Bacteria:40	PRK12847, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
CDD:237229	282	PRK	Bacteria:225	PRK12848, ubiA, 4-hydroxybenzoate octaprenyltransferase; Reviewed.
CDD:237230	542	PRK	Bacteria:160,nodiv:1	PRK12849, groEL, chaperonin GroEL; Reviewed.
CDD:237233	482	PRK	Bacteria:108	PRK12853, PRK12853, glucose-6-phosphate 1-dehydrogenase; Provisional.
CDD:237234	484	PRK	Bacteria:26	PRK12854, PRK12854, glucose-6-phosphate 1-dehydrogenase; Provisional.
CDD:237236	340	PRK	Bacteria:28	PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
CDD:183799	763	PRK	Bacteria:89,nodiv:1	PRK12862, PRK12862, malic enzyme; Reviewed.
CDD:183800	94	PRK	Bacteria:60	PRK12863, PRK12863, YciI-like protein; Reviewed.
CDD:183801	89	PRK	Bacteria:30	PRK12864, PRK12864, YciI-like protein; Reviewed.
CDD:237240	290	PRK	Bacteria:24	PRK12870, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
CDD:237241	285	PRK	Bacteria:19	PRK12872, ubiA, prenyltransferase; Reviewed.
CDD:237243	282	PRK	Bacteria:13	PRK12875, ubiA, prenyltransferase; Reviewed.
CDD:183808	314	PRK	Bacteria:55	PRK12878, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
CDD:237245	325	PRK	Bacteria:83	PRK12879, PRK12879, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed.
CDD:237246	889	PRK	Bacteria:78	PRK12881, acnA, aconitate hydratase; Provisional.
CDD:183811	276	PRK	Bacteria:17	PRK12882, ubiA, prenyltransferase; Reviewed.
CDD:183812	279	PRK	Bacteria:12	PRK12884, ubiA, prenyltransferase; Reviewed.
CDD:183813	308	PRK	Bacteria:18	PRK12887, ubiA, tocopherol phytyltransferase; Reviewed.
CDD:237248	414	PRK	Bacteria:40	PRK12890, PRK12890, allantoate amidohydrolase; Reviewed.
CDD:237250	412	PRK	Bacteria:63,nodiv:1	PRK12893, PRK12893, allantoate amidohydrolase; Reviewed.
CDD:237252	255	PRK	Bacteria:111	PRK12896, PRK12896, methionine aminopeptidase; Reviewed.
CDD:237253	656	PRK	Bacteria:14	PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
CDD:237256	1112	PRK	Bacteria:25	PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
CDD:237258	925	PRK	Bacteria:18	PRK12903, secA, preprotein translocase subunit SecA; Reviewed.
CDD:237259	830	PRK	Bacteria:665,nodiv:2	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.
CDD:183829	305	PRK	Bacteria:109	PRK12921, PRK12921, 2-dehydropantoate 2-reductase; Provisional.
CDD:237261	290	PRK	Bacteria:68	PRK12928, PRK12928, lipoyl synthase; Provisional.
CDD:183833	250	PRK	Bacteria:48	PRK12939, PRK12939, short chain dehydrogenase; Provisional.
CDD:237262	466	PRK	Bacteria:105	PRK12997, PRK12997, PTS system ascorbate-specific transporter subunit IIC; Reviewed.
CDD:237263	1146	PRK	Bacteria:241,nodiv:1	PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
CDD:183836	399	PRK	Bacteria:79	PRK13004, PRK13004, peptidase; Reviewed.
CDD:237264	352	PRK	Bacteria:89	PRK13007, PRK13007, succinyl-diaminopimelate desuccinylase; Reviewed.
CDD:237265	375	PRK	Bacteria:445,nodiv:1	PRK13009, PRK13009, succinyl-diaminopimelate desuccinylase; Reviewed.
CDD:237266	286	PRK	Bacteria:52,nodiv:1	PRK13011, PRK13011, formyltetrahydrofolate deformylase; Reviewed.
CDD:237267	896	PRK	Bacteria:59	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional.
CDD:237269	186	PRK	Bacteria:46	PRK13014, PRK13014, methionine sulfoxide reductase A; Provisional.
CDD:237270	146	PRK	Bacteria:56,nodiv:1	PRK13015, PRK13015, 3-dehydroquinate dehydratase; Reviewed.
CDD:237272	596	PRK	Bacteria:62	PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
CDD:237273	378	PRK	Bacteria:59	PRK13018, PRK13018, cell division protein FtsZ; Provisional.
CDD:183845	94	PRK	Bacteria:51	PRK13019, clpS, ATP-dependent Clp protease adaptor; Reviewed.
CDD:183846	206	PRK	Bacteria:53	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional.
CDD:237275	289	PRK	Bacteria:561,nodiv:1	PRK13022, secF, preprotein translocase subunit SecF; Reviewed.
CDD:237276	755	PRK	Bacteria:141	PRK13024, PRK13024, bifunctional preprotein translocase subunit SecD/SecF; Reviewed.
CDD:237277	774	PRK	Bacteria:50	PRK13026, PRK13026, acyl-CoA dehydrogenase; Reviewed.
CDD:183851	402	PRK	Bacteria:71	PRK13028, PRK13028, tryptophan synthase subunit beta; Provisional.
CDD:237279	1159	PRK	Bacteria:41	PRK13030, PRK13030, 2-oxoacid ferredoxin oxidoreductase; Provisional.
CDD:237280	416	PRK	Bacteria:94	PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
CDD:237281	300	PRK	Bacteria:115	PRK13054, PRK13054, lipid kinase; Reviewed.
CDD:237282	334	PRK	Bacteria:72	PRK13055, PRK13055, putative lipid kinase; Reviewed.
CDD:183857	287	PRK	Bacteria:31	PRK13057, PRK13057, putative lipid kinase; Reviewed.
CDD:237285	258	PRK	Bacteria:703,nodiv:2	PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
CDD:237286	244	PRK	Bacteria:17	PRK13125, trpA, tryptophan synthase subunit alpha; Provisional.
CDD:237287	56	PRK	Bacteria:37	PRK13130, PRK13130, H/ACA RNA-protein complex component Nop10p; Reviewed.
CDD:237288	205	PRK	Bacteria:224	PRK13141, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional.
CDD:237289	200	PRK	Bacteria:57	PRK13143, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional.
CDD:237290	209	PRK	Bacteria:237,nodiv:1	PRK13146, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional.
CDD:183872	73	PRK	Bacteria:51	PRK13149, PRK13149, H/ACA RNA-protein complex component Gar1; Reviewed.
CDD:183874	160	PRK	Bacteria:123	PRK13165, PRK13165, cytochrome c-type biogenesis protein CcmE; Reviewed.
CDD:237291	443	PRK	Bacteria:257	PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
CDD:183876	110	PRK	Bacteria:130	PRK13169, PRK13169, DNA replication intiation control protein YabA; Reviewed.
CDD:183877	196	PRK	Bacteria:155	PRK13170, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional.
CDD:183878	199	PRK	Bacteria:54	PRK13181, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional.
CDD:237292	175	PRK	Bacteria:32	PRK13182, racA, polar chromosome segregation protein; Reviewed.
CDD:237293	270	PRK	Bacteria:84	PRK13185, chlL, protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional.
CDD:237294	295	PRK	Bacteria:534,nodiv:2	PRK13186, lpxC, UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed.
CDD:237296	464	PRK	Bacteria:42	PRK13188, PRK13188, bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed.
CDD:237297	222	PRK	Bacteria:48	PRK13189, PRK13189, peroxiredoxin; Provisional.
CDD:183886	208	PRK	Bacteria:27	PRK13192, PRK13192, bifunctional urease subunit gamma/beta; Reviewed.
CDD:237299	215	PRK	Bacteria:139	PRK13197, PRK13197, pyrrolidone-carboxylate peptidase; Provisional.
CDD:237303	102	PRK	Bacteria:144,nodiv:1	PRK13203, ureB, urease subunit beta; Reviewed.
CDD:237305	568	PRK	Bacteria:301,nodiv:1	PRK13207, ureC, urease subunit alpha; Reviewed.
CDD:237306	800	PRK	Bacteria:148	PRK13208, valS, valyl-tRNA synthetase; Reviewed.
CDD:237307	283	PRK	Bacteria:76	PRK13209, PRK13209, L-xylulose 5-phosphate 3-epimerase; Reviewed.
CDD:237308	284	PRK	Bacteria:140	PRK13210, PRK13210, putative L-xylulose 5-phosphate 3-epimerase; Reviewed.
CDD:237309	478	PRK	Bacteria:35	PRK13211, PRK13211, N-acetylglucosamine-binding protein A; Reviewed.
CDD:237310	226	PRK	Bacteria:204,nodiv:1	PRK13222, PRK13222, phosphoglycolate phosphatase; Provisional.
CDD:237314	460	PRK	Bacteria:124	PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional.
CDD:183911	206	PRK	Bacteria:17,Environmental:1	PRK13239, PRK13239, alkylmercury lyase; Provisional.
CDD:183913	100	PRK	Bacteria:236,nodiv:1	PRK13241, ureA, urease subunit gamma; Provisional.
CDD:237315	238	PRK	Bacteria:17	PRK13247, PRK13247, dihydrobiliverdin:ferredoxin oxidoreductase; Provisional.
CDD:183917	75	PRK	Bacteria:41	PRK13251, PRK13251, transcription attenuation protein MtrB; Provisional.
CDD:183918	488	PRK	Bacteria:171	PRK13252, PRK13252, betaine aldehyde dehydrogenase; Provisional.
CDD:237316	92	PRK	Bacteria:130	PRK13253, PRK13253, citrate lyase subunit gamma; Provisional.
CDD:237317	148	PRK	Bacteria:144	PRK13254, PRK13254, cytochrome c-type biogenesis protein CcmE; Reviewed.
CDD:183921	218	PRK	Bacteria:69	PRK13255, PRK13255, thiopurine S-methyltransferase; Reviewed.
CDD:237319	336	PRK	Bacteria:85	PRK13257, PRK13257, allantoicase; Provisional.
CDD:237320	114	PRK	Bacteria:275,nodiv:1	PRK13258, PRK13258, 7-cyano-7-deazaguanine reductase; Provisional.
CDD:237321	94	PRK	Bacteria:111	PRK13259, PRK13259, regulatory protein SpoVG; Reviewed.
CDD:237322	159	PRK	Bacteria:148,nodiv:1	PRK13261, ureE, urease accessory protein UreE; Provisional.
CDD:183930	177	PRK	Bacteria:47	PRK13264, PRK13264, 3-hydroxyanthranilate 3,4-dioxygenase; Provisional.
CDD:237324	225	PRK	Bacteria:38	PRK13266, PRK13266, Thf1-like protein; Reviewed.
CDD:237325	179	PRK	Bacteria:26	PRK13267, PRK13267, archaemetzincin-like protein; Reviewed.
CDD:237327	476	PRK	Bacteria:160	PRK13273, mdoD, glucan biosynthesis protein D; Provisional.
CDD:237328	516	PRK	Bacteria:184	PRK13274, mdoG, glucan biosynthesis protein G; Provisional.
CDD:183939	67	PRK	Bacteria:20	PRK13275, mtrF, tetrahydromethanopterin S-methyltransferase subunit F; Provisional.
CDD:183941	366	PRK	Bacteria:31	PRK13277, PRK13277, 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional.
CDD:237329	358	PRK	Bacteria:48	PRK13278, purP, 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; Provisional.
CDD:237330	552	PRK	Bacteria:103	PRK13279, arnT, 4-amino-4-deoxy-L-arabinose transferase; Provisional.
CDD:237331	269	PRK	Bacteria:31	PRK13280, PRK13280, N-glycosylase/DNA lyase; Provisional.
CDD:237332	442	PRK	Bacteria:189	PRK13281, PRK13281, succinylarginine dihydrolase; Provisional.
CDD:237334	148	PRK	Bacteria:79	PRK13285, PRK13285, flagellar assembly protein FliW; Provisional.
CDD:237336	214	PRK	Bacteria:44	PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
CDD:237337	399	PRK	Bacteria:193	PRK13289, PRK13289, bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional.
CDD:183953	125	PRK	Bacteria:92	PRK13290, ectC, L-ectoine synthase; Reviewed.
CDD:183954	173	PRK	Bacteria:41	PRK13291, PRK13291, metal-dependent hydrolase; Provisional.
CDD:183956	245	PRK	Bacteria:30	PRK13293, PRK13293, F420-0--gamma-glutamyl ligase; Reviewed.
CDD:183957	448	PRK	Bacteria:45	PRK13294, PRK13294, F420-0--gamma-glutamyl ligase; Provisional.
CDD:237339	394	PRK	Bacteria:123	PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
CDD:237340	447	PRK	Bacteria:78	PRK13300, PRK13300, tRNA CCA-pyrophosphorylase; Provisional.
CDD:237342	265	PRK	Bacteria:56	PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
CDD:237343	265	PRK	Bacteria:20	PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
CDD:237344	216	PRK	Bacteria:152	PRK13306, ulaD, 3-keto-L-gulonate-6-phosphate decarboxylase; Provisional.
CDD:183964	391	PRK	Bacteria:26	PRK13307, PRK13307, bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase; Provisional.
CDD:237346	277	PRK	Bacteria:51	PRK13317, PRK13317, pantothenate kinase; Provisional.
CDD:237347	258	PRK	Bacteria:180	PRK13318, PRK13318, pantothenate kinase; Reviewed.
CDD:237348	244	PRK	Bacteria:30	PRK13320, PRK13320, pantothenate kinase; Reviewed.
CDD:237349	256	PRK	Bacteria:48	PRK13321, PRK13321, pantothenate kinase; Reviewed.
CDD:237350	246	PRK	Bacteria:31	PRK13322, PRK13322, pantothenate kinase; Reviewed.
CDD:237352	255	PRK	Bacteria:39	PRK13328, PRK13328, pantothenate kinase; Reviewed.
CDD:183979	249	PRK	Bacteria:21	PRK13329, PRK13329, pantothenate kinase; Reviewed.
CDD:237353	251	PRK	Bacteria:15	PRK13331, PRK13331, pantothenate kinase; Reviewed.
CDD:183981	206	PRK	Bacteria:27	PRK13333, PRK13333, pantothenate kinase; Reviewed.
CDD:183984	406	PRK	Bacteria:46	PRK13340, PRK13340, alanine racemase; Reviewed.
CDD:237354	725	PRK	Bacteria:19	PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed.
CDD:237355	413	PRK	Bacteria:795,nodiv:1	PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
CDD:183987	502	PRK	Bacteria:40	PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
CDD:237356	453	PRK	Bacteria:30	PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.
CDD:237357	294	PRK	Bacteria:33	PRK13348, PRK13348, chromosome replication initiation inhibitor protein; Provisional.
CDD:237358	687	PRK	Bacteria:44	PRK13351, PRK13351, elongation factor G; Reviewed.
CDD:237359	431	PRK	Bacteria:213	PRK13352, PRK13352, thiamine biosynthesis protein ThiC; Provisional.
CDD:183992	473	PRK	Bacteria:37	PRK13353, PRK13353, aspartate ammonia-lyase; Provisional.
CDD:237360	410	PRK	Bacteria:96	PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
CDD:237362	286	PRK	Bacteria:49,nodiv:1	PRK13356, PRK13356, aminotransferase; Provisional.
CDD:237363	356	PRK	Bacteria:331	PRK13357, PRK13357, branched-chain amino acid aminotransferase; Provisional.
CDD:237364	329	PRK	Bacteria:32	PRK13361, PRK13361, molybdenum cofactor biosynthesis protein A; Provisional.
CDD:184001	306	PRK	Bacteria:32	PRK13362, PRK13362, protoheme IX farnesyltransferase; Provisional.
CDD:184007	238	PRK	Bacteria:31	PRK13368, PRK13368, 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional.
CDD:237365	502	PRK	Bacteria:29,nodiv:1	PRK13369, PRK13369, glycerol-3-phosphate dehydrogenase; Provisional.
CDD:237366	313	PRK	Bacteria:55	PRK13370, mhpB, 3-(2,3-dihydroxyphenyl)propionate dioxygenase; Provisional.
CDD:237367	387	PRK	Bacteria:48	PRK13371, PRK13371, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional.
CDD:237370	144	PRK	Bacteria:30	PRK13380, PRK13380, glycine cleavage system protein H; Provisional.
CDD:237371	404	PRK	Bacteria:47	PRK13381, PRK13381, peptidase T; Provisional.
CDD:237372	236	PRK	Bacteria:33	PRK13386, fliH, flagellar assembly protein H; Provisional.
CDD:237374	540	PRK	Bacteria:22	PRK13388, PRK13388, acyl-CoA synthetase; Provisional.
CDD:237378	584	PRK	Bacteria:28	PRK13406, bchD, magnesium chelatase subunit D; Provisional.
CDD:184037	590	PRK	Bacteria:75	PRK13409, PRK13409, putative ATPase RIL; Provisional.
CDD:237386	181	PRK	Bacteria:75	PRK13429, PRK13429, F0F1 ATP synthase subunit delta; Provisional.
CDD:237387	271	PRK	Bacteria:39	PRK13430, PRK13430, F0F1 ATP synthase subunit delta; Provisional.
CDD:184052	145	PRK	Bacteria:16,nodiv:1	PRK13435, PRK13435, response regulator; Provisional.
CDD:184056	136	PRK	Bacteria:28	PRK13446, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
CDD:184057	136	PRK	Bacteria:20	PRK13447, PRK13447, F0F1 ATP synthase subunit epsilon; Provisional.
CDD:237391	475	PRK	Bacteria:123	PRK13473, PRK13473, gamma-aminobutyraldehyde dehydrogenase; Provisional.
CDD:237392	178	PRK	Bacteria:38	PRK13474, PRK13474, cytochrome b6-f complex iron-sulfur subunit; Provisional.
CDD:237393	512	PRK	Bacteria:36	PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase; Provisional.
CDD:184075	267	PRK	Bacteria:107	PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional.
CDD:184076	368	PRK	Bacteria:92	PRK13479, PRK13479, 2-aminoethylphosphonate--pyruvate transaminase; Provisional.
CDD:237395	352	PRK	Bacteria:162	PRK13482, PRK13482, DNA integrity scanning protein DisA; Provisional.
CDD:237396	201	PRK	Bacteria:41	PRK13487, PRK13487, chemoreceptor glutamine deamidase CheD; Provisional.
CDD:237397	157	PRK	Bacteria:21	PRK13488, PRK13488, chemoreceptor glutamine deamidase CheD; Provisional.
CDD:237401	345	PRK	Bacteria:91	PRK13499, PRK13499, rhamnose-proton symporter; Provisional.
CDD:237402	569	PRK	Bacteria:251	PRK13504, PRK13504, sulfite reductase subunit beta; Provisional.
CDD:237403	557	PRK	Bacteria:214	PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
CDD:237404	578	PRK	Bacteria:36	PRK13506, PRK13506, formate--tetrahydrofolate ligase; Provisional.
CDD:184100	251	PRK	Bacteria:79	PRK13509, PRK13509, transcriptional repressor UlaR; Provisional.
CDD:184101	95	PRK	Bacteria:81	PRK13510, PRK13510, sulfur transfer complex subunit TusB; Provisional.
CDD:184102	469	PRK	Bacteria:68	PRK13511, PRK13511, 6-phospho-beta-galactosidase; Provisional.
CDD:237406	371	PRK	Bacteria:31	PRK13515, PRK13515, carboxylate-amine ligase; Provisional.
CDD:237407	373	PRK	Bacteria:123	PRK13516, PRK13516, gamma-glutamyl:cysteine ligase; Provisional.
CDD:237408	373	PRK	Bacteria:52	PRK13517, PRK13517, carboxylate-amine ligase; Provisional.
CDD:237409	371	PRK	Bacteria:43	PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
CDD:237410	744	PRK	Bacteria:85	PRK13524, PRK13524, outer membrane receptor FepA; Provisional.
CDD:237411	189	PRK	Bacteria:178	PRK13525, PRK13525, glutamine amidotransferase subunit PdxT; Provisional.
CDD:237412	200	PRK	Bacteria:58	PRK13527, PRK13527, glutamine amidotransferase subunit PdxT; Provisional.
CDD:237414	563	PRK	Bacteria:297,nodiv:1	PRK13529, PRK13529, malate dehydrogenase; Provisional.
CDD:184118	498	PRK	Bacteria:94	PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
CDD:237416	830	PRK	Bacteria:181	PRK13532, PRK13532, nitrate reductase catalytic subunit; Provisional.
CDD:237417	487	PRK	Bacteria:44	PRK13533, PRK13533, 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional.
CDD:237418	639	PRK	Bacteria:24	PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional.
CDD:184125	204	PRK	Bacteria:159	PRK13538, PRK13538, cytochrome c biogenesis protein CcmA; Provisional.
CDD:237421	207	PRK	Bacteria:64	PRK13539, PRK13539, cytochrome c biogenesis protein CcmA; Provisional.
CDD:237422	258	PRK	Bacteria:143	PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
CDD:184134	506	PRK	Bacteria:109	PRK13549, PRK13549, xylose transporter ATP-binding subunit; Provisional.
CDD:184135	362	PRK	Bacteria:79	PRK13551, PRK13551, agmatine deiminase; Provisional.
CDD:184136	239	PRK	Bacteria:61	PRK13552, frdB, fumarate reductase iron-sulfur subunit; Provisional.
CDD:237423	258	PRK	Bacteria:25	PRK13553, PRK13553, fumarate reductase cytochrome b-556 subunit; Provisional.
CDD:237425	540	PRK	Bacteria:23	PRK13557, PRK13557, histidine kinase; Provisional.
CDD:237428	520	PRK	Bacteria:179	PRK13564, PRK13564, anthranilate synthase component I; Provisional.
CDD:184146	490	PRK	Bacteria:108	PRK13565, PRK13565, anthranilate synthase component I; Provisional.
CDD:237429	720	PRK	Bacteria:54	PRK13566, PRK13566, anthranilate synthase; Provisional.
CDD:184150	506	PRK	Bacteria:14	PRK13569, PRK13569, anthranilate synthase component I; Provisional.
CDD:237431	455	PRK	Bacteria:62	PRK13570, PRK13570, anthranilate synthase component I; Provisional.
CDD:184152	506	PRK	Bacteria:45	PRK13571, PRK13571, anthranilate synthase component I; Provisional.
CDD:237434	720	PRK	Bacteria:119	PRK13578, PRK13578, ornithine decarboxylase; Provisional.
CDD:237435	370	PRK	Bacteria:47,nodiv:1	PRK13579, gcvT, glycine cleavage system aminomethyltransferase T; Provisional.
CDD:237436	526	PRK	Bacteria:393	PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase; Provisional.
CDD:237437	205	PRK	Bacteria:48	PRK13582, thrH, phosphoserine phosphatase; Provisional.
CDD:237438	228	PRK	Bacteria:35	PRK13583, hisG, ATP phosphoribosyltransferase catalytic subunit; Provisional.
CDD:184165	241	PRK	Bacteria:34	PRK13585, PRK13585, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional.
CDD:237441	433	PRK	Bacteria:118	PRK13596, PRK13596, NADH dehydrogenase I subunit F; Provisional.
CDD:237443	303	PRK	Bacteria:115	PRK13606, PRK13606, LPPG:FO 2-phospho-L-lactate transferase; Provisional.
CDD:237444	443	PRK	Bacteria:141	PRK13607, PRK13607, proline dipeptidase; Provisional.
CDD:237446	113	PRK	Bacteria:33	PRK13612, PRK13612, photosystem II reaction center protein Psb28; Provisional.
CDD:237449	591	PRK	Bacteria:36	PRK13616, PRK13616, lipoprotein LpqB; Provisional.
CDD:184186	115	PRK	Bacteria:242,nodiv:1	PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA; Provisional.
CDD:184190	402	PRK	Bacteria:240	PRK13628, PRK13628, serine/threonine transporter SstT; Provisional.
CDD:237452	271	PRK	Bacteria:21	PRK13632, cbiO, cobalt transporter ATP-binding subunit; Provisional.
CDD:184195	279	PRK	Bacteria:47	PRK13635, cbiO, cobalt transporter ATP-binding subunit; Provisional.
CDD:237458	355	PRK	Bacteria:69	PRK13654, PRK13654, magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional.
CDD:237459	494	PRK	Bacteria:39	PRK13655, PRK13655, phosphoenolpyruvate carboxylase; Provisional.
CDD:237460	398	PRK	Bacteria:152,nodiv:1	PRK13656, PRK13656, trans-2-enoyl-CoA reductase; Provisional.
CDD:184214	588	PRK	Bacteria:49,nodiv:1	PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter; Provisional.
CDD:184216	103	PRK	Bacteria:86	PRK13659, PRK13659, hypothetical protein; Provisional.
CDD:237461	182	PRK	Bacteria:148	PRK13660, PRK13660, hypothetical protein; Provisional.
CDD:184218	182	PRK	Bacteria:101	PRK13661, PRK13661, hypothetical protein; Provisional.
CDD:184219	177	PRK	Bacteria:144	PRK13662, PRK13662, hypothetical protein; Provisional.
CDD:184220	493	PRK	Bacteria:86	PRK13663, PRK13663, hypothetical protein; Provisional.
CDD:237462	316	PRK	Bacteria:101	PRK13665, PRK13665, hypothetical protein; Provisional.
CDD:184223	92	PRK	Bacteria:74	PRK13666, PRK13666, hypothetical protein; Provisional.
CDD:184224	70	PRK	Bacteria:120	PRK13667, PRK13667, hypothetical protein; Provisional.
CDD:237463	267	PRK	Bacteria:72	PRK13668, PRK13668, hypothetical protein; Provisional.
CDD:184226	78	PRK	Bacteria:69	PRK13669, PRK13669, hypothetical protein; Provisional.
CDD:237464	388	PRK	Bacteria:157	PRK13670, PRK13670, hypothetical protein; Provisional.
CDD:184229	71	PRK	Bacteria:138	PRK13672, PRK13672, hypothetical protein; Provisional.
CDD:237465	118	PRK	Bacteria:67	PRK13673, PRK13673, hypothetical protein; Provisional.
CDD:237466	271	PRK	Bacteria:168	PRK13674, PRK13674, putative GTP cyclohydrolase; Provisional.
CDD:184232	308	PRK	Bacteria:46	PRK13675, PRK13675, GTP cyclohydrolase; Provisional.
CDD:237467	114	PRK	Bacteria:119	PRK13676, PRK13676, hypothetical protein; Provisional.
CDD:184235	95	PRK	Bacteria:144	PRK13678, PRK13678, hypothetical protein; Provisional.
CDD:184236	168	PRK	Bacteria:61	PRK13679, PRK13679, hypothetical protein; Provisional.
CDD:184237	117	PRK	Bacteria:74	PRK13680, PRK13680, hypothetical protein; Provisional.
CDD:184239	51	PRK	Bacteria:198,nodiv:1	PRK13682, PRK13682, hypothetical protein; Provisional.
CDD:184240	87	PRK	Bacteria:38	PRK13683, PRK13683, hypothetical protein; Provisional.
CDD:237468	334	PRK	Bacteria:37	PRK13684, PRK13684, Ycf48-like protein; Provisional.
CDD:184244	85	PRK	Bacteria:61,nodiv:1	PRK13687, PRK13687, hypothetical protein; Provisional.
CDD:237470	156	PRK	Bacteria:51	PRK13688, PRK13688, hypothetical protein; Provisional.
CDD:237471	75	PRK	Bacteria:142	PRK13689, PRK13689, hypothetical protein; Provisional.
CDD:237472	184	PRK	Bacteria:149	PRK13690, PRK13690, hypothetical protein; Provisional.
CDD:237475	174	PRK	Bacteria:31	PRK13695, PRK13695, putative NTPase; Provisional.
CDD:237476	62	PRK	Bacteria:19	PRK13696, PRK13696, hypothetical protein; Provisional.
CDD:184258	85	PRK	Bacteria:54	PRK13702, PRK13702, replication protein; Provisional.
CDD:184260	240	PRK	Bacteria:37	PRK13704, PRK13704, plasmid SOS inhibition protein A; Provisional.
CDD:184263	101	PRK	Bacteria:36	PRK13707, PRK13707, conjugal transfer pilus assembly protein TraL; Provisional.
CDD:184269	118	PRK	Bacteria:28	PRK13713, PRK13713, conjugal transfer protein TraM; Provisional.
CDD:237484	181	PRK	Bacteria:27	PRK13728, PRK13728, conjugal transfer protein TrbB; Provisional.
CDD:184285	171	PRK	Bacteria:28	PRK13733, PRK13733, conjugal transfer protein TraV; Provisional.
CDD:184296	262	PRK	Bacteria:48,Environmental:1	PRK13746, PRK13746, aminoglycoside resistance protein; Provisional.
CDD:237491	485	PRK	Bacteria:17	PRK13759, PRK13759, arylsulfatase; Provisional.
CDD:237492	231	PRK	Bacteria:79	PRK13760, PRK13760, putative RNA-associated protein; Provisional.
CDD:184308	248	PRK	Bacteria:81	PRK13761, PRK13761, hypothetical protein; Provisional.
CDD:237493	322	PRK	Bacteria:71	PRK13762, PRK13762, tRNA-modifying enzyme; Provisional.
CDD:237494	180	PRK	Bacteria:75	PRK13763, PRK13763, putative RNA-processing protein; Provisional.
CDD:184311	602	PRK	Bacteria:72	PRK13764, PRK13764, ATPase; Provisional.
CDD:237495	637	PRK	Bacteria:39	PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
CDD:237496	773	PRK	Bacteria:48	PRK13766, PRK13766, Hef nuclease; Provisional.
CDD:237497	876	PRK	Bacteria:51	PRK13767, PRK13767, ATP-dependent helicase; Provisional.
CDD:237498	253	PRK	Bacteria:34	PRK13768, PRK13768, GTPase; Provisional.
CDD:237500	318	PRK	Bacteria:20	PRK13776, PRK13776, formimidoylglutamase; Provisional.
CDD:237501	185	PRK	Bacteria:39	PRK13777, PRK13777, transcriptional regulator Hpr; Provisional.
CDD:184320	314	PRK	Bacteria:157	PRK13778, paaA, phenylacetate-CoA oxygenase subunit PaaA; Provisional.
CDD:237504	95	PRK	Bacteria:127	PRK13781, paaB, phenylacetate-CoA oxygenase subunit PaaB; Provisional.
CDD:237509	479	PRK	Bacteria:17	PRK13794, PRK13794, hypothetical protein; Provisional.
CDD:237510	636	PRK	Bacteria:18	PRK13795, PRK13795, hypothetical protein; Provisional.
CDD:237511	365	PRK	Bacteria:141	PRK13796, PRK13796, GTPase YqeH; Provisional.
CDD:184333	166	PRK	Bacteria:35	PRK13798, PRK13798, putative OHCU decarboxylase; Provisional.
CDD:237514	961	PRK	Bacteria:88	PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
CDD:237515	862	PRK	Bacteria:336	PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional.
CDD:237517	756	PRK	Bacteria:59	PRK13807, PRK13807, maltose phosphorylase; Provisional.
CDD:237520	215	PRK	Bacteria:18	PRK13813, PRK13813, orotidine 5'-phosphate decarboxylase; Provisional.
CDD:237521	394	PRK	Bacteria:44	PRK13820, PRK13820, argininosuccinate synthase; Provisional.
CDD:237522	641	PRK	Bacteria:24,nodiv:1	PRK13822, PRK13822, conjugal transfer coupling protein TraG; Provisional.
CDD:184348	94	PRK	Bacteria:37,Environmental:1,nodiv:1	PRK13823, PRK13823, conjugal transfer protein TrbD; Provisional.
CDD:184349	404	PRK	Bacteria:36,nodiv:1	PRK13824, PRK13824, replication initiation protein RepC; Provisional.
CDD:237523	388	PRK	Bacteria:19,nodiv:1	PRK13825, PRK13825, conjugal transfer protein TraB; Provisional.
CDD:184351	161	PRK	Bacteria:36	PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional.
CDD:237526	828	PRK	Bacteria:13,nodiv:1	PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional.
CDD:172365	176	PRK	Bacteria:12,nodiv:1	PRK13838, PRK13838, conjugal transfer pilin processing protease TraF; Provisional.
CDD:237530	207	PRK	Bacteria:11,nodiv:1	PRK13843, PRK13843, conjugal transfer protein TraH; Provisional.
CDD:184356	228	PRK	Bacteria:47	PRK13872, PRK13872, conjugal transfer protein TrbF; Provisional.
CDD:237536	811	PRK	Bacteria:43	PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
CDD:184358	230	PRK	Bacteria:45	PRK13874, PRK13874, conjugal transfer protein TrbJ; Provisional.
CDD:237537	440	PRK	Bacteria:41	PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
CDD:237538	663	PRK	Bacteria:41	PRK13876, PRK13876, conjugal transfer coupling protein TraG; Provisional.
CDD:184361	114	PRK	Bacteria:27,Environmental:1	PRK13877, PRK13877, conjugal transfer relaxosome component TraJ; Provisional.
CDD:237539	746	PRK	Bacteria:22,Environmental:1	PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
CDD:184363	253	PRK	Bacteria:37,Environmental:1	PRK13879, PRK13879, conjugal transfer protein TrbJ; Provisional.
CDD:237542	232	PRK	Bacteria:24,Environmental:1	PRK13882, PRK13882, conjugal transfer protein TrbP; Provisional.
CDD:184367	151	PRK	Bacteria:24,Environmental:1	PRK13883, PRK13883, conjugal transfer protein TrbH; Provisional.
CDD:184368	178	PRK	Bacteria:25,Environmental:1	PRK13884, PRK13884, conjugal transfer peptidase TraF; Provisional.
CDD:237546	988	PRK	Bacteria:17	PRK13889, PRK13889, conjugal transfer relaxase TraA; Provisional.
CDD:184378	144	PRK	Bacteria:24,Environmental:1	PRK13895, PRK13895, conjugal transfer protein TraM; Provisional.
CDD:237551	900	PRK	Bacteria:83	PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
CDD:237552	363	PRK	Bacteria:52	PRK13903, murB, UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional.
CDD:184384	257	PRK	Bacteria:29	PRK13904, murB, UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional.
CDD:237553	298	PRK	Bacteria:336,nodiv:1	PRK13905, murB, UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional.
CDD:184387	204	PRK	Bacteria:29	PRK13908, PRK13908, putative recombination protein RecO; Provisional.
CDD:237554	910	PRK	Bacteria:27	PRK13909, PRK13909, putative recombination protein RecB; Provisional.
CDD:237556	306	PRK	Bacteria:53	PRK13915, PRK13915, putative glucosyl-3-phosphoglycerate synthase; Provisional.
CDD:237560	276	PRK	Bacteria:603,nodiv:1	PRK13922, PRK13922, rod shape-determining protein MreC; Provisional.
CDD:237561	170	PRK	Bacteria:12	PRK13923, PRK13923, putative spore coat protein regulator protein YlbO; Provisional.
CDD:184399	198	PRK	Bacteria:22	PRK13925, rnhB, ribonuclease HII; Provisional.
CDD:237562	334	PRK	Bacteria:628,nodiv:1	PRK13927, PRK13927, rod shape-determining protein MreB; Provisional.
CDD:237563	336	PRK	Bacteria:85	PRK13928, PRK13928, rod shape-determining protein Mbl; Provisional.
CDD:237564	335	PRK	Bacteria:192	PRK13930, PRK13930, rod shape-determining protein MreB; Provisional.
CDD:237567	197	PRK	Bacteria:47,nodiv:1	PRK13936, PRK13936, phosphoheptose isomerase; Provisional.
CDD:184408	188	PRK	Bacteria:73	PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
CDD:184410	282	PRK	Bacteria:30	PRK13945, PRK13945, formamidopyrimidine-DNA glycosylase; Provisional.
CDD:184411	184	PRK	Bacteria:47,nodiv:1	PRK13946, PRK13946, shikimate kinase; Provisional.
CDD:237569	142	PRK	Bacteria:104	PRK13952, mscL, large-conductance mechanosensitive channel; Provisional.
CDD:237570	341	PRK	Bacteria:20	PRK13959, PRK13959, phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional.
CDD:237571	296	PRK	Bacteria:205	PRK13961, PRK13961, phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional.
CDD:184428	333	PRK	Bacteria:48,nodiv:1	PRK13971, PRK13971, hydroxyproline-2-epimerase; Provisional.
CDD:184429	213	PRK	Bacteria:42	PRK13973, PRK13973, thymidylate kinase; Provisional.
CDD:237575	576	PRK	Bacteria:143	PRK13977, PRK13977, myosin-cross-reactive antigen; Provisional.
CDD:184435	265	PRK	Bacteria:75	PRK13980, PRK13980, NAD synthetase; Provisional.
CDD:237577	540	PRK	Bacteria:164	PRK13981, PRK13981, NAD synthetase; Provisional.
CDD:237578	400	PRK	Bacteria:48	PRK13983, PRK13983, diaminopimelate aminotransferase; Provisional.
CDD:184450	404	PRK	Bacteria:234	PRK14012, PRK14012, cysteine desulfurase; Provisional.
CDD:237583	338	PRK	Bacteria:133,nodiv:1	PRK14013, PRK14013, hypothetical protein; Provisional.
CDD:237584	301	PRK	Bacteria:172,nodiv:1	PRK14014, PRK14014, putative acyltransferase; Provisional.
CDD:237585	875	PRK	Bacteria:395,nodiv:1	PRK14015, pepN, aminopeptidase N; Provisional.
CDD:237586	727	PRK	Bacteria:101	PRK14016, PRK14016, cyanophycin synthetase; Provisional.
CDD:184455	382	PRK	Bacteria:137	PRK14017, PRK14017, galactonate dehydratase; Provisional.
CDD:237587	367	PRK	Bacteria:75	PRK14019, PRK14019, bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional.
CDD:237588	481	PRK	Bacteria:69	PRK14022, PRK14022, UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional.
CDD:237589	241	PRK	Bacteria:76	PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
CDD:184465	447	PRK	Bacteria:35	PRK14032, PRK14032, citrate synthase; Provisional.
CDD:237590	375	PRK	Bacteria:38	PRK14033, PRK14033, citrate synthase; Provisional.
CDD:237591	377	PRK	Bacteria:45	PRK14036, PRK14036, citrate synthase; Provisional.
CDD:237592	593	PRK	Bacteria:87	PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
CDD:237597	172	PRK	Bacteria:219	PRK14054, PRK14054, methionine sulfoxide reductase A; Provisional.
CDD:237598	578	PRK	Bacteria:35	PRK14056, PRK14056, phenylalanine 4-monooxygenase; Provisional.
CDD:237599	268	PRK	Bacteria:43	PRK14058, PRK14058, acetylglutamate/acetylaminoadipate kinase; Provisional.
CDD:184482	251	PRK	Bacteria:43	PRK14059, PRK14059, hypothetical protein; Provisional.
CDD:237600	416	PRK	Bacteria:86,nodiv:1	PRK14072, PRK14072, 6-phosphofructokinase; Provisional.
CDD:237603	601	PRK	Bacteria:31	PRK14083, PRK14083, HSP90 family protein; Provisional.
CDD:237604	382	PRK	Bacteria:38	PRK14085, PRK14085, imidazolonepropionase; Provisional.
CDD:237606	347	PRK	Bacteria:29	PRK14089, PRK14089, ipid-A-disaccharide synthase; Provisional.
CDD:237608	533	PRK	Bacteria:31	PRK14095, pgi, glucose-6-phosphate isomerase; Provisional.
CDD:237609	528	PRK	Bacteria:54	PRK14096, pgi, glucose-6-phosphate isomerase; Provisional.
CDD:184504	448	PRK	Bacteria:200	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional.
CDD:184511	450	PRK	Bacteria:19	PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional.
CDD:237612	986	PRK	Bacteria:39,nodiv:1	PRK14108, PRK14108, bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional.
CDD:237613	1007	PRK	Bacteria:89	PRK14109, PRK14109, bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional.
CDD:184516	247	PRK	Bacteria:236	PRK14115, gpmA, phosphoglyceromutase; Provisional.
CDD:237615	390	PRK	Bacteria:27	PRK14121, PRK14121, tRNA (guanine-N(7)-)-methyltransferase; Provisional.
CDD:184523	103	PRK	Bacteria:19	PRK14125, PRK14125, cell division suppressor protein YneA; Provisional.
CDD:237616	109	PRK	Bacteria:38	PRK14127, PRK14127, cell division protein GpsB; Provisional.
CDD:237617	376	PRK	Bacteria:75	PRK14131, PRK14131, N-acetylneuraminic acid mutarotase; Provisional.
CDD:237618	126	PRK	Bacteria:15	PRK14132, PRK14132, riboflavin kinase; Provisional.
CDD:237619	263	PRK	Bacteria:125	PRK14135, recX, recombination regulator RecX; Provisional.
CDD:237621	185	PRK	Bacteria:61	PRK14139, PRK14139, heat shock protein GrpE; Provisional.
CDD:237622	191	PRK	Bacteria:66	PRK14140, PRK14140, heat shock protein GrpE; Provisional.
CDD:172630	209	PRK	Bacteria:37,nodiv:1	PRK14141, PRK14141, heat shock protein GrpE; Provisional.
CDD:237624	238	PRK	Bacteria:19	PRK14143, PRK14143, heat shock protein GrpE; Provisional.
CDD:184539	193	PRK	Bacteria:80	PRK14150, PRK14150, heat shock protein GrpE; Provisional.
CDD:184558	296	PRK	Bacteria:59,nodiv:1	PRK14188, PRK14188, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional.
CDD:184560	284	PRK	Bacteria:46	PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional.
CDD:184564	127	PRK	Bacteria:143	PRK14196, PRK14196, chromosome condensation membrane protein; Provisional.
CDD:184582	272	PRK	Bacteria:80	PRK14236, PRK14236, phosphate transporter ATP-binding protein; Provisional.
CDD:237663	374	PRK	Bacteria:37	PRK14293, PRK14293, chaperone protein DnaJ; Provisional.
CDD:184614	450	PRK	Bacteria:38	PRK14314, glmM, phosphoglucosamine mutase; Provisional.
CDD:237669	448	PRK	Bacteria:75,nodiv:1	PRK14315, glmM, phosphoglucosamine mutase; Provisional.
CDD:237670	448	PRK	Bacteria:175	PRK14316, glmM, phosphoglucosamine mutase; Provisional.
CDD:237671	465	PRK	Bacteria:25	PRK14317, glmM, phosphoglucosamine mutase; Provisional.
CDD:237672	448	PRK	Bacteria:61	PRK14318, glmM, phosphoglucosamine mutase; Provisional.
CDD:237673	444	PRK	Bacteria:397,nodiv:2	PRK14325, PRK14325, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional.
CDD:237675	439	PRK	Bacteria:37	PRK14328, PRK14328, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional.
CDD:237676	467	PRK	Bacteria:24	PRK14329, PRK14329, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional.
CDD:237680	213	PRK	Bacteria:62,nodiv:1	PRK14341, PRK14341, lipoate-protein ligase B; Provisional.
CDD:237681	213	PRK	Bacteria:193,nodiv:1	PRK14342, PRK14342, lipoate-protein ligase B; Provisional.
CDD:184638	234	PRK	Bacteria:45	PRK14345, PRK14345, lipoate-protein ligase B; Provisional.
CDD:184641	482	PRK	Bacteria:58	PRK14352, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional.
CDD:184642	446	PRK	Bacteria:67	PRK14353, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional.
CDD:184643	458	PRK	Bacteria:155	PRK14354, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional.
CDD:237689	430	PRK	Bacteria:27	PRK14359, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional.
CDD:184646	450	PRK	Bacteria:35	PRK14360, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional.
CDD:237705	201	PRK	Bacteria:14	PRK14404, PRK14404, membrane protein; Provisional.
CDD:237709	199	PRK	Bacteria:27	PRK14419, PRK14419, membrane protein; Provisional.
CDD:184675	92	PRK	Bacteria:69	PRK14426, PRK14426, acylphosphatase; Provisional.
CDD:184686	342	PRK	Bacteria:33	PRK14454, PRK14454, ribosomal RNA large subunit methyltransferase N; Provisional.
CDD:184688	345	PRK	Bacteria:30	PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase N; Provisional.
CDD:184689	373	PRK	Bacteria:82	PRK14459, PRK14459, ribosomal RNA large subunit methyltransferase N; Provisional.
CDD:237722	455	PRK	Bacteria:71	PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis protein NifN; Provisional.
CDD:184699	475	PRK	Bacteria:37	PRK14478, PRK14478, nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional.
CDD:237723	568	PRK	Bacteria:96	PRK14479, PRK14479, dihydroxyacetone kinase; Provisional.
CDD:237724	331	PRK	Bacteria:116	PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK; Provisional.
CDD:172956	329	PRK	Bacteria:42	PRK14483, PRK14483, DhaKLM operon coactivator DhaQ; Provisional.
CDD:184702	124	PRK	Bacteria:69	PRK14484, PRK14484, phosphotransferase mannnose-specific family component IIA; Provisional.
CDD:237725	217	PRK	Bacteria:207	PRK14487, PRK14487, cbb3-type cytochrome c oxidase subunit II; Provisional.
CDD:237726	473	PRK	Bacteria:211,nodiv:1	PRK14488, PRK14488, cbb3-type cytochrome c oxidase subunit I; Provisional.
CDD:237729	597	PRK	Bacteria:35	PRK14491, PRK14491, putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional.
CDD:237730	274	PRK	Bacteria:17	PRK14493, PRK14493, putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional.
CDD:237731	229	PRK	Bacteria:24	PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional.
CDD:237732	633	PRK	Bacteria:88	PRK14498, PRK14498, putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional.
CDD:184712	726	PRK	Bacteria:25	PRK14501, PRK14501, putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB; Provisional.
CDD:237738	497	PRK	Bacteria:173	PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional.
CDD:237740	879	PRK	Bacteria:61	PRK14511, PRK14511, maltooligosyl trehalose synthase; Provisional.
CDD:184724	155	PRK	Bacteria:56	PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
CDD:237750	84	PRK	Bacteria:62	PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
CDD:237751	69	PRK	Bacteria:60	PRK14549, PRK14549, 50S ribosomal protein L29P; Provisional.
CDD:237753	414	PRK	Bacteria:35	PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional.
CDD:184740	108	PRK	Bacteria:100	PRK14553, PRK14553, hypothetical protein; Provisional.
CDD:237754	422	PRK	Bacteria:63	PRK14554, PRK14554, putative pseudouridylate synthase; Provisional.
CDD:237755	145	PRK	Bacteria:53	PRK14555, PRK14555, hypothetical protein; Provisional.
CDD:237756	645	PRK	Bacteria:12	PRK14559, PRK14559, putative protein serine/threonine phosphatase; Provisional.
CDD:237757	160	PRK	Bacteria:55	PRK14560, PRK14560, putative RNA-binding protein; Provisional.
CDD:184745	194	PRK	Bacteria:49	PRK14561, PRK14561, hypothetical protein; Provisional.
CDD:184746	204	PRK	Bacteria:55	PRK14562, PRK14562, haloacid dehalogenase superfamily protein; Provisional.
CDD:237765	290	PRK	Bacteria:75,nodiv:1	PRK14608, PRK14608, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:237766	269	PRK	Bacteria:15	PRK14609, PRK14609, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional.
CDD:237771	308	PRK	Bacteria:19	PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional.
CDD:237786	137	PRK	Bacteria:37	PRK14673, PRK14673, hypothetical protein; Provisional.
CDD:237800	504	PRK	Bacteria:14	PRK14716, PRK14716, bacteriophage N4 adsorption protein B; Provisional.
CDD:237804	608	PRK	Bacteria:25	PRK14725, PRK14725, pyruvate kinase; Provisional.
CDD:184807	195	PRK	Bacteria:30	PRK14730, coaE, dephospho-CoA kinase; Provisional.
CDD:173193	208	PRK	Bacteria:11	PRK14731, coaE, dephospho-CoA kinase; Provisional.
CDD:237810	209	PRK	Bacteria:31	PRK14764, PRK14764, lipoprotein signal peptidase; Provisional.
CDD:237816	200	PRK	Bacteria:19	PRK14788, PRK14788, lipoprotein signal peptidase; Provisional.
CDD:237817	146	PRK	Bacteria:26	PRK14791, PRK14791, lipoprotein signal peptidase; Provisional.
CDD:237818	159	PRK	Bacteria:14	PRK14792, PRK14792, lipoprotein signal peptidase; Provisional.
CDD:184824	161	PRK	Bacteria:25	PRK14796, PRK14796, lipoprotein signal peptidase; Provisional.
CDD:184825	150	PRK	Bacteria:62	PRK14797, PRK14797, lipoprotein signal peptidase; Provisional.
CDD:237820	735	PRK	Bacteria:34	PRK14806, PRK14806, bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional.
CDD:184834	184	PRK	Bacteria:22	PRK14821, PRK14821, putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional.
CDD:184835	200	PRK	Bacteria:86	PRK14822, PRK14822, nucleoside-triphosphatase; Provisional.
CDD:184840	251	PRK	Bacteria:149	PRK14830, PRK14830, undecaprenyl pyrophosphate synthase; Provisional.
CDD:184841	249	PRK	Bacteria:34	PRK14831, PRK14831, undecaprenyl pyrophosphate synthase; Provisional.
CDD:184855	423	PRK	Bacteria:20	PRK14853, nhaA, pH-dependent sodium/proton antiporter; Provisional.
CDD:184859	90	PRK	Bacteria:22	PRK14857, tatA, twin arginine translocase protein A; Provisional.
CDD:237837	61	PRK	Bacteria:37	PRK14861, tatA, twin arginine translocase protein A; Provisional.
CDD:237838	440	PRK	Bacteria:273	PRK14862, rimO, ribosomal protein S12 methylthiotransferase; Provisional.
CDD:184866	104	PRK	Bacteria:88	PRK14864, PRK14864, putative biofilm stress and motility protein A; Provisional.
CDD:237840	451	PRK	Bacteria:19	PRK14866, PRK14866, hypothetical protein; Provisional.
CDD:237843	546	PRK	Bacteria:77	PRK14869, PRK14869, putative manganese-dependent inorganic pyrophosphatase; Provisional.
CDD:237844	665	PRK	Bacteria:61	PRK14873, PRK14873, primosome assembly protein PriA; Provisional.
CDD:237845	334	PRK	Bacteria:268,nodiv:1	PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase; Provisional.
CDD:184875	371	PRK	Bacteria:49	PRK14875, PRK14875, acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional.
CDD:184878	323	PRK	Bacteria:37	PRK14878, PRK14878, UGMP family protein; Provisional.
CDD:237847	211	PRK	Bacteria:41	PRK14879, PRK14879, serine/threonine protein kinase; Provisional.
CDD:237848	167	PRK	Bacteria:45	PRK14886, PRK14886, KEOPS complex Cgi121-like subunit; Provisional.
CDD:237849	84	PRK	Bacteria:33	PRK14887, PRK14887, KEOPS complex Pcc1-like subunit; Provisional.
CDD:237850	59	PRK	Bacteria:29	PRK14888, PRK14888, KEOPS complex Pcc1-like subunit; Provisional.
CDD:184883	143	PRK	Bacteria:16	PRK14889, PRK14889, VKOR family protein; Provisional.
CDD:184884	59	PRK	Bacteria:62	PRK14890, PRK14890, putative Zn-ribbon RNA-binding protein; Provisional.
CDD:184886	99	PRK	Bacteria:21	PRK14892, PRK14892, putative transcription elongation factor Elf1; Provisional.
CDD:237852	258	PRK	Bacteria:53	PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional.
CDD:237856	434	PRK	Bacteria:35	PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
CDD:237857	444	PRK	Bacteria:185	PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
CDD:237858	445	PRK	Bacteria:11	PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
CDD:237859	1000	PRK	Bacteria:23	PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional.
CDD:237860	756	PRK	Bacteria:488,nodiv:2	PRK14939, gyrB, DNA gyrase subunit B; Provisional.
CDD:237862	620	PRK	Bacteria:31	PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional.
CDD:237863	944	PRK	Bacteria:18	PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional.
CDD:237865	618	PRK	Bacteria:15	PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional.
CDD:237872	188	PRK	Bacteria:46	PRK14968, PRK14968, putative methyltransferase; Provisional.
CDD:237875	336	PRK	Bacteria:52	PRK14974, PRK14974, cell division protein FtsY; Provisional.
CDD:237876	553	PRK	Bacteria:44	PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional.
CDD:237877	281	PRK	Bacteria:30	PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
CDD:184943	112	PRK	Bacteria:60	PRK14981, PRK14981, DNA-directed RNA polymerase subunit F; Provisional.
CDD:237879	231	PRK	Bacteria:37	PRK14983, PRK14983, aldehyde decarbonylase; Provisional.
CDD:237883	1031	PRK	Bacteria:45	PRK14991, PRK14991, tetrathionate reductase subunit A; Provisional.
CDD:237885	389	PRK	Bacteria:53	PRK15033, PRK15033, tricarballylate utilization protein B; Provisional.
CDD:237886	219	PRK	Bacteria:56	PRK15042, pduD, propanediol dehydratase medium subunit; Provisional.
CDD:237887	349	PRK	Bacteria:48	PRK15046, PRK15046, 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional.
CDD:237888	296	PRK	Bacteria:48	PRK15050, PRK15050, 2-aminoethylphosphonate transport system permease PhnU; Provisional.
CDD:237890	344	PRK	Bacteria:50	PRK15055, PRK15055, anaerobic sulfite reductase subunit A; Provisional.
CDD:237891	726	PRK	Bacteria:404,nodiv:1	PRK15061, PRK15061, catalase/hydroperoxidase HPI(I); Provisional.
CDD:237892	364	PRK	Bacteria:390	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional.
CDD:237893	428	PRK	Bacteria:360,nodiv:1	PRK15063, PRK15063, isocitrate lyase; Provisional.
CDD:237894	530	PRK	Bacteria:229	PRK15064, PRK15064, ABC transporter ATP-binding protein; Provisional.
CDD:237895	262	PRK	Bacteria:211	PRK15065, PRK15065, PTS system mannose-specific transporter subunit IIC; Provisional.
CDD:237896	257	PRK	Bacteria:246,nodiv:1	PRK15066, PRK15066, inner membrane transport permease; Provisional.
CDD:237897	461	PRK	Bacteria:242	PRK15067, PRK15067, ethanolamine ammonia lyase large subunit; Provisional.
CDD:237898	322	PRK	Bacteria:225	PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
CDD:237899	211	PRK	Bacteria:133	PRK15070, PRK15070, propanediol utilization phosphotransacylase; Provisional.
CDD:237900	356	PRK	Bacteria:153	PRK15071, PRK15071, lipopolysaccharide ABC transporter permease; Provisional.
CDD:237901	404	PRK	Bacteria:125,nodiv:1	PRK15072, PRK15072, bifunctional D-altronate/D-mannonate dehydratase; Provisional.
CDD:237902	434	PRK	Bacteria:99	PRK15075, PRK15075, citrate-proton symporter; Provisional.
CDD:185035	431	PRK	Bacteria:108,nodiv:1	PRK15076, PRK15076, alpha-galactosidase; Provisional.
CDD:237903	379	PRK	Bacteria:92	PRK15078, PRK15078, polysaccharide export protein Wza; Provisional.
CDD:237904	267	PRK	Bacteria:110	PRK15080, PRK15080, ethanolamine utilization protein EutJ; Provisional.
CDD:185042	133	PRK	Bacteria:81	PRK15084, PRK15084, formate hydrogenlyase maturation protein HycH; Provisional.
CDD:237906	372	PRK	Bacteria:104	PRK15086, PRK15086, ethanolamine utilization protein EutH; Provisional.
CDD:185045	322	PRK	Bacteria:106	PRK15088, PRK15088, PTS system mannose-specific transporter subunits IIAB; Provisional.
CDD:185046	257	PRK	Bacteria:100	PRK15090, PRK15090, DNA-binding transcriptional regulator KdgR; Provisional.
CDD:237907	310	PRK	Bacteria:94	PRK15092, PRK15092, DNA-binding transcriptional repressor LrhA; Provisional.
CDD:185056	961	PRK	Bacteria:99	PRK15101, PRK15101, protease3; Provisional.
CDD:237910	419	PRK	Bacteria:95	PRK15103, PRK15103, paraquat-inducible membrane protein A; Provisional.
CDD:185068	214	PRK	Bacteria:90	PRK15113, PRK15113, glutathione S-transferase; Provisional.
CDD:185076	289	PRK	Bacteria:96	PRK15121, PRK15121, right oriC-binding transcriptional activator; Provisional.
CDD:237914	903	PRK	Bacteria:85	PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
CDD:237915	268	PRK	Bacteria:83	PRK15123, PRK15123, lipopolysaccharide core heptose(I) kinase RfaP; Provisional.
CDD:185085	389	PRK	Bacteria:91	PRK15131, PRK15131, mannose-6-phosphate isomerase; Provisional.
CDD:237929	496	PRK	Bacteria:88	PRK15238, PRK15238, inner membrane transporter YjeM; Provisional.
CDD:237931	271	PRK	Bacteria:20	PRK15251, PRK15251, cytolethal distending toxin subunit CdtB; Provisional.
CDD:237933	197	PRK	Bacteria:41	PRK15262, PRK15262, putative fimbrial protein StaF; Provisional.
CDD:185171	196	PRK	Bacteria:38	PRK15263, PRK15263, putative fimbrial protein StaE; Provisional.
CDD:237942	517	PRK	Bacteria:330	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional.
CDD:237946	686	PRK	Bacteria:42	PRK15337, PRK15337, type III secretion system protein InvA; Provisional.
CDD:237951	921	PRK	Bacteria:35	PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional.
CDD:237955	536	PRK	Bacteria:135	PRK15389, PRK15389, fumarate hydratase; Provisional.
CDD:185292	296	PRK	Bacteria:103	PRK15394, PRK15394, 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional.
CDD:185295	239	PRK	Bacteria:108	PRK15397, PRK15397, nicotinamide riboside transporter PnuC; Provisional.
CDD:237956	465	PRK	Bacteria:96	PRK15398, PRK15398, aldehyde dehydrogenase EutE; Provisional.
CDD:237957	213	PRK	Bacteria:149	PRK15401, PRK15401, alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional.
CDD:185300	406	PRK	Bacteria:104	PRK15402, PRK15402, multidrug efflux system translocase MdfA; Provisional.
CDD:237959	369	PRK	Bacteria:140	PRK15404, PRK15404, leucine ABC transporter subunit substrate-binding protein LivK; Provisional.
CDD:237960	438	PRK	Bacteria:77	PRK15407, PRK15407, lipopolysaccharide biosynthesis protein RfbH; Provisional.
CDD:185313	266	PRK	Bacteria:70	PRK15415, PRK15415, propanediol utilization protein PduB; Provisional.
CDD:237964	570	PRK	Bacteria:60	PRK15426, PRK15426, putative diguanylate cyclase YedQ; Provisional.
CDD:185340	138	PRK	Bacteria:64	PRK15443, pduE, propanediol dehydratase small subunit; Provisional.
CDD:185341	554	PRK	Bacteria:64	PRK15444, pduC, propanediol dehydratase large subunit; Provisional.
CDD:185342	427	PRK	Bacteria:179	PRK15445, PRK15445, arsenical pump membrane protein; Provisional.
CDD:237967	383	PRK	Bacteria:171	PRK15446, PRK15446, phosphonate metabolism protein PhnM; Provisional.
CDD:237968	301	PRK	Bacteria:209,nodiv:1	PRK15447, PRK15447, putative protease; Provisional.
CDD:237969	443	PRK	Bacteria:222	PRK15452, PRK15452, putative protease; Provisional.
CDD:237970	290	PRK	Bacteria:232	PRK15453, PRK15453, phosphoribulokinase; Provisional.
CDD:185352	644	PRK	Bacteria:241	PRK15455, PRK15455, PrkA family serine protein kinase; Provisional.
CDD:237972	986	PRK	Bacteria:33	PRK15483, PRK15483, type III restriction-modification system StyLTI enzyme res; Provisional.
CDD:237973	759	PRK	Bacteria:36	PRK15488, PRK15488, thiosulfate reductase PhsA; Provisional.
CDD:240229	821	EUK	Invertebrates:10	PTZ00014, PTZ00014, myosin-A; Provisional.
CDD:185406	121	EUK	Invertebrates:12	PTZ00030, PTZ00030, 60S ribosomal protein L20; Provisional.
CDD:173331	124	EUK	Invertebrates:20	PTZ00034, PTZ00034, 40S ribosomal protein S10; Provisional.
CDD:185407	337	EUK	Invertebrates:22	PTZ00035, PTZ00035, Rad51 protein; Provisional.
CDD:240239	120	EUK	Invertebrates:22	PTZ00041, PTZ00041, 60S ribosomal protein L35a; Provisional.
CDD:240242	358	EUK	Invertebrates:1	PTZ00046, PTZ00046, rifin; Provisional.
CDD:240245	421	EUK	Invertebrates:14	PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase; Provisional.
CDD:240246	470	EUK	Invertebrates:20	PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
CDD:240253	202	EUK	Invertebrates:24	PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
CDD:240254	300	EUK	Invertebrates:24	PTZ00069, PTZ00069, 60S ribosomal protein L5; Provisional.
CDD:240256	132	EUK	Invertebrates:23	PTZ00071, PTZ00071, 40S ribosomal protein S24; Provisional.
CDD:185429	135	EUK	Invertebrates:24	PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
CDD:240258	476	EUK	Invertebrates:23	PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
CDD:185434	85	EUK	Invertebrates:22	PTZ00083, PTZ00083, 40S ribosomal protein S27; Provisional.
CDD:240260	220	EUK	Invertebrates:24	PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
CDD:240263	898	EUK	Invertebrates:18	PTZ00092, PTZ00092, aconitate hydratase-like protein; Provisional.
CDD:240264	452	EUK	Invertebrates:19	PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
CDD:185442	143	EUK	Invertebrates:24	PTZ00096, PTZ00096, 40S ribosomal protein S15; Provisional.
CDD:240268	398	EUK	Invertebrates:24	PTZ00104, PTZ00104, S-adenosylmethionine synthase; Provisional.
CDD:240269	140	EUK	Invertebrates:24	PTZ00105, PTZ00105, 60S ribosomal protein L12; Provisional.
CDD:240270	464	EUK	Invertebrates:15	PTZ00107, PTZ00107, hexokinase; Provisional.
CDD:240271	1388	EUK	Invertebrates:19	PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
CDD:185455	555	EUK	Invertebrates:24	PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
CDD:185458	154	EUK	Invertebrates:17	PTZ00120, PTZ00120, D-tyrosyl-tRNA(Tyr) deacylase; Provisional.
CDD:240279	299	EUK	Invertebrates:13	PTZ00122, PTZ00122, phosphoglycerate mutase; Provisional.
CDD:240280	236	EUK	Invertebrates:15	PTZ00123, PTZ00123, phosphoglycerate mutase like-protein; Provisional.
CDD:240282	383	EUK	Invertebrates:16	PTZ00126, PTZ00126, tyrosyl-tRNA synthetase; Provisional.
CDD:240283	403	EUK	Invertebrates:17	PTZ00127, PTZ00127, cytochrome c oxidase assembly protein; Provisional.
CDD:185464	232	EUK	Invertebrates:17	PTZ00128, PTZ00128, cytochrome c oxidase assembly protein-like; Provisional.
CDD:185469	154	EUK	Invertebrates:24	PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
CDD:240285	310	EUK	Invertebrates:19	PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
CDD:240289	418	EUK	Invertebrates:17	PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional.
CDD:240291	293	EUK	Invertebrates:23	PTZ00146, PTZ00146, fibrillarin; Provisional.
CDD:240292	205	EUK	Invertebrates:24	PTZ00148, PTZ00148, 40S ribosomal protein S8; Provisional.
CDD:240295	134	EUK	Invertebrates:23	PTZ00154, PTZ00154, 40S ribosomal protein S17; Provisional.
CDD:240297	133	EUK	Invertebrates:24	PTZ00159, PTZ00159, 60S ribosomal protein L32; Provisional.
CDD:185489	147	EUK	Invertebrates:23	PTZ00160, PTZ00160, 60S ribosomal protein L27a; Provisional.
CDD:240299	514	EUK	Invertebrates:16	PTZ00164, PTZ00164, bifunctional dihydrofolate reductase-thymidylate synthase; Provisional.
CDD:240301	1054	EUK	Invertebrates:17	PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional.
CDD:240303	228	EUK	Invertebrates:17	PTZ00170, PTZ00170, D-ribulose-5-phosphate 3-epimerase; Provisional.
CDD:240304	148	EUK	Invertebrates:10	PTZ00171, PTZ00171, acyl carrier protein; Provisional.
CDD:185497	108	EUK	Invertebrates:22	PTZ00172, PTZ00172, 40S ribosomal protein S26; Provisional.
CDD:240305	247	EUK	Invertebrates:22	PTZ00174, PTZ00174, phosphomannomutase; Provisional.
CDD:185500	270	EUK	Invertebrates:23	PTZ00175, PTZ00175, diphthine synthase; Provisional.
CDD:240306	181	EUK	Invertebrates:23	PTZ00178, PTZ00178, 60S ribosomal protein L17; Provisional.
CDD:185502	355	EUK	Invertebrates:18	PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase; Provisional.
CDD:240309	160	EUK	Invertebrates:24	PTZ00189, PTZ00189, 60S ribosomal protein L21; Provisional.
CDD:185507	145	EUK	Invertebrates:22	PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
CDD:185509	98	EUK	Invertebrates:23	PTZ00196, PTZ00196, 60S ribosomal protein L36; Provisional.
CDD:173474	122	EUK	Invertebrates:19	PTZ00198, PTZ00198, 60S ribosomal protein L22; Provisional.
CDD:240310	448	EUK	Invertebrates:3	PTZ00200, PTZ00200, cysteine proteinase; Provisional.
CDD:185514	533	EUK	Invertebrates:24	PTZ00212, PTZ00212, T-complex protein 1 subunit beta; Provisional.
CDD:185516	151	EUK	Invertebrates:12	PTZ00215, PTZ00215, ribose 5-phosphate isomerase; Provisional.
CDD:240316	700	EUK	Invertebrates:5	PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional.
CDD:240317	393	EUK	Invertebrates:24	PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
CDD:185519	474	EUK	Invertebrates:23	PTZ00219, PTZ00219, Sec61 alpha  subunit; Provisional.
CDD:173487	164	EUK	Invertebrates:14	PTZ00236, PTZ00236, mitochondrial import inner membrane translocase subunit tim17; Provisional.
CDD:240326	158	EUK	Invertebrates:22	PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional.
CDD:185524	166	EUK	Invertebrates:13	PTZ00242, PTZ00242, protein tyrosine phosphatase; Provisional.
CDD:240328	345	EUK	Invertebrates:9	PTZ00247, PTZ00247, adenosine kinase; Provisional.
CDD:240329	319	EUK	Invertebrates:17	PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional.
CDD:240331	249	EUK	Invertebrates:24	PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional.
CDD:240334	390	EUK	Invertebrates:24	PTZ00258, PTZ00258, GTP-binding protein; Provisional.
CDD:240335	434	EUK	Invertebrates:11	PTZ00259, PTZ00259, endonuclease G; Provisional.
CDD:185539	459	EUK	Invertebrates:10	PTZ00286, PTZ00286, 6-phospho-1-fructokinase; Provisional.
CDD:240348	504	EUK	Invertebrates:20	PTZ00294, PTZ00294, glycerol kinase-like protein; Provisional.
CDD:240349	640	EUK	Invertebrates:15	PTZ00295, PTZ00295, glucosamine-fructose-6-phosphate aminotransferase; Provisional.
CDD:240352	585	EUK	Invertebrates:18	PTZ00302, PTZ00302, N-acetylglucosamine-phosphate mutase; Provisional.
CDD:185549	561	EUK	Invertebrates:18	PTZ00311, PTZ00311, phosphoenolpyruvate carboxykinase; Provisional.
CDD:240355	495	EUK	Invertebrates:17	PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase; Provisional.
CDD:240357	559	EUK	Invertebrates:12	PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
CDD:240360	321	EUK	Invertebrates:5	PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
CDD:240361	494	EUK	Invertebrates:23	PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain; Provisional.
CDD:240362	460	EUK	Invertebrates:23	PTZ00327, PTZ00327, eukaryotic translation initiation factor 2 gamma subunit; Provisional.
CDD:240363	212	EUK	Invertebrates:12	PTZ00331, PTZ00331, alpha/beta hydrolase; Provisional.
CDD:240365	255	EUK	Invertebrates:23	PTZ00333, PTZ00333, triosephosphate isomerase; Provisional.
CDD:240367	294	EUK	Invertebrates:20	PTZ00338, PTZ00338, dimethyladenosine transferase-like protein; Provisional.
CDD:240369	345	EUK	Invertebrates:18	PTZ00340, PTZ00340, O-sialoglycoprotein endopeptidase-like protein; Provisional.
CDD:240376	436	EUK	Invertebrates:13	PTZ00350, PTZ00350, adenylosuccinate synthetase; Provisional.
CDD:240377	212	EUK	Invertebrates:13	PTZ00352, PTZ00352, 60S ribosomal protein L13; Provisional.
CDD:173547	334	EUK	Invertebrates:9	PTZ00354, PTZ00354, alcohol dehydrogenase; Provisional.
CDD:185573	115	EUK	Invertebrates:14	PTZ00356, PTZ00356, peptidyl-prolyl cis-trans isomerase (PPIase); Provisional.
CDD:240378	367	EUK	Invertebrates:1	PTZ00358, PTZ00358, hypothetical protein; Provisional.
CDD:185577	443	EUK	Invertebrates:20	PTZ00363, PTZ00363, rab-GDP dissociation inhibitor; Provisional.
CDD:240383	392	EUK	Invertebrates:1	PTZ00366, PTZ00366, Surface antigen  (SAG) superfamily; Provisional.
CDD:240386	296	EUK	Invertebrates:1	PTZ00370, PTZ00370, STEVOR; Provisional.
CDD:240387	465	EUK	Invertebrates:20	PTZ00371, PTZ00371, aspartyl aminopeptidase; Provisional.
CDD:240388	413	EUK	Invertebrates:12	PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
CDD:240390	404	EUK	Invertebrates:18	PTZ00376, PTZ00376, aspartate aminotransferase; Provisional.
CDD:240391	481	EUK	Invertebrates:15	PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
CDD:240392	493	EUK	Invertebrates:9	PTZ00381, PTZ00381, aldehyde dehydrogenase family protein; Provisional.
CDD:185592	184	EUK	Invertebrates:24	PTZ00389, PTZ00389, 40S ribosomal protein S7; Provisional.
CDD:240400	251	EUK	Invertebrates:19	PTZ00396, PTZ00396, Casein kinase II subunit beta; Provisional.
CDD:240402	651	EUK	Invertebrates:22	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
CDD:240411	995	EUK	Invertebrates:20	PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein; Provisional.
CDD:185612	552	EUK	Invertebrates:13	PTZ00430, PTZ00430, glucose-6-phosphate isomerase; Provisional.
CDD:240417	413	EUK	Invertebrates:18	PTZ00435, PTZ00435, isocitrate dehydrogenase; Provisional.
CDD:240436	352	EUK	Invertebrates:8	PTZ00486, PTZ00486, apyrase Superfamily; Provisional.
CDD:240439	850	EUK	Invertebrates:8	PTZ00491, PTZ00491, major vault protein; Provisional.
CDD:129113	63	EUKprk	Bacteria:4,Plants:5	TIGR00001, rpmI_bact, ribosomal protein L35.  This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:129114	78	EUKprk	Bacteria:3,Plants:5,Primates:1	TIGR00002, S16, ribosomal protein S16.  This model describes ribosomal S16 of bacteria and organelles [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:129116	124	EUKprk	Bacteria:8,Invertebrates:1,Plants:2,Rodents:1	TIGR00004, TIGR00004, reactive intermediate/imine deaminase.  This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by ...
CDD:161659	299	PRK	Bacteria:3	TIGR00005, rluA_subfam, pseudouridine synthase, RluA family.  In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine [Protein synthesis, tRNA and rRNA base modification].
CDD:232779	230	PRK	Bacteria:13	TIGR00007, TIGR00007, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase.  This protein family consists of HisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, the enzyme catalyzing the fourth step in histidine biosynthesis. It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase ...
CDD:199985	56	EUKprk	Bacteria:9,Plants:1	TIGR00009, L28, ribosomal protein L28.  This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:232780	252	PRK	Bacteria:3	TIGR00010, TIGR00010, hydrolase, TatD family.  PSI-BLAST, starting with a urease alpha subunit, finds a large superfamily of proteins, including a number of different enzymes that act as hydrolases at C-N bonds other than peptide bonds (EC 3.5.-.-), many uncharacterized proteins, and the members of this family. Several genomes have multiple paralogs related to this family. However, a set of 17 proteins can be found, one each from 17 of the first 20 genomes, such ...
CDD:232781	152	PRK	Bacteria:14	TIGR00011, YbaK_EbsC, Cys-tRNA(Pro) deacylase.  This model represents the YbaK family, bacterial proteins whose full length sequence is homologous to an insertion domain in proline--tRNA ligases. The domain deacylates mischarged tRNAs. The YbaK protein of Haemophilus influenzae (HI1434) likewise deacylates Ala-tRNA(Pro), but not the correctly charged Pro-tRNA(Pro). A crystallographic study of HI1434 suggests a nucleotide binding function. Previously, a member of ...
CDD:129124	55	EUKprk	Bacteria:10,Invertebrates:2,Plants:3	TIGR00012, L29, ribosomal protein L29.  This model describes a ribosomal large subunit protein, called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:232786	218	EUKprk	Bacteria:16,Invertebrates:1,Plants:2,Primates:1	TIGR00021, rpiA, ribose 5-phosphate isomerase.  This model describes ribose 5-phosphate isomerase, an enzyme of the non-oxidative branch of the pentose phosphate pathway [Energy metabolism, Pentose phosphate pathway].
CDD:211538	113	PRK	Bacteria:5	TIGR00026, hi_GC_TIGR00026, deazaflavin-dependent oxidoreductase, nitroreductase family.  This model represents a family of proteins found in paralogous families in the genera Mycobacterium and Streptomyces. Seven members are in Mycobacterium tuberculosis. Member protein Rv3547 has been characterized as a deazaflavin-dependent nitroreductase [Unknown function, Enzymes of unknown specificity].
CDD:232789	260	PRK	Bacteria:9	TIGR00027, mthyl_TIGR00027, methyltransferase, TIGR00027 family.  This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other ...
CDD:232790	142	miss	miss	TIGR00028, Mtu_PIN_fam, Mycobacterium tuberculosis PIN domain family.  Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
CDD:129141	58	EUKprk	Bacteria:7,Environmental:1,Invertebrates:1,Primates:1	TIGR00030, S21p, ribosomal protein S21.  This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:232792	351	EUKprk	Bacteria:1,Plants:1	TIGR00033, aroC, chorismate synthase.  Homotetramer (noted in E.coli) suggests reason for good conservation [Amino acid biosynthesis, Aromatic amino acid family].
CDD:213496	184	PRK	Bacteria:19	TIGR00038, efp, translation elongation factor P.  function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, ...
CDD:232793	124	EUKprk	Bacteria:1,Invertebrates:2,Primates:1	TIGR00039, 6PTHBS, 6-pyruvoyl tetrahydropterin synthase/QueD family protein.  This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble ...
CDD:232794	158	PRK	Bacteria:3	TIGR00040, yfcE, phosphoesterase, MJ0936 family.  Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown ...
CDD:161676	195	EUKprk	Bacteria:2,Plants:2	TIGR00041, DTMP_kinase, thymidylate kinase.  Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions].
CDD:232795	184	PRK	Bacteria:2	TIGR00042, TIGR00042, non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family.  Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine, which can be a natural product of monooxygenase activity on adenine. Methanococcus jannaschii MJ0226 and E. coli RdgB are also characterized as pyrophosphatases active against non-standard purines NTPs. E. coli RdgB appears to act by intercepting non-canonical ...
CDD:232796	110	EUKprk	Bacteria:19,Primates:1,nodiv:1	TIGR00043, TIGR00043, probable rRNA maturation factor YbeY.  This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect [Protein synthesis, Other].
CDD:232797	375	PRK	Bacteria:8	TIGR00045, TIGR00045, glycerate kinase.  The only characterized member of this family so far is the glycerate kinase GlxK (EC 2.7.1.31) of E. coli. This enzyme acts after glyoxylate carboligase and 2-hydroxy-3-oxopropionate reductase (tartronate semialdehyde reductase) in the conversion of glyoxylate to 3-phosphoglycerate (the D-glycerate pathway) as a part of allantoin degradation [Energy metabolism, Other].
CDD:129157	240	PRK	Bacteria:3	TIGR00046, TIGR00046, RNA methyltransferase, RsmE family.  Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA [Protein synthesis, tRNA and rRNA base modification].
CDD:232799	105	EUKprk	Bacteria:16,Invertebrates:2,Plants:3	TIGR00049, TIGR00049, Iron-sulfur cluster assembly accessory protein.  Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS ...
CDD:232802	201	PRK	Bacteria:2	TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family.  Has paralogs, but YrdC called a tRNA modification protein. Ref 2 authors say probably heteromultimeric complex. Paralogs may mean its does the final binding to the tRNA [Protein synthesis, tRNA and rRNA base modification].
CDD:232804	272	PRK	Bacteria:8	TIGR00064, ftsY, signal recognition particle-docking protein FtsY.  There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein [Protein fate, Protein and peptide secretion and trafficking].
CDD:232805	349	PRK	Bacteria:4	TIGR00065, ftsZ, cell division protein FtsZ.  This family consists of cell division protein FtsZ, a GTPase found in bacteria, the chloroplast of plants, and in archaebacteria. Structurally similar to tubulin, FtsZ undergoes GTP-dependent polymerization into filaments that form a cytoskeleton involved in septum synthesis [Cellular processes, Cell division].
CDD:232808	393	EUKprk	Bacteria:42,Plants:2	TIGR00069, hisD, histidinol dehydrogenase.  This model describes a polypeptide sequence catalyzing the final step in histidine biosynthesis, found sometimes as an independent protein and sometimes as a part of a multifunctional protein [Amino acid biosynthesis, Histidine family].
CDD:232809	182	PRK	Bacteria:17	TIGR00070, hisG, ATP phosphoribosyltransferase.  Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension [Amino acid biosynthesis, Histidine family].
CDD:232810	227	EUKprk	Bacteria:2,Plants:1	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase.  Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs [Protein synthesis, tRNA and rRNA base modification].
CDD:199990	145	PRK	Bacteria:52	TIGR00072, hydrog_prot, hydrogenase maturation protease.  HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.
CDD:129184	76	PRK	Bacteria:3	TIGR00074, hypC_hupF, hydrogenase assembly chaperone HypC/HupF.  See Medline:98153179 for function. This protein is suggested by act as a chaperone for a hydrogenase large subunit, holding the precursor form before metallocenter nickel incorporation. [SS 12/31/03] More recently proposed additional function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PMID:12441107. Added ...
CDD:232813	166	miss	miss	TIGR00077, lspA, lipoprotein signal peptidase.  Alternate name: lipoprotein signal peptidase [Protein fate, Protein and peptide secretion and trafficking].
CDD:232814	265	EUKprk	Bacteria:7,Plants:1,Primates:1	TIGR00078, nadC, nicotinate-nucleotide pyrophosphorylase.  Synonym: quinolinate phosphoribosyltransferase (decarboxylating) [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides].
CDD:232815	161	PRK	Bacteria:4	TIGR00079, pept_deformyl, peptide deformylase.  Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, is a metalloenzyme that uses water to release formate from the N-terminal formyl-L-methionine of bacterial and chloroplast peptides. This enzyme should not be confused with formylmethionine deformylase (EC 3.5.1.31) which is active on free N-formyl methionine and has been reported from rat intestine [Protein fate, Protein modification and repair].
CDD:129193	191	PRK	Bacteria:1	TIGR00084, ruvA, Holliday junction DNA helicase, RuvA subunit.  RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions [DNA metabolism, DNA replication, ...
CDD:129194	144	PRK	Bacteria:7	TIGR00086, smpB, SsrA-binding protein.  This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the ...
CDD:232819	244	EUKprk	Bacteria:2,Plants:2	TIGR00087, surE, 5'/3'-nucleotidase SurE.  This protein family originally was named SurE because of its role in stationary phase survivalin Escherichia coli. In E. coli, surE is next to pcm, an L-isoaspartyl protein repair methyltransferase that is also required for stationary phase survival. Recent work (PMID:15489502) shows that viewing SurE as an acid phosphatase (3.1.3.2) is not accurate. Rather, SurE in E. coli, Thermotoga maritima, and Pyrobaculum ...
CDD:232820	429	PRK	Bacteria:4	TIGR00089, TIGR00089, radical SAM methylthiotransferase, MiaB/RimO family.  This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is ...
CDD:161702	99	PRK	Bacteria:89	TIGR00090, iojap_ybeB, iojap-like ribosome-associated protein.  This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown [Unknown ...
CDD:161703	194	EUKprk	Bacteria:3,Plants:1	TIGR00091, TIGR00091, tRNA (guanine-N(7)-)-methyltransferase.  This predicted S-adenosylmethionine-dependent methyltransferase is found in a single copy in most Bacteria. It is also found, with a short amino-terminal extension in eukaryotes. Its function is unknown. In E. coli, this protein flanks the DNA repair protein MutY, also called micA [Protein synthesis, tRNA and rRNA base modification].
CDD:232821	128	PRK	Bacteria:3	TIGR00093, TIGR00093, pseudouridine synthase.  This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc [Protein synthesis, tRNA and rRNA base modification].
CDD:232822	387	PRK	Bacteria:1	TIGR00094, tRNA_TruD_broad, tRNA pseudouridine synthase, TruD family.  an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa [Protein synthesis, tRNA and rRNA base modification].
CDD:232823	254	EUKprk	Bacteria:4,Plants:1	TIGR00097, HMP-P_kinase, phosphomethylpyrimidine kinase.  This model represents phosphomethylpyrimidine kinase, the ThiD protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a ...
CDD:232824	256	PRK	Bacteria:9	TIGR00099, Cof-subfamily, Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily.  This subfamily of sequences falls within the Class-IIB subfamily (TIGR01484) of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. The use of the name "Cof" as an identifier here is arbitrary and refers to the E. coli Cof protein. This subfamily is notable for the large number of recent paralogs in many species. Listeria, for instance, has 12, ...
CDD:232825	115	PRK	Bacteria:1	TIGR00100, hypA, hydrogenase nickel insertion protein HypA.  CXXC-~12X-CXXC and genetically seems a regulatory protein. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes [Protein fate, Protein modification and repair].
CDD:129211	68	PRK	Bacteria:6	TIGR00105, L31, ribosomal protein L31.  This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:232829	245	EUKprk	Bacteria:10,Plants:2	TIGR00112, proC, pyrroline-5-carboxylate reductase.  This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs [Amino acid biosynthesis, Glutamate family].
CDD:232831	408	PRK	Bacteria:63,Synthetic:1	TIGR00115, tig, trigger factor.  Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome [Protein ...
CDD:232834	237	PRK	Bacteria:1	TIGR00121, birA_ligase, birA, biotin-[acetyl-CoA-carboxylase] ligase region.  This model represents the biotin--acetyl-CoA-carboxylase ligase region of biotin--acetyl-CoA-carboxylase ligase. In Escherichia coli and some other species, this enzyme is part of a bifunction protein BirA that includes a small, N-terminal biotin operon repressor domain. Proteins identified by this model should not be called bifunctional unless they are also identified by birA_repr_reg ...
CDD:232837	66	EUKprk	Bacteria:17,Invertebrates:2,Plants:2,Primates:1,Rodents:1	TIGR00125, cyt_tran_rel, cytidyltransferase-like domain.  Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these ...
CDD:232842	460	PRK	Bacteria:2	TIGR00132, gatA, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit.  In many species, Gln--tRNA ligase is missing. tRNA(Gln) is misacylated with Glu after which a heterotrimeric amidotransferase converts Glu to Gln. This model represents the amidase chain of that heterotrimer, encoded by the gatA gene. In the Archaea, Asn--tRNA ligase is also missing. This amidase subunit may also function in the conversion of Asp-tRNA(Asn) to Asn-tRNA(Asn), presumably ...
CDD:232843	478	EUKprk	Bacteria:1,Plants:1	TIGR00133, gatB, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit.  The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include ...
CDD:129241	93	PRK	Bacteria:3	TIGR00135, gatC, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit.  Archaea, organelles, and many bacteria charge Gln-tRNA by first misacylating it with Glu and then amidating Glu to Gln. This small protein is part of the amidotransferase heterotrimer and appears to be important to the stability of the amidase subunit encode by gatA, but its function may not be required in every organism that expresses gatA and gatB. The seed alignment for This model does ...
CDD:211555	181	PRK	Bacteria:7	TIGR00138, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase GidB.  GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, ...
CDD:129246	134	PRK	Bacteria:10	TIGR00140, hupD, hydrogenase expression/formation protein.  valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease [Protein fate, Protein modification and repair].
CDD:129252	438	PRK	Bacteria:1	TIGR00148, TIGR00148, UbiD family decarboxylase.  The member of this family in E. coli is UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family described by This model, however, is broad enough that it is likely to contain several different decarboxylases. Found in bacteria, archaea, and yeast, with two members in A. fulgidus. No homologs were detected besides those classified as orthologs. The member from H. pylori has a C-terminal extension of just over ...
CDD:129255	155	PRK	Bacteria:3	TIGR00151, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.  Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:129256	188	PRK	Bacteria:2	TIGR00152, TIGR00152, dephospho-CoA kinase.  This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A].
CDD:129270	93	PRK	Bacteria:2	TIGR00166, S6, ribosomal protein S6.  The ribosomal protein S6 ortholog family, including yeast MRP17, shows more than two-fold length variation from 95 residues in Bacillus subtilis to 215 in Mycoplasma pneumoniae. This length variation comes primarily from poorly conserved C-terminal extensions that are particularly long in the Mycoplasmas. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6 ...
CDD:232852	288	EUKprk	Bacteria:3,Plants:1	TIGR00167, cbbA, ketose-bisphosphate aldolase.  This model is under revision. Proteins found by this model include fructose-bisphosphate and tagatose-bisphosphate aldolase [Energy metabolism, Glycolysis/gluconeogenesis].
CDD:232855	430	PRK	Bacteria:35	TIGR00173, menD, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.  MenD was thought until recently to act as SHCHC synthase, but has recently been shown to act instead as SEPHCHC synthase. Conversion of SEPHCHC into SHCHC and pyruvate may occur spontaneously but is catalyzed efficiently, at least in some organisms, by MenH (see TIGR03695). 2-oxoglutarate decarboxylase/SHCHC synthase (menD) is a thiamine pyrophosphate enzyme involved in ...
CDD:232857	155	PRK	Bacteria:6	TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis protein MobB.  This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin].
CDD:232858	144	EUKprk	Bacteria:10,Invertebrates:1,Plants:1,Primates:1,Rodents:1	TIGR00177, molyb_syn, molybdenum cofactor synthesis domain.  The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by This model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine ...
CDD:232860	187	PRK	Bacteria:7	TIGR00180, parB_part, ParB/RepB/Spo0J family partition protein.  This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during ...
CDD:232861	591	PRK	Bacteria:6	TIGR00181, pepF, oligoendopeptidase F.  This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PMID:8757883), with the name difference reflecting a difference in species of origin rather activity; ...
CDD:129290	237	PRK	Bacteria:1	TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3.  this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification].
CDD:211560	111	PRK	Bacteria:3	TIGR00188, rnpA, ribonuclease P protein component, eubacterial.  This peptide is the protein component of a ribonucleoprotein that cleaves the leader sequence from each tRNA precursor to leave the mature 5'-terminus. The catalytic site is in the RNA component, M1 RNA. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead [Transcription, RNA processing].
CDD:232865	271	EUKprk	Bacteria:4,Invertebrates:1,Primates:1	TIGR00189, tesB, acyl-CoA thioesterase II.  Function: hydrolyzes a broad range of acyl-CoA thioesters. Physiological function is not known. Subunit: homotetramer [Fatty acid and phospholipid metabolism, Biosynthesis].
CDD:129295	302	EUKprk	Bacteria:1,Plants:1	TIGR00191, thrB, homoserine kinase.  Homoserine kinase is part of the threonine biosynthetic pathway.Homoserine kinase is a member of the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase) and shares with them an amino-terminal domain probably related to ATP binding.P.aeruginosa homoserine kinase seems not to be homologous (see PROSITE:PDOC0054) [Amino acid biosynthesis, Aspartate family].
CDD:232867	574	PRK	Bacteria:1	TIGR00194, uvrC, excinuclease ABC, C subunit.  This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments [DNA metabolism, DNA replication, recombination, and repair].
CDD:232868	271	PRK	Bacteria:2	TIGR00196, yjeF_cterm, yjeF C-terminal region, hydroxyethylthiazole kinase-related.  E. coli yjeF has full-length orthologs in a number of species, all of unknown function. However, yeast YNL200C is homologous and corresponds to the N-terminal region while yeast YKL151C and B. subtilis yxkO correspond to this C-terminal region only [Unknown function, General].
CDD:232869	205	EUK	Plants:1	TIGR00197, yjeF_nterm, yjeF N-terminal region.  The protein region corresponding to This model shows no clear homology to any protein of known function. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO ...
CDD:232876	292	PRK	Bacteria:11	TIGR00212, hemC, porphobilinogen deaminase.  Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:232878	280	PRK	Bacteria:4	TIGR00216, ispH_lytB, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming).  The IspH protein (previously designated LytB) has now been recognized as the last enzyme in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory ...
CDD:232883	334	PRK	Bacteria:2	TIGR00225, prc, C-terminal peptidase (prc).  A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in ...
CDD:232884	124	PRK	Bacteria:7	TIGR00229, sensory_box, PAS domain S-box.  The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain ...
CDD:232886	162	EUKprk	Bacteria:4,Invertebrates:1,Plants:1,Primates:1,Rodents:1	TIGR00231, small_GTP, small GTP-binding protein domain.  Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small ...
CDD:232888	327	EUKprk	Bacteria:9,Plants:1,Primates:1	TIGR00233, trpS, tryptophanyl-tRNA synthetase.  This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this model [Protein synthesis, tRNA aminoacylation].
CDD:232889	377	EUKprk	Bacteria:2,Plants:1	TIGR00234, tyrS, tyrosyl-tRNA synthetase.  This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples [Protein synthesis, tRNA aminoacylation].
CDD:232895	165	PRK	Bacteria:2	TIGR00254, GGDEF, diguanylate cyclase (GGDEF) domain.  The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a ...
CDD:232896	328	EUKprk	Bacteria:1,Plants:1	TIGR00260, thrC, threonine synthase.  Involved in threonine biosynthesis it catalyses the reaction O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE + ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor. the enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes. the pyridoxal-phosphate binding site is a Lys (K) residues present at residue 70 of the model [Amino acid biosynthesis, Aspartate family].
CDD:161792	256	PRK	Bacteria:3	TIGR00262, trpA, tryptophan synthase, alpha subunit.  Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA ...
CDD:232901	400	PRK	Bacteria:32	TIGR00275, TIGR00275, flavoprotein, HI0933 family.  The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae [Unknown function, Enzymes of unknown specificity].
CDD:213520	337	PRK	Bacteria:47	TIGR00276, TIGR00276, epoxyqueuosine reductase.  This model was rebuilt to exclude archaeal homologs, now that there is new information that bacterial members are epoxyqueuosine reductase, QueG, involved in queuosine biosynthesis for tRNA maturation [Protein synthesis, tRNA and rRNA base modification].
CDD:232902	80	PRK	Bacteria:5	TIGR00277, HDIG, uncharacterized domain HDIG.  This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG. For proteins scoring above the trusted cutoff, confidence is high both that the domain is present and that the model produces an essentially correct ...
CDD:232906	288	PRK	Bacteria:8	TIGR00287, cas1, CRISPR-associated endonuclease Cas1.  This model identifies CRISPR-associated protein Cas1, the most universal CRISPR system protein. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Cas1 is a metal-dependent DNA-specific endonuclease [Mobile and extrachromosomal element functions, Other].
CDD:129394	126	EUKprk	Bacteria:4,Invertebrates:1,Plants:1,Primates:1	TIGR00293, TIGR00293, prefoldin, archaeal alpha subunit/eukaryotic subunit 5.  Members of this protein family, rich in coiled coil regions, are molecular chaperones in the class of the prefoldin (GimC) alpha subunit. Prefoldin is a hexamer of two alpha and four beta subunits. This protein appears universal in the archaea but is restricted to Aquifex aeolicus among bacteria so far. Eukaryotes have several related proteins; only ...
CDD:232919	319	EUKprk	Bacteria:26,Environmental:1,Invertebrates:22,Plants:18,Vertebrates:2	TIGR00322, diphth2_R, diphthamide biosynthesis enzyme Dph1/Dph2 domain.  Archaea and Eukaryotes, but not Eubacteria, share the property of having a covalently modified residue, 2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine, as a part of a cytosolic protein. The modified His, termed diphthamide, is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. ...
CDD:129428	347	PRK	Bacteria:3	TIGR00328, flhB, flagellar biosynthetic protein FlhB.  FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff ...
CDD:129429	305	PRK	Bacteria:2	TIGR00329, gcp_kae1, metallohydrolase, glycoprotease/Kae1 family.  This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this ...
CDD:232922	337	PRK	Bacteria:10	TIGR00331, hrcA, heat shock gene repressor HrcA.  HrcA represses the class I heat shock operons groE and dnaK; overproduction prevents induction of these operons by heat shock while deletion allows constitutive expression even at low temperatures. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene [Regulatory functions, DNA interactions].
CDD:232928	383	EUKprk	Bacteria:3,Plants:4	TIGR00339, sopT, ATP sulphurylase.  This enzyme forms adenosine 5'-phosphosulfate (APS) from ATP and free sulfate, the first step in the formation of the activated sulfate donor 3'-phosphoadenylylsulfate (PAPS). In some cases, it is found in a bifunctional protein in which the other domain, APS kinase, catalyzes the second and final step, the phosphorylation of APS to PAPS; the combined ATP sulfurylase/APS kinase may be called PAPS synthase. Members of ...
CDD:232931	851	EUK	Plants:1	TIGR00344, alaS, alanine--tRNA ligase.  The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP) [Protein synthesis, tRNA aminoacylation].
CDD:129447	166	PRK	Bacteria:4	TIGR00347, bioD, dethiobiotin synthase.  Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin].
CDD:232933	667	PRK	Bacteria:2	TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR family.  This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site ...
CDD:232941	405	PRK	Bacteria:20	TIGR00362, DnaA, chromosomal replication initiator protein DnaA.  DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006) [DNA metabolism, DNA replication, recombination, and repair].
CDD:188046	97	PRK	Bacteria:80	TIGR00365, TIGR00365, monothiol glutaredoxin, Grx4 family.  The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation [Energy metabolism, Electron transport].
CDD:161843	117	PRK	Bacteria:4	TIGR00369, unchar_dom_1, uncharacterized domain 1.  Most proteins containing this domain consist almost entirely of a single copy of this domain. A protein from C. elegans consists of two tandem copies of the domain. The domain is also found as the N-terminal region of an apparent initiation factor eIF-2B alpha subunit of Aquifex aeolicus. The function of the domain is unknown.
CDD:232944	178	PRK	Bacteria:7	TIGR00372, cas4, CRISPR-associated protein Cas4.  This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the ...
CDD:129470	319	miss	miss	TIGR00374, TIGR00374, conserved hypothetical protein.  This model is built on a superfamily of proteins in the Archaea and in Aquifex aeolicus. The authenticity of homology can be seen in the presence of motifs in the alignment that include residues relatively rare among these sequences, even though the alignment includes long regions of low-complexity hydrophobic sequences. One apparent fusion protein contains a Glycos_transf_2 region in the N-terminal half of the ...
CDD:129473	108	PRK	Bacteria:10	TIGR00377, ant_ant_sig, anti-anti-sigma factor.  This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif ...
CDD:232950	220	PRK	Bacteria:2	TIGR00384, dhsB, succinate dehydrogenase and fumarate reductase iron-sulfur protein.  Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also ...
CDD:232953	861	PRK	Bacteria:3	TIGR00392, ileS, isoleucyl-tRNA synthetase.  The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms [Protein synthesis, tRNA aminoacylation].
CDD:232957	530	EUKprk	Bacteria:2,Plants:1	TIGR00398, metG, methionyl-tRNA synthetase.  The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to This model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast ...
CDD:232965	418	miss	miss	TIGR00414, serS, seryl-tRNA synthetase.  This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model [Protein synthesis, tRNA aminoacylation].
CDD:232967	563	PRK	Bacteria:2	TIGR00418, thrS, threonyl-tRNA synthetase.  This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether. [Protein synthesis, tRNA aminoacylation].
CDD:232969	861	PRK	Bacteria:1	TIGR00422, valS, valyl-tRNA synthetase.  The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase [Protein synthesis, tRNA aminoacylation].
CDD:232973	296	PRK	Bacteria:67	TIGR00433, bioB, biotin synthase.  Catalyzes the last step of the biotin biosynthesis pathway. All members of the seed alignment are in the immediate gene neighborhood of a bioA gene [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin].
CDD:232974	464	PRK	Bacteria:3	TIGR00435, cysS, cysteinyl-tRNA synthetase.  This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for ...
CDD:232975	591	miss	miss	TIGR00437, feoB, ferrous iron transporter FeoB.  FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum [Transport and binding proteins, Cations and iron carrying compounds].
CDD:213530	397	PRK	Bacteria:39	TIGR00442, hisS, histidyl-tRNA synthetase.  This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA ...
CDD:232978	313	PRK	Bacteria:13	TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase, regulatory subunit.  Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit [Amino acid biosynthesis, Histidine family].
CDD:213531	188	PRK	Bacteria:1	TIGR00447, pth, peptidyl-tRNA hydrolase.  The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function [Protein synthesis, Other].
CDD:213532	217	PRK	Bacteria:12	TIGR00453, ispD, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.  Members of this protein family are 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, the IspD protein of the deoxyxylulose pathway of IPP biosynthesis. In about twenty percent of bacterial genomes, this protein occurs as IspDF, a bifunctional fusion protein [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:232981	566	EUKprk	Bacteria:1,Plants:2	TIGR00456, argS, arginyl-tRNA synthetase.  This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus ...
CDD:232984	290	PRK	Bacteria:46,nodiv:1	TIGR00462, genX, EF-P lysine aminoacylase GenX.  Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located ...
CDD:232986	470	PRK	Bacteria:1	TIGR00464, gltX_bact, glutamyl-tRNA synthetase, bacterial family.  The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This model models just the bacterial and mitochondrial forms of the enzyme. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may ...
CDD:232988	293	EUKprk	Bacteria:1,Plants:1	TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit.  Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An ...
CDD:232990	797	PRK	Bacteria:13	TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial.  Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a ...
CDD:232992	454	PRK	Bacteria:6	TIGR00474, selA, seryl-tRNA(sec) selenium transferase.  In bacteria, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing ...
CDD:232994	193	EUKprk	Bacteria:5,Primates:1	TIGR00482, TIGR00482, nicotinate (nicotinamide) nucleotide adenylyltransferase.  This model represents the predominant bacterial/eukaryotic adenylyltransferase for nicotinamide-nucleotide, its deamido form nicotinate nucleotide, or both. The first activity, nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1), synthesizes NAD by the salvage pathway, while the second, nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) synthesizes the immediate ...
CDD:213534	249	PRK	Bacteria:1	TIGR00486, YbgI_SA1388, dinuclear metal center protein, YbgI/SA1388 family.  The characterization of this family of uncharacterized proteins as orthologous is tentative. Members are found in all three domains of life. Several members (from Bacillus subtilis, Listeria monocytogenes, and Mycobacterium tuberculosis - all classified as Firmicutes within the Eubacteria) share a long insert relative to other members [Unknown function, General].
CDD:129583	367	PRK	Bacteria:1	TIGR00492, alr, alanine racemase.  This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or ...
CDD:232998	496	EUKprk	Bacteria:2,Plants:1	TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial.  This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms [Protein synthesis, tRNA aminoacylation].
CDD:129591	247	PRK	Bacteria:1	TIGR00500, met_pdase_I, methionine aminopeptidase, type I.  Methionine aminopeptidase is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. This model describes type I. The role of this protein in general is to produce the mature form of cytosolic proteins by removing the N-terminal methionine ...
CDD:233000	417	PRK	Bacteria:75	TIGR00508, bioA, adenosylmethionine-8-amino-7-oxononanoate transaminase.  All members of the seed alignment have been demonstrated experimentally to act as EC 2.6.1.62, an enzyme in the biotin biosynthetic pathway. Alternate names include 7,8-diaminopelargonic acid aminotransferase, DAPA aminotransferase, and adenosylmethionine-8-amino-7-oxononanoate aminotransferase. The gene symbol is bioA in E. coli and BIO3 in S. cerevisiae [Biosynthesis of cofactors, ...
CDD:233003	331	EUKprk	Bacteria:7,Invertebrates:2,Plants:3,Primates:1,Vertebrates:1	TIGR00512, salvage_mtnA, S-methyl-5-thioribose-1-phosphate isomerase.  The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now ...
CDD:233006	390	PRK	Bacteria:1	TIGR00521, coaBC_dfp, phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase.  This model represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather ...
CDD:213537	116	PRK	Bacteria:4	TIGR00525, folB, dihydroneopterin aldolase.  This model describes a bacterial dihydroneopterin aldolase, shown to form homo-octamers in E. coli. The equivalent activity is catalyzed by domains of larger folate biosynthesis proteins in other systems. The closely related parologous enzyme in E. coli, dihydroneopterin triphosphate epimerase, which is also homo-octameric, and dihydroneopterin aldolase domains of larger proteins, score below the trusted cutoff but may ...
CDD:233009	118	EUKprk	Bacteria:2,Plants:2	TIGR00526, folB_dom, FolB domain.  Two paralogous genes of E. coli, folB (dihydroneopterin aldolase) and folX (d-erythro-7,8-dihydroneopterin triphosphate epimerase) are homologous to each other and homo-octameric. In Pneumocystis carinii, a multifunctional enzyme of folate synthesis has an N-terminal region active as dihydroneopterin aldolase. This region consists of two tandem sequences each homologous to folB and forms tetramers.
CDD:129621	130	PRK	Bacteria:1	TIGR00530, AGP_acyltrn, 1-acyl-sn-glycerol-3-phosphate acyltransferases.  This model describes the core homologous region of a collection of related proteins, several of which are known to act as 1-acyl-sn-glycerol-3-phosphate acyltransferases (EC 2.3.1.51). Proteins scoring above the trusted cutoff are likely to have the same general activity. However, there is variation among characterized members as to whether the acyl group can be donated by acyl carrier protein ...
CDD:129627	284	miss	miss	TIGR00536, hemK_fam, HemK family putative methylases.  The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are ...
CDD:233013	367	PRK	Bacteria:15	TIGR00540, TPR_hemY_coli, heme biosynthesis-associated TPR protein.  Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated ...
CDD:233014	351	EUKprk	Bacteria:7,Plants:1	TIGR00543, isochor_syn, isochorismate synthases.  This enzyme interconverts chorismate and isochorismate. In E. coli, different loci encode isochorismate synthases for the pathways of menaquinone biosynthesis and enterobactin biosynthesis (via salicilate) and fail to complement each other. Among isochorismate synthases, the N-terminal domain is poorly conserved [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone].
CDD:233016	391	PRK	Bacteria:8	TIGR00546, lnt, apolipoprotein N-acyltransferase.  This enzyme transfers the acyl group to lipoproteins in the lgt/lsp/lnt system which is found broadly in bacteria but not in archaea. This model represents one component of the "lipoprotein lgt/lsp/lnt system" genome property [Protein fate, Protein modification and repair].
CDD:233017	274	EUKprk	Bacteria:10,Invertebrates:1,Plants:1	TIGR00549, mevalon_kin, mevalonate kinase.  This model represents mevalonate kinase, the third step in the mevalonate pathway of isopentanyl pyrophosphate (IPP) biosynthesis. IPP is a common intermediate for a number of pathways including cholesterol biosynthesis. This model covers enzymes from eukaryotes, archaea and bacteria. The related enzyme from the same pathway, phosphmevalonate kinase, serves as an outgroup for this clade. ...
CDD:233019	250	PRK	Bacteria:3	TIGR00552, nadE, NAD+ synthetase.  NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of ...
CDD:233020	328	PRK	Bacteria:6	TIGR00553, pabB, aminodeoxychorismate synthase, component I, bacterial clade.  Members of this family, aminodeoxychorismate synthase, component I (PabB), were designated para-aminobenzoate synthase component I until it was recognized that PabC, a lyase, completes the pathway of PABA synthesis. This family is closely related to anthranilate synthase component I (trpE), and both act on chorismate. The clade of PabB enzymes represented by this model includes sequences ...
CDD:233022	128	EUKprk	Bacteria:4,Plants:2	TIGR00556, pantethn_trn, phosphopantetheine--protein transferase domain.  This model models a domain active in transferring the phophopantetheine prosthetic group to its attachment site on enzymes and carrier proteins. Many members of this family are small proteins that act on the acyl carrier protein involved in fatty acid biosynthesis. Some members are domains of larger proteins involved specialized pathways for the synthesis of unusual molecules ...
CDD:233023	320	PRK	Bacteria:61	TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.  This model represents PdxA, an NAD+-dependent 4-hydroxythreonine 4-phosphate dehydrogenase (EC 1.1.1.262) active in pyridoxal phosphate biosynthesis [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine].
CDD:211586	190	EUKprk	Bacteria:79,Invertebrates:2,Plants:1	TIGR00558, pdxH, pyridoxamine-phosphate oxidase.  This model is similar to Pyridox_oxidase from PFAM but is designed to find only true pyridoxamine-phosphate oxidase and to ignore the related protein PhzG involved in phenazine biosynthesis. This protein from E. coli was characterized as a homodimer with two FMN per dimer [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine].
CDD:233024	182	PRK	Bacteria:3	TIGR00560, pgsA, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase.  Alternate names: phosphatidylglycerophosphate synthase; glycerophosphate phosphatidyltransferase; PGP synthase. A number of related enzymes are quite similar in both sequence and catalytic activity, including Saccharamyces cerevisiae YDL142c, now known to be a cardiolipin synthase. There may be problems with incorrect transitive annotation of near homologs as authentic ...
CDD:233026	454	EUKprk	Bacteria:6,Plants:1	TIGR00564, trpE_most, anthranilate synthase component I, non-proteobacterial lineages.  This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. Archaeal enzymes have been excluded from this model (and are now found in TIGR01820) as have a clade of enzymes ...
CDD:233028	266	PRK	Bacteria:3,Phages:1,Viruses:1	TIGR00571, dam, DNA adenine methylase (dam).  All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family ...
CDD:233029	514	EUKprk	Bacteria:3,Plants:1,Primates:1,Rodents:1,Vertebrates:1,Viruses:1	TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1).  All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, ...
CDD:233030	652	PRK	Bacteria:7	TIGR00575, dnlj, DNA ligase, NAD-dependent.  All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at ...
CDD:129666	141	EUKprk	Bacteria:9,Invertebrates:1,Phages:2,Plants:3,Primates:1,Viruses:7	TIGR00576, dut, deoxyuridine 5'-triphosphate nucleotidohydrolase (dut).  The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 ...
CDD:233031	272	EUKprk	Bacteria:9,Plants:1	TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg).  All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233032	926	PRK	Bacteria:3	TIGR00580, mfd, transcription-repair coupling factor (mfd).  All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic ...
CDD:233035	312	EUKprk	Bacteria:5,Invertebrates:1,Plants:3,Primates:1	TIGR00585, mutl, DNA mismatch repair protein MutL.  All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233036	274	EUKprk	Bacteria:2,Invertebrates:1,Plants:2	TIGR00587, nfo, apurinic endonuclease (APN1).  All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:213542	80	EUKprk	Bacteria:4,Invertebrates:1,Plants:1,Primates:1	TIGR00589, ogt, O-6-methylguanine DNA methyltransferase.  All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, ...
CDD:233038	887	PRK	Bacteria:7	TIGR00593, pola, DNA polymerase I.  All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233039	1022	PRK	Bacteria:3	TIGR00594, polc, DNA-directed DNA polymerase III (polc).  All proteins in this family for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233040	505	PRK	Bacteria:3	TIGR00595, priA, primosomal protein N'.  All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233047	705	EUK	Invertebrates:2,Plants:1,Vertebrates:1	TIGR00604, rad3, DNA repair helicase (rad3).  All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233050	1087	PRK	Bacteria:5	TIGR00609, recB, exodeoxyribonuclease V, beta subunit.  The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) ...
CDD:233051	365	PRK	Bacteria:8	TIGR00611, recf, recF protein.  All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233053	241	PRK	Bacteria:11	TIGR00613, reco, DNA repair protein RecO.  All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair [DNA metabolism, DNA replication, recombination, and repair].
CDD:233054	195	PRK	Bacteria:2	TIGR00615, recR, recombination protein RecR.  All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233056	253	PRK	Bacteria:2	TIGR00619, sbcd, exonuclease SbcD.  All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic ...
CDD:233057	164	EUKprk	Bacteria:6,Environmental:1,Primates:1,Rodents:1	TIGR00621, ssb, single stranded DNA-binding protein (ssb).  All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233060	212	EUKprk	Bacteria:4,Invertebrates:1,Plants:1,Primates:1,Rodents:1,Viruses:20	TIGR00628, ung, uracil-DNA glycosylase.  All proteins in this family for which functions are known are uracil-DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233062	925	PRK	Bacteria:6	TIGR00630, uvra, excinuclease ABC, A subunit.  This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA ...
CDD:233063	655	PRK	Bacteria:7	TIGR00631, uvrb, excinuclease ABC, B subunit.  All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233064	255	EUKprk	Bacteria:6,Invertebrates:2,Mammals:1,Plants:1,Primates:1	TIGR00633, xth, exodeoxyribonuclease III (xth).  All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:129721	305	PRK	Bacteria:3	TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.  All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex ...
CDD:213544	171	PRK	Bacteria:6	TIGR00636, PduO_Nterm, ATP:cob(I)alamin adenosyltransferase.  This model represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin ...
CDD:233066	69	PRK	Bacteria:5	TIGR00638, Mop, molybdenum-pterin binding domain.  This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins [Transport and binding proteins, Anions].
CDD:233069	630	EUK	Plants:1	TIGR00643, recG, ATP-dependent DNA helicase RecG.  [DNA metabolism, DNA replication, recombination, and repair].
CDD:233070	539	PRK	Bacteria:6,Phages:1	TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ.  All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair [DNA metabolism, DNA replication, recombination, and repair].
CDD:213546	268	PRK	Bacteria:2	TIGR00652, DapF, diaminopimelate epimerase.  [Amino acid biosynthesis, Aspartate family].
CDD:233073	459	PRK	Bacteria:5	TIGR00653, GlnA, glutamine synthetase, type I.  Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta ...
CDD:233076	441	PRK	Bacteria:5	TIGR00657, asp_kinases, aspartate kinase.  Aspartate kinase catalyzes a first step in the biosynthesis from Asp of Lys (and its precursor diaminopimelate), Met, and Thr. In E. coli, a distinct isozyme is inhibited by each of the three amino acid products. The Met-sensitive (I) and Thr-sensitive (II) forms are bifunctional enzymes fused to homoserine dehydrogenases and form homotetramers, while the Lys-sensitive form (III) is a monofunctional homodimer.The ...
CDD:233078	367	PRK	Bacteria:2	TIGR00663, dnan, DNA polymerase III, beta subunit.  All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233080	434	PRK	Bacteria:134	TIGR00665, DnaB, replicative DNA helicase.  This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The ...
CDD:233083	301	PRK	Bacteria:7	TIGR00670, asp_carb_tr, aspartate carbamoyltransferase.  Aspartate transcarbamylase (ATCase) is an alternate name.PyrB encodes the catalytic chain of aspartate carbamoyltransferase, an enzyme of pyrimidine biosynthesis, which organizes into trimers. In some species, including E. coli and the Archaea but excluding Bacillus subtilis, a regulatory subunit PyrI is also present in an allosterically regulated hexameric holoenzyme. Several molecular weight classes of ...
CDD:233084	243	PRK	Bacteria:2	TIGR00671, baf, pantothenate kinase, type III.  This model describes a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterized member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in E. coli [Biosynthesis of cofactors, prosthetic groups, and carriers, ...
CDD:129757	285	PRK	Bacteria:3	TIGR00674, dapA, dihydrodipicolinate synthase.  Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias ...
CDD:233085	315	PRK	Bacteria:13,Phages:1	TIGR00675, dcm, DNA-methyltransferase (dcm).  All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].
CDD:233086	272	PRK	Bacteria:16,nodiv:1	TIGR00676, fadh2, 5,10-methylenetetrahydrofolate reductase, prokaryotic form.  The enzyme activities methylenetetrahydrofolate reductase (EC 1.5.1.20) and 5,10-methylenetetrahydrofolate reductase (FADH) (EC 1.7.99.5) differ in that 1.5.1.20 (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while 1.7.99.5 (assigned in many bacteria) is flexible with respect to the acceptor; both convert 5-methyltetrahydrofolate to ...
CDD:233087	188	PRK	Bacteria:31	TIGR00678, holB, DNA polymerase III, delta' subunit.  This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to ...
CDD:233088	300	PRK	Bacteria:42	TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase.  Members of this family are the bifunctional enzyme, HPr kinase/phosphatase. All members of the seed alignment (n=57) have a gene tightly clustered with a gene for the phospocarrier protein HPr, its target [Regulatory functions, Protein interactions, Signal transduction, PTS].
CDD:213552	683	miss	miss	TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/SpoT family.  The functions of E. coli RelA and SpoT differ somewhat. RelA (EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the ...
CDD:233094	196	PRK	Bacteria:10	TIGR00693, thiE, thiamine-phosphate pyrophosphorylase.  This model represents the thiamine-phosphate pyrophosphorylase, ThiE, of a number of bacteria, and N-terminal domains of bifunctional thiamine proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the C-terminal domain corresponds to the bacterial hydroxyethylthiazole kinase (EC 2.7.1.50), ThiM. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory ...
CDD:188074	249	PRK	Bacteria:4	TIGR00694, thiM, hydroxyethylthiazole kinase.  This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine].
CDD:129780	202	PRK	Bacteria:2	TIGR00697, TIGR00697, conserved hypothetical integral membrane protein.  All known members of this family are proteins or 210-250 amino acids in length. Conserved regions of hydrophobicity suggest that all members of the family are integral membrane proteins [Hypothetical proteins, Conserved].
CDD:233100	423	PRK	Bacteria:3	TIGR00713, hemL, glutamate-1-semialdehyde-2,1-aminomutase.  This enzyme, glutamate-1-semialdehyde-2,1-aminomutase (glutamate-1-semialdehyde aminotransferase, GSA aminotransferase), contains a pyridoxal phosphate attached at a Lys residue at position 283 of the seed alignment. It is in the family of class III aminotransferases [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:188076	450	PRK	Bacteria:10	TIGR00720, sda_mono, L-serine dehydratase, iron-sulfur-dependent, single chain form.  This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and ...
CDD:233104	221	PRK	Bacteria:2	TIGR00726, TIGR00726, uncharacterized protein, YfiH family.  PSI-BLAST converges on members of this family of uncharacterized bacterial proteins and shows no significant similarity to any characterized protein. No completed genome to date has two members. Members of the family have been crystallized but the function is unknown [Unknown function, General].
CDD:233105	606	EUKprk	Bacteria:3,Plants:5	TIGR00728, OPT_sfam, oligopeptide transporter, OPT superfamily.  This superfamily has two main branches. One branch contains a tetrapeptide transporter demonstrated experimentally in three different species of yeast. The other family contains EspB of Myxococcus xanthus, a protein required for normal rather than delayed sporulation after cellular aggregation; its role is unknown but is compatible with transport of a signalling molecule. Homology between ...
CDD:233106	176	PRK	Bacteria:1	TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-form.  This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family ...
CDD:129815	220	PRK	Bacteria:1	TIGR00732, dprA, DNA protecting protein DprA.  Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA ...
CDD:129820	319	PRK	Bacteria:1	TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.  This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter ...
CDD:129821	132	PRK	Bacteria:9	TIGR00738, rrf2_super, Rrf2 family protein.  This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency [Unknown function, General].
CDD:233109	84	miss	miss	TIGR00739, yajC, preprotein translocase, YajC subunit.  While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this ...
CDD:129824	95	PRK	Bacteria:4	TIGR00741, yfiA, ribosomal subunit interface protein.  This model includes a small protein encoded by one of two genes, both downstream of the gene rpoN for sigma 54, whose deletion leads to increased expression from sigma 54-dependent promoters. It also includes the N-terminal half of a light-repressed protein LtrA of Synechococcus PCC 7002 and the N-terminal region (after removal of the transit peptide) of a larger plastid-specific ribosomal protein of spinach. The ...
CDD:233111	293	PRK	Bacteria:8	TIGR00745, apbA_panE, 2-dehydropantoate 2-reductase.  This model describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes ...
CDD:233115	253	PRK	Bacteria:13	TIGR00755, ksgA, dimethyladenosine transferase.  In both E. coli and Saccharomyces cerevisiae, this protein is responsible for the dimethylation of two adjacent adenosine residues in a conserved hairpin of 16S rRNA in bacteria, 18S rRNA in eukaryotes. This adjacent dimethylation is the only rRNA modification shared by bacteria and eukaryotes. A single member of this family is present in each of the first 20 completed microbial genomes. This protein is essential in ...
CDD:213555	35	EUK	Invertebrates:2,Plants:9,Primates:1	TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif).  This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this ...
CDD:233116	414	PRK	Bacteria:4	TIGR00757, RNaseEG, ribonuclease, Rne/Rng family.  This model describes ribonuclease G (formerly CafA, cytoplasmic axial filament protein A), the N-terminal domain of ribonuclease E in which ribonuclease activity resides, and related proteins. In E. coli, both RNase E and RNase G have been shown to play a role in the maturation of the 5' end of 16S RNA. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but ...
CDD:233118	231	EUKprk	Bacteria:5,Plants:1	TIGR00761, argB, acetylglutamate kinase.  This model describes N-acetylglutamate kinases (ArgB) of many prokaryotes and the N-acetylglutamate kinase domains of multifunctional proteins from yeasts. This enzyme is the second step in the "acetylated" ornithine biosynthesis pathway. A related group of enzymes representing the first step of the pathway contain a homologous domain and are excluded from this model [Amino acid biosynthesis, Glutamate family].
CDD:213558	275	PRK	Bacteria:73	TIGR00762, DegV, EDD domain protein, DegV family.  This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of ...
CDD:233119	775	EUKprk	Bacteria:1,Invertebrates:1,Plants:2,Primates:1	TIGR00763, lon, ATP-dependent protease La.  This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:233121	277	EUKprk	Bacteria:3,Primates:1	TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family.  This family, related to bacterial glutathione synthetases, contains at least two different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii ...
CDD:213559	50	PRK	Bacteria:8	TIGR00778, ahpD_dom, alkylhydroperoxidase AhpD family core domain.  This model represents a 51-residue core region of homology among a family of mostly uncharacterized proteins of 110 to 227 amino acids. Most members of this family contain the motif EXXXXXX[SA]XXXXXC[VIL]XCXXXH. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized ...
CDD:233126	444	EUKprk	Bacteria:4,Plants:1	TIGR00785, dass, anion transporter.  The Divalent Anion:Na+ Symporter (DASS) Family (TC 2.A.47) Functionally characterized proteins of the DASS family transport (1) organic di- and tricarboxylates of the Krebs Cycle as well as dicarboxylate amino acid, (2) inorganic sulfate and (3) phosphate. The animal NaDC-1 cotransport 3 Na+ with each dicarboxylate. Protonated tricarboxylates are also cotransported with 3Na+ [Transport and binding proteins, Anions, ...
CDD:129868	405	PRK	Bacteria:11	TIGR00786, dctM, TRAP transporter, DctM subunit.  The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family (TC 2.A.56)- DctM subunit TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterized. This system is the DctPQM system of Rhodobacter capsulatus (Forward et ...
CDD:129869	257	PRK	Bacteria:7	TIGR00787, dctP, tripartite ATP-independent periplasmic transporter solute receptor, DctP family.  TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model ...
CDD:162039	239	EUKprk	Bacteria:6,Invertebrates:1,Plants:1	TIGR00790, fnt, formate/nitrite transporter.  The Formate-Nitrite Transporter (FNT) Family (TC 2.A.44)The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite. The homologous yeast protein may function as a short chain aliphatic carboxylate H+ symporter,transporting formate, acetate and propionate, and functioning primarily as an acetate uptake permease. The ...
CDD:233128	437	PRK	Bacteria:12	TIGR00792, gph, sugar (Glycoside-Pentoside-Hexuronide) transporter.  The Glycoside-Pentoside-Hexuronide (GPH):Cation Symporter Family (TC 2.A.2) GPH:cation symporters catalyze uptake of sugars in symport with a monovalent cation (H+ or Na+). Members of this family includes transporters for melibiose, lactose, raffinose, glucuronides, pentosides and isoprimeverose. Mutants of two groups of these symporters (the melibiose permeases of enteric bacteria, and the ...
CDD:233129	378	PRK	Bacteria:6	TIGR00796, livcs, branched-chain amino acid uptake carrier.  The Branched Chain Amino Acid:Cation Symporter (LIVCS) Family (TC 2.A.26) Characterized members of this family transport all three of the branched chain aliphatic amino acids (leucine (L), isoleucine (I) and valine (V)). They function by a Na+ or H+ symport mechanism and display 12 putative transmembrane helical spanners [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233130	342	EUKprk	Bacteria:11,Plants:1	TIGR00797, matE, putative efflux protein, MATE family.  The Multi Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS ...
CDD:129880	318	EUK	Invertebrates:2,Plants:2,Rodents:1	TIGR00798, mtc, tricarboxylate carrier.  The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably ...
CDD:233132	442	EUKprk	Bacteria:5,Plants:3	TIGR00800, ncs1, NCS1 nucleoside transporter family.  The Nucleobase:Cation Symporter-1 (NCS1) Family (TC 2.A.39) The NCS1 family consists of bacterial and yeast transporters for nucleobases including purines and pyrimidines. Members of this family possess twelve putative transmembrane a-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport mechanism [Transport and binding proteins, Nucleosides, ...
CDD:233133	412	EUKprk	Bacteria:7,Plants:2	TIGR00801, ncs2, uracil-xanthine permease.  The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40) Most of the functionally characterized members of the NCS2 family are transporters specific for nucleobases including both purines and pyrimidines. However, two closely related rat members of the family, SVCT1 and SVCT2, localized to different tissues of the body, cotransport L-ascorbate and Na+ with a high degree of specificity and high affinity for ...
CDD:129885	222	EUK	Invertebrates:2,Mammals:1,Plants:3,Primates:1,Rodents:1	TIGR00803, nst, UDP-galactose transporter.  The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10)Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the ...
CDD:233135	401	EUKprk	Bacteria:3,Invertebrates:1,Mammals:1,Primates:1,Rodents:2	TIGR00804, nupC, nucleoside transporter.  The Concentrative Nucleoside Transporter (CNT) Family (TC 2.A.41) Members of the CNT family mediate nucleoside uptake. In bacteria they are energized by H+ symport, but in mammals they are energized by Na+ symport. The different transporters exhibit differing specificities for nucleosides. The E. coli NupC permease transports all nucleosides (both ribo- and ...
CDD:213562	73	PRK	Bacteria:63	TIGR00810, secG, protein translocase, SecG subunit.  This family of proteins forms a complex with SecY and SecE. SecA then recruits the SecYEG complex to form an active protein translocation channel [Protein fate, Protein and peptide secretion and trafficking].
CDD:233138	407	EUKprk	Bacteria:7,Invertebrates:1,Mammals:4,Primates:1,Rodents:2	TIGR00813, sss, transporter, SSS family.  The Solute:Sodium Symporter (SSS) Family (TC 2.A.21) Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, nucleosides, inositols, vitamins, urea or anions, depending on the system. Members of the SSS family have been identified in bacteria, archaea and animals, and all functionally well characterized members catalyze ...
CDD:162054	563	EUKprk	Bacteria:2,Plants:6,Primates:1,Rodents:2	TIGR00815, sulP, high affinity sulphate transporter 1.  The SulP family is a large and ubiquitous family with over 30 sequenced members derived from bacteria, fungi, plants and animals. Many organisms including Bacillus subtilis, Synechocystis sp, Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans possess multiple SulP family paralogues. Many of these proteins are functionally characterized, and all are sulfate ...
CDD:233142	88	PRK	Bacteria:8	TIGR00826, EIIB_glc, PTS system, glucose-like IIB component.  The PTS Glucose-Glucoside (Glc) Family (TC 4.A.1) Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose ...
CDD:129910	121	PRK	Bacteria:9	TIGR00830, PTBA, PTS system, glucose subfamily, IIA component.  These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are ...
CDD:213563	328	PRK	Bacteria:9	TIGR00832, acr3, arsenical-resistance protein.  The Arsenical Resistance-3 (ACR3) Family (TC 2.A.59) The first protein of the ACR3 family functionally characterized was the ACR3 protein of Saccharomyces cerevisiae. It is present in the yeast plasma membrane and pumps arsenite out of the cell in response to the pmf. Similar proteins are found in bacteria, often as part of a four gene operon with an regulatory protein ArsR, a protein of unknown function ArsH, and an ...
CDD:233144	425	PRK	Bacteria:6	TIGR00835, agcS, amino acid carrier protein.  The Alanine or Glycine: Cation Symporter (AGCS) Family (TC 2.A.25) Members of the AGCS family transport alanine and/or glycine in symport with Na+ and or H+.
CDD:233145	403	EUKprk	Bacteria:4,Invertebrates:1,Plants:3	TIGR00836, amt, ammonium transporter.  The Ammonium Transporter (Amt) Family (TC 2.A.49) All functionally characterized members of the Amt family are ammonia or ammonium uptake transporters. Some, but not others, also transport methylammonium. The mechanism of energy coupling, if any, to methyl-NH2 or NH3 uptake by the AmtB protein of E. coli is not entirely clear. NH4+ uniport driven by the pmf, energy independent NH3 facilitation, and ...
CDD:233146	381	PRK	Bacteria:4	TIGR00837, araaP, aromatic amino acid transport protein.  The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- tyrosine/tryptophan subfamily (TC 2.A.42.1) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for aromatic amino acid transporters and includes the tyrosine permease, TyrP, of E. coli, and the tryptophan transporters TnaB and Mtr of E. coli [Transport and ...
CDD:129918	455	PRK	Bacteria:1	TIGR00838, argH, argininosuccinate lyase.  This model describes argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens [Amino acid biosynthesis, Glutamate family].
CDD:188087	286	EUKprk	Bacteria:3,Mammals:1,Plants:1,Primates:1,Rodents:3	TIGR00841, bass, bile acid transporter.  The Bile Acid:Na+ Symporter (BASS) Family (TC 2.A.28) Functionally characterized members of the BASS family catalyze Na+:bile acid symport. These systems have been identified in intestinal, liver and kidney tissues of animals. These symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts. Functionally ...
CDD:213565	452	PRK	Bacteria:3	TIGR00842, bcct, choline/carnitine/betaine transport.  The Betaine/Carnitine/Choline Transporter (BCCT) Family (TC 2.A.15) Proteins of the BCCT family share the common functional feature of transporting molecules with a quaternary ammonium group [R-N+(CH3)3]. The BCCT family includes transporters for carnitine, choline and glycine betaine. BCCT transporters have 12 putative TMS, and are energized by pmf-driven proton symport. Some of these permeases exhibit ...
CDD:233150	129	PRK	Bacteria:9	TIGR00848, fruA, PTS system, fructose subfamily, IIA component.  4.A.2 The PTS Fructose-Mannitol (Fru) Family Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities. The fructose ...
CDD:233151	289	PRK	Bacteria:2	TIGR00852, pts-Glc, PTS system, maltose and glucose-specific subfamily, IIC component.  The PTS Glucose-Glucoside (Glc) Family (TC 4.A.1) Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this ...
CDD:233153	411	PRK	Bacteria:4	TIGR00857, pyrC_multi, dihydroorotase, multifunctional complex type.  In contrast to the homodimeric type of dihydroorotase found in E. coli, this class tends to appear in a large, multifunctional complex with aspartate transcarbamoylase. Homologous domains appear in multifunctional proteins of higher eukaryotes. In some species, including Pseudomonas putida and P. aeruginosa, this protein is inactive but is required as a non-catalytic subunit of aspartate ...
CDD:129937	360	PRK	Bacteria:4	TIGR00858, bioF, 8-amino-7-oxononanoate synthase.  7-keto-8-aminopelargonic acid synthetase is an alternate name. This model represents 8-amino-7-oxononanoate synthase, the BioF protein of biotin biosynthesis. This model is based on a careful phylogenetic analysis to separate members of this family from 2-amino-3-ketobutyrate and other related pyridoxal phosphate-dependent enzymes. In several species, including Staphylococcus and Coxiella, a candidate ...
CDD:233154	595	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:2	TIGR00859, ENaC, sodium channel transporter.  The Epithelial Na+ Channel (ENaC) Family (TC 1.A.06)The ENaC family consists of sodium channels from animals and has no recognizable homologues in other eukaryotes or bacteria. The vertebrate ENaC proteins from epithelial cells cluster tightly together on the phylogenetic tree: voltage-insensitive ENaC homologues are also found in the brain. Eleven sequenced C. elegans proteins, ...
CDD:233155	459	EUK	Invertebrates:6,Mammals:1,Primates:1,Rodents:4,Vertebrates:3	TIGR00860, LIC, Cation transporter family protein.  The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels ...
CDD:233156	216	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Plants:4,Primates:1,Rodents:1	TIGR00861, MIP, MIP family channel proteins.  1.A.8 The Major Intrinsic Protein (MIP) FamilyThe MIP family is large and diverse, possessing over 100 members that all form transmembrane channels. These channel proteins function in water, smallcarbohydrate (e.g., glycerol), urea, NH3, CO2 and possibly ion transport by an energy independent mechanism. They are found ubiquitously in bacteria, archaeaand ...
CDD:233161	743	EUK	Invertebrates:3,Mammals:2,Primates:1,Rodents:2	TIGR00870, trp, transient-receptor-potential calcium channel protein.  The Transient Receptor Potential Ca2+ Channel (TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also been called the store-operated calcium channel (SOC) family. The prototypical members include the Drosophila retinal proteinsTRP and TRPL (Montell and Rubin, 1989; Hardie and Minke, 1993). SOC members of the family mediate the entry of extracellular Ca2+ into ...
CDD:233162	482	EUKprk	Bacteria:1,Plants:2,Primates:1,Rodents:1	TIGR00871, zwf, glucose-6-phosphate 1-dehydrogenase.  This enzyme (EC 1.1.1.49) acts on glucose 6-phospate and reduces NADP(+). An alternate name appearing in the literature for the human enzyme, based on a slower activity with beta-D-glucose, is glucose 1-dehydrogenase (EC 1.1.1.47), but that name more properly describes a subfamily of the short chain dehydrogenases/reductases family. This is a well-studied enzyme family, with ...
CDD:233164	422	EUKprk	Bacteria:4,Primates:1	TIGR00877, purD, phosphoribosylamine--glycine ligase.  Alternate name: glycinamide ribonucleotide synthetase (GARS). This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:162083	332	PRK	Bacteria:1	TIGR00878, purM, phosphoribosylaminoimidazole synthetase.  Alternate name: phosphoribosylformylglycinamidine cyclo-ligase; AIRS; AIR synthase This enzyme is found as a homodimeric monofunctional protein in prokaryotes and as part of a larger, multifunctional protein, sometimes with two copies of this enzyme in tandem, in eukaryotes [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:233165	481	EUKprk	Bacteria:1,Invertebrates:2,Plants:4,Primates:1,Rodents:1	TIGR00879, SP, MFS transporter, sugar porter (SP) family.  This model represent the sugar porter subfamily of the major facilitator superfamily (pfam00083) [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].
CDD:233166	141	EUKprk	Bacteria:5,Invertebrates:1,Plants:4,Primates:1,Rodents:1	TIGR00880, 2_A_01_02, Multidrug resistance protein.  
CDD:233167	379	EUKprk	Bacteria:3,Invertebrates:1,Primates:1	TIGR00881, 2A0104, phosphoglycerate transporter family protein.  [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].
CDD:233168	394	PRK	Bacteria:5	TIGR00883, 2A0106, metabolite-proton symporter.  This model represents the metabolite:H+ symport subfamily of the major facilitator superfamily (pfam00083), including citrate-H+ symporters, dicarboxylate:H+ symporters, the proline/glycine-betaine transporter ProP, etc [Transport and binding proteins, Unknown substrate].
CDD:233170	366	EUKprk	Bacteria:8,Plants:5	TIGR00886, 2A0108, nitrite extrusion protein (nitrite facilitator).  [Transport and binding proteins, Anions].
CDD:129966	188	EUKprk	Bacteria:1,Plants:1	TIGR00888, guaA_Nterm, GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit.  This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This N-terminal region would be the smaller subunit [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:233174	399	EUKprk	Bacteria:4,Plants:1	TIGR00893, 2A0114, D-galactonate transporter.  [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].
CDD:233175	398	PRK	Bacteria:7	TIGR00895, 2A0115, benzoate transport.  [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].
CDD:233176	505	EUK	Invertebrates:1,Mammals:2,Plants:1,Primates:1,Rodents:2	TIGR00898, 2A0119, cation transport protein.  [Transport and binding proteins, Cations and iron carrying compounds].
CDD:162098	365	PRK	Bacteria:8	TIGR00900, 2A0121, H+ Antiporter protein.  [Transport and binding proteins, Cations and iron carrying compounds].
CDD:129983	473	PRK	Bacteria:3	TIGR00905, 2A0302, transporter, basic amino acid/polyamine antiporter (APA) family.  This family includes several families of antiporters that, rather commonly, are encoded next to decarboxylases that convert one of the antiporter substrates into the other. This arrangement allows a cycle that can remove proteins from the cytoplasm and thereby protect against acidic conditions [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233180	359	PRK	Bacteria:9	TIGR00912, 2A0309, spore germination protein (amino acid permease).  This model describes spore germination protein GerKB and paralogs from Bacillus subtilis, Clostridium tetani, and other known or predicted endospore-forming members of the Firmicutes (low-GC Gram positive bacteria). Members show some similarity to amino acid permeases [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233181	478	EUK	Plants:2	TIGR00913, 2A0310, amino acid permease (yeast).  [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233183	192	PRK	Bacteria:8	TIGR00916, 2A0604s01, protein-export membrane protein, SecD/SecF family.  The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins [Protein fate, Protein and peptide secretion and trafficking].
CDD:233188	172	PRK	Bacteria:3	TIGR00922, nusG, transcription termination/antitermination factor NusG.  NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA ...
CDD:233192	435	EUKprk	Bacteria:2,Invertebrates:1	TIGR00928, purB, adenylosuccinate lyase.  This family consists of adenylosuccinate lyase, the enzyme that catalyzes step 8 in the purine biosynthesis pathway for de novo synthesis of IMP and also the final reaction in the two-step sequence from IMP to AMP [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:233193	785	PRK	Bacteria:7	TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase, VirB4 family.  Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).
CDD:233194	953	EUK	Invertebrates:1,Mammals:3,Plants:2,Primates:1,Rodents:2,Vertebrates:2	TIGR00930, 2a30, K-Cl cotransporter.  [Transport and binding proteins, Other].
CDD:233195	273	EUKprk	Bacteria:5,Plants:1	TIGR00932, 2a37, transporter, monovalent cation:proton antiporter-2 (CPA2) family.  [Transport and binding proteins, Cations and iron carrying compounds].
CDD:233196	390	PRK	Bacteria:5	TIGR00933, 2a38, potassium uptake protein, TrkH family.  The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake ...
CDD:233199	437	EUK	Invertebrates:3,Plants:2,Primates:1,Rodents:2	TIGR00939, 2a57, Equilibrative Nucleoside Transporter (ENT).  [Transport and binding proteins, Nucleosides, purines and pyrimidines].
CDD:233202	215	EUKprk	Bacteria:3,Invertebrates:1,Plants:4	TIGR00945, tatC, Twin arginine targeting (Tat) protein translocase TatC.  This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane. A related model (TIGR01912) represents the archaeal clade of this family. TatC is often found in a gene cluster with the two other ...
CDD:233203	321	EUKprk	Bacteria:2,Plants:2	TIGR00946, 2a69, he Auxin Efflux Carrier (AEC) Family.  [Transport and binding proteins, Other].
CDD:233204	185	PRK	Bacteria:3	TIGR00949, 2A76, The Resistance to Homoserine/Threonine (RhtB) Family protein.  [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233205	260	PRK	Bacteria:3	TIGR00950, 2A78, Carboxylate/Amino Acid/Amine Transporter.  [Transport and binding proteins, Amino acids, peptides and amines].
CDD:130027	86	PRK	Bacteria:2	TIGR00952, S15_bact, ribosomal protein S15, bacterial/organelle.  This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233207	617	EUK	Invertebrates:10,Plants:1,Primates:1,Rodents:1	TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein.  [Transport and binding proteins, Other].
CDD:233210	428	PRK	Bacteria:3	TIGR00959, ffh, signal recognition particle protein.  This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle [Protein fate, Protein and peptide secretion and trafficking].
CDD:233212	745	EUKprk	Bacteria:7,Plants:5	TIGR00963, secA, preprotein translocase, SecA subunit.  The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus. This model excludes SecA2 of the accessory secretory system [Protein fate, Protein and peptide secretion and trafficking].
CDD:213575	55	PRK	Bacteria:15	TIGR00964, secE_bact, preprotein translocase, SecE subunit, bacterial.  This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC [Protein fate, Protein and peptide secretion and trafficking].
CDD:233213	246	miss	miss	TIGR00966, 3a0501s07, protein-export membrane protein SecF.  This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein [Protein fate, Protein and peptide secretion and trafficking].
CDD:233214	410	EUKprk	Bacteria:11,Mammals:1,Plants:3,Rodents:1	TIGR00967, 3a0501s007, preprotein translocase, SecY subunit.  Members of this protein family are the SecY component of the SecYEG translocon, or protein translocation pore, which is driven by the ATPase SecA. This model does not discriminate bacterial from archaeal forms [Protein fate, Protein and peptide secretion and trafficking].
CDD:188099	247	PRK	Bacteria:7	TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding protein.  This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members ...
CDD:233217	271	PRK	Bacteria:13	TIGR00974, 3a0107s02c, phosphate ABC transporter, permease protein PstA.  This model describes PtsA, one of a pair of permease proteins in the ABC (high affinity) phosphate transporter. In a number of species, this permease is fused with the PtsC protein (TIGR02138). In the model bacterium Escherichia coli, this transport system is induced when the concentration of extrallular inorganic phosphate is low. A constitutive, lower affinity transporter operates otherwise ...
CDD:233219	550	PRK	Bacteria:4	TIGR00976, /NonD, putative hydrolase, CocE/NonD family.  This model represents a protein subfamily that includes the cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). This family shows extensive, low-level similarity to a family of xaa-pro dipeptidyl-peptidases, and local similarity by PSI-BLAST to many other hydrolases [Unknown function, Enzymes of unknown specificity].
CDD:233227	291	PRK	Bacteria:10	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein.  Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells [Cellular processes, Pathogenesis].
CDD:130070	178	PRK	Bacteria:5	TIGR00997, ispZ, intracellular septation protein A.  This partially characterized protein, whose absence can cause a cell division defect in an intracellularly replicating bacterium, is found only so far only in the Proteobacteria [Cellular processes, Cell division].
CDD:233230	457	PRK	Bacteria:9	TIGR01000, bacteriocin_acc, bacteriocin secretion accessory protein.  This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193 [Transport and binding proteins, Other].
CDD:200064	82	PRK	Bacteria:16	TIGR01003, PTS_HPr_family, Phosphotransferase System HPr (HPr) Family.  The HPr family are bacterial proteins (or domains of proteins) which function in phosphoryl transfer system (PTS) systems. They include energy-coupling components which catalyze sugar uptake via a group translocation mechanism. The functions of most of these proteins are not known, but they presumably function in PTS-related regulatory capacities. All seed members are stand-alone HPr proteins, ...
CDD:130082	211	EUKprk	Bacteria:4,Plants:1	TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type.  This model describes the bacterial type of ribosomal protein S3. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. This model recognizes all bacterial forms and many chloroplast forms above the trusted cutoff score. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea [Protein synthesis, Ribosomal ...
CDD:130084	225	PRK	Bacteria:3	TIGR01011, rpsB_bact, ribosomal protein S2, bacterial type.  This model describes the bacterial, ribosomal, and chloroplast forms of ribosomal protein S2. TIGR01012 describes the archaeal and cytosolic forms [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:200066	200	EUKprk	Bacteria:2,Plants:2	TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle type.  This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:130093	154	EUKprk	Bacteria:1,Plants:1	TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle type.  This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233236	54	PRK	Bacteria:1	TIGR01023, rpmG_bact, ribosomal protein L33, bacterial type.  This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:130096	113	PRK	Bacteria:2	TIGR01024, rplS_bact, ribosomal protein L19, bacterial type.  This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:162163	363	PRK	Bacteria:4	TIGR01027, proB, glutamate 5-kinase.  Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family [Amino acid biosynthesis, Glutamate family].
CDD:233238	154	EUKprk	Bacteria:2,Invertebrates:1,Plants:2	TIGR01029, rpsG_bact, ribosomal protein S7, bacterial/organelle.  This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5). The eukaryotic and archaeal branch is described by model TIGR01028 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233239	55	PRK	Bacteria:19	TIGR01031, rpmF_bact, ribosomal protein L32.  This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus [Protein synthesis, Ribosomal proteins: synthesis and ...
CDD:233240	238	PRK	Bacteria:2	TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR family.  This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein [Regulatory functions, DNA interactions].
CDD:233242	417	miss	miss	TIGR01035, hemA, glutamyl-tRNA reductase.  This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:233248	414	PRK	Bacteria:8	TIGR01048, lysA, diaminopimelate decarboxylase.  This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis [Amino acid biosynthesis, Aspartate family].
CDD:130121	99	EUKprk	Bacteria:4,Plants:4	TIGR01049, rpsJ_bact, ribosomal protein S10, bacterial/organelle.  This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial ...
CDD:130122	92	EUK	Plants:5	TIGR01050, rpsS_bact, ribosomal protein S19, bacterial/organelle.  The homologous protein of the eukaryotic cytosol and of the Archaea may be designated S15 or S19 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233249	610	PRK	Bacteria:1	TIGR01051, topA_bact, DNA topoisomerase I, bacterial.  This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events [DNA metabolism, DNA replication, recombination, and repair].
CDD:233254	654	PRK	Bacteria:1	TIGR01059, gyrB, DNA gyrase, B subunit.  This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB [DNA metabolism, DNA replication, recombination, and repair].
CDD:233256	800	miss	miss	TIGR01063, gyrA, DNA gyrase, A subunit.  This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV [DNA metabolism, DNA replication, recombination, and repair].
CDD:233257	473	EUKprk	Bacteria:3,Invertebrates:1,Mammals:1,Plants:1,Vertebrates:1	TIGR01064, pyruv_kin, pyruvate kinase.  This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars [Energy metabolism, Glycolysis/gluconeogenesis].
CDD:233258	204	EUKprk	Bacteria:2,Invertebrates:1,Primates:1	TIGR01065, hlyIII, channel protein, hemolysin III family.  This family includes proteins from pathogenic and non-pathogenic bacteria, Homo sapiens and Drosophila. In Bacillus cereus, a pathogen, it has been show to function as a channel-forming cytolysin. The human protein is expressed preferentially in mature macrophages, consistent with a role cytolytic role.
CDD:162186	140	EUKprk	Bacteria:2,Plants:2	TIGR01066, rplM_bact, ribosomal protein L13, bacterial type.  This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:130139	122	EUKprk	Bacteria:2,Invertebrates:1	TIGR01067, rplN_bact, ribosomal protein L14, bacterial/organelle.  This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:200072	101	EUKprk	Bacteria:4,Plants:1	TIGR01068, thioredoxin, thioredoxin.  Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by This model. Any protein that hits once with a score greater than the second (per domain) trusted cutoff may be taken as thioredoxin [Energy metabolism, Electron transport].
CDD:233260	145	PRK	Bacteria:2	TIGR01071, rplO_bact, ribosomal protein L15, bacterial/organelle.  [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:162190	416	PRK	Bacteria:6	TIGR01072, murA, UDP-N-acetylglucosamine 1-carboxyvinyltransferase.  [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].
CDD:233263	104	EUKprk	Bacteria:4,Plants:1	TIGR01079, rplX_bact, ribosomal protein L24, bacterial/organelle.  This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233264	448	PRK	Bacteria:6	TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase.  This model describes the MurC protein in bacterial peptidoglycan (murein) biosynthesis. In a few species (Mycobacterium leprae, the Chlamydia), the amino acid may be L-serine or glycine instead of L-alanine. A related protein, UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by model TIGR01081 [Cell envelope, Biosynthesis and degradation of ...
CDD:130155	191	PRK	Bacteria:9	TIGR01083, nth, endonuclease III.  This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY [DNA metabolism, DNA replication, recombination, and repair].
CDD:233265	464	PRK	Bacteria:3	TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase.  Most members of this family are EC 6.3.2.13, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase. An exception is Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is EC 6.3.2.7. The Mycobacteria, part of the closest neighboring branch outside of the low-GC Gram-positive bacteria, use diaminopimelate. A close homolog, scoring just below ...
CDD:233266	433	PRK	Bacteria:3	TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase.  [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].
CDD:233267	169	EUKprk	Bacteria:3,Plants:1,Primates:1	TIGR01090, apt, adenine phosphoribosyltransferase.  A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for This model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage. The trusted cutoff score is made high for this reason. Most proteins scoring between the trusted and noise cutoffs are likely to act as adenine phosphotransferase ...
CDD:130163	207	PRK	Bacteria:9	TIGR01091, upp, uracil phosphoribosyltransferase.  A fairly deep split in phylogenetic and UPGMA trees separates this mostly prokaryotic set of uracil phosphoribosyltransferases from a mostly eukaryotic set that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides].
CDD:233268	228	EUKprk	Bacteria:5,Plants:3	TIGR01093, aroD, 3-dehydroquinate dehydratase, type I.  This model detects 3-dehydroquinate dehydratase, type I, either as a monofunctional protein or as a domain of a larger, multifunctional protein. It is often found fused to shikimate 5-dehydrogenase (EC 1.1.1.25), and sometimes additional domains. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by the model TIGR01088 [Amino acid biosynthesis, Aromatic amino acid family].
CDD:233269	250	PRK	Bacteria:6	TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding periplasmic protein.  [Transport and binding proteins, Amino acids, peptides and amines].
CDD:233270	250	PRK	Bacteria:23	TIGR01097, PhnE, phosphonate ABC transporter, permease protein PhnE.  Phosphonates are a class of compound analogous to organic phosphates, but in which the C-O-P linkage is replaced by a direct, stable C-P bond. Some bacteria can utilize phosphonates as a source of phosphorus. This family consists of permease proteins of known or predicted phosphonate ABC transporters. Often this protein is found as a duplicated pair, occasionally as a fused pair. Certain "second" ...
CDD:233271	254	PRK	Bacteria:10	TIGR01098, 3A0109s03R, phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein.  Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a ...
CDD:233272	260	PRK	Bacteria:6	TIGR01099, galU, UTP-glucose-1-phosphate uridylyltransferase.  Built to distinquish between the highly similar genes galU and galF [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides].
CDD:162204	289	EUK	Mammals:3,Primates:1,Rodents:3,Vertebrates:4	TIGR01107, Na_K_ATPase_bet, Sodium Potassium ATPase beta subunit.  This model describes the Na+/K+ ATPase beta subunit in eukaryotes. Na+/K+ ATPase(also called Sodium-Potassium pump) is intimately associated with the plasma membrane. It couples the energy released by the hydrolysis of ATP to extrude 3 Na+ ions, with the concomitant uptake of 2K+ ions, against their ionic gradients [Transport and binding proteins, Cations and iron ...
CDD:200074	102	EUK	Invertebrates:4,Plants:4,Primates:1,Rodents:1	TIGR01126, pdi_dom, protein disulfide-isomerase domain.  This model describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK [Protein fate, Protein folding and stabilization].
CDD:233280	302	PRK	Bacteria:22,Environmental:1	TIGR01128, holA, DNA polymerase III, delta subunit.  DNA polymerase III delta (holA) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex subassembly of DNA polymerase III ...
CDD:233281	397	PRK	Bacteria:1	TIGR01129, secD, protein-export membrane protein SecD.  Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed and score between the trusted and noise cutoffs. SecD from Mycobacterium tuberculosis has a long Pro-rich insert [Protein fate, Protein and peptide secretion and trafficking].
CDD:233282	462	EUK	Invertebrates:5,Plants:5,Primates:1	TIGR01130, ER_PDI_fam, protein disulfide isomerase, eukaryotic.  This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to ...
CDD:233283	226	EUKprk	Bacteria:2,Invertebrates:18,Mammals:1,Plants:9,Vertebrates:1	TIGR01131, ATP_synt_6_or_A, ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes).  Bacterial forms should be designated ATP synthase, F0 subunit A; eukaryotic (chloroplast and mitochondrial) forms should be designated ATP synthase, F0 subunit 6. The F1/F0 ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and mitochondria and chloroplast. This enzyme is principally involved in ...
CDD:233284	348	PRK	Bacteria:7	TIGR01133, murG, undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase.  RM 8449890 RT The final step of peptidoglycan subunit assembly in Escherichia coli occurs in the cytoplasm. RA Bupp K, van Heijenoort J. RL J Bacteriol 1993 Mar;175(6):1841-3 [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].
CDD:233285	442	PRK	Bacteria:11	TIGR01134, purF, amidophosphoribosyltransferase.  Alternate name: glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:130205	607	PRK	Bacteria:7	TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase (isomerizing).  The member from Methanococcus jannaschii contains an intein [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Central intermediary metabolism, Amino sugars].
CDD:233286	299	EUKprk	Bacteria:9,Plants:1	TIGR01136, cysKM, cysteine synthase.  This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the ...
CDD:233289	330	PRK	Bacteria:30	TIGR01140, L_thr_O3P_dcar, L-threonine-O-3-phosphate decarboxylase.  This family contains pyridoxal phosphate-binding class II aminotransferases (see pfam00222) closely related to, yet distinct from, histidinol-phosphate aminotransferase (HisC). It is found in cobalamin biosynthesis operons in Salmonella typhimurium and Bacillus halodurans (each of which also has HisC) and has been shown to have L-threonine-O-3-phosphate decarboxylase activity in Salmonella. ...
CDD:233290	346	PRK	Bacteria:9,Synthetic:1	TIGR01141, hisC, histidinol-phosphate aminotransferase.  Alternate names: histidinol-phosphate transaminase; imidazole acetol-phosphate transaminase Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme [Amino acid biosynthesis, Histidine family].
CDD:233291	417	PRK	Bacteria:12	TIGR01143, murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase.  This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus ...
CDD:130215	172	EUKprk	Bacteria:4,Plants:2	TIGR01145, ATP_synt_delta, ATP synthase, F1 delta subunit.  This model describes the ATP synthase delta subunit in bacteria, mitochondria, and chloroplasts. It is sometimes called OSCP for Oligomycin Sensitivity Conferring Protein. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP ...
CDD:233292	286	EUKprk	Bacteria:9,Mammals:1,Plants:3,Primates:1	TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit.  This model describes the ATP synthase gamma subunit in bacteria and its equivalents in organelles, namely, mitochondria and chloroplast. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involed in the synthesis of ATP from ADP and inorganic ...
CDD:130226	101	PRK	Bacteria:5	TIGR01158, SUI1_rel, translation initation factor SUI1, putative, prokaryotic.  This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met [Protein synthesis, Translation factors].
CDD:233295	352	EUKprk	Bacteria:5,Plants:1	TIGR01161, purK, phosphoribosylaminoimidazole carboxylase, PurK protein.  Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase, which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is ...
CDD:130230	156	EUKprk	Bacteria:15,Invertebrates:2,Plants:2,Primates:1,Rodents:1	TIGR01162, purE, phosphoribosylaminoimidazole carboxylase, PurE protein.  Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:130231	210	PRK	Bacteria:8	TIGR01163, rpe, ribulose-phosphate 3-epimerase.  This family consists of Ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archebacteria, fungi and plants [Energy metabolism, Pentose phosphate pathway].
CDD:213590	34	PRK	Bacteria:98	TIGR01167, LPXTG_anchor, LPXTG-motif cell wall anchor domain.  This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common ...
CDD:233297	39	PRK	Bacteria:27	TIGR01168, YSIRK_signal, Gram-positive signal peptide, YSIRK family.  Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology. There is a strong correlation between proteins carrying this region at the ...
CDD:211630	227	EUKprk	Bacteria:4,Plants:1	TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.  This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:162234	273	EUKprk	Bacteria:4,Plants:2	TIGR01171, rplB_bact, ribosomal protein L2, bacterial/organellar.  This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:200082	162	PRK	Bacteria:9	TIGR01172, cysE, serine O-acetyltransferase.  Cysteine biosynthesis [Amino acid biosynthesis, Serine family].
CDD:233299	451	PRK	Bacteria:8	TIGR01173, glmU, UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase.  This protein is a bifunctional enzyme, GlmU, which catalyzes last two reactions in the four-step pathway of UDP-N-acetylglucosamine biosynthesis from fructose-6-phosphate. Its reaction product is required from peptidoglycan biosynthesis, LPS biosynthesis in species with LPS, and certain other processes [Cell envelope, Biosynthesis and degradation of murein sacculus ...
CDD:233300	371	PRK	Bacteria:5	TIGR01174, ftsA, cell division protein FtsA.  This bacterial cell division protein interacts with FtsZ, the bacterial homolog of tubulin. It is an ATP-binding protein and shows structural similarities to actin and heat shock cognate protein 70 [Cellular processes, Cell division].
CDD:213592	328	PRK	Bacteria:5	TIGR01179, galE, UDP-glucose-4-epimerase GalE.  Alternate name: UDPgalactose 4-epimerase This enzyme interconverts UDP-glucose and UDP-galactose. A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded from This model and described by a separate model [Energy metabolism, Sugars].
CDD:162241	204	PRK	Bacteria:6	TIGR01182, eda, Entner-Doudoroff aldolase.  2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida [Amino acid biosynthesis, Glutamate family, Energy metabolism, Entner-Doudoroff].
CDD:233305	198	PRK	Bacteria:6	TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA.  This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This ...
CDD:233307	82	PRK	Bacteria:4	TIGR01195, oadG_fam, sodium pump decarboxylases, gamma subunit.  This model finds the subfamily of distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
CDD:233308	233	EUKprk	Bacteria:3,Plants:1,Primates:1	TIGR01198, pgl, 6-phosphogluconolactonase.  This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with [Energy metabolism, Pentose phosphate pathway].
CDD:233309	227	PRK	Bacteria:29,Environmental:1	TIGR01200, GLPGLI, GLPGLI family protein.  This protein family was first noted as a paralogous set in Porphyromonas gingivalis, but it is more widely distributed among the Bacteroidetes. The protein family is now renamed GLPGLI after its best-conserved motif.
CDD:200084	145	PRK	Bacteria:4	TIGR01201, HU_rel, DNA-binding protein, histone-like, putative.  This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe [DNA metabolism, Chromosome-associated proteins].
CDD:130270	166	EUKprk	Bacteria:3,Invertebrates:3,Primates:1	TIGR01203, HGPRTase, hypoxanthine phosphoribosyltransferase.  Alternate name: hypoxanthine-guanine phosphoribosyltransferase. Sequence differences as small as a single residue can affect whether members of this family act on hypoxanthine and guanine or hypoxanthine only. The designation of this model as equivalog reflects hypoxanthine specificity and does not reflect whether or not guanine can replace hypoxanthine [Purines, pyrimidines, ...
CDD:233310	315	PRK	Bacteria:9	TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase.  This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment ...
CDD:200085	287	PRK	Bacteria:5	TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase.  This enzyme catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS core antigen, O-antigen, etc [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides].
CDD:130283	130	EUKprk	Bacteria:7,Plants:2	TIGR01216, ATP_synt_epsi, ATP synthase, F1 epsilon subunit (delta in mitochondria).  This model describes one of the five types of subunits in the F1 part of F1/F0 ATP synthases. Members of this family are designated epsilon in bacterial and chloroplast systems but designated delta in mitochondria, where the counterpart of the bacterial delta subunit is designated OSCP. In a few cases (Propionigenium modestum, Acetobacterium woodii) scoring above the ...
CDD:233317	208	PRK	Bacteria:24	TIGR01218, Gpos_tandem_5TM, tandem five-transmembrane protein.  Members of this family of proteins, with average length of 210, have no invariant residues but five predicted transmembrane segments. Strangely, most members occur in groups of consecutive paralogous genes. A striking example is a set of eleven encoded consecutively, head-to-tail, in Staphylococcus aureus strain COL.
CDD:233320	217	PRK	Bacteria:4	TIGR01222, minC, septum site-determining protein MinC.  The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs [Cellular processes, Cell division].
CDD:233327	495	EUKprk	Bacteria:1,Plants:1	TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.  HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:233329	330	EUKprk	Bacteria:7,Plants:1	TIGR01245, trpD, anthranilate phosphoribosyltransferase.  In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino acid family].
CDD:130318	308	EUKprk	Bacteria:9,Primates:1	TIGR01251, ribP_PPkin, ribose-phosphate pyrophosphokinase.  Alternate name: phosphoribosylpyrophosphate synthetase In some systems, close homologs lacking enzymatic activity exist and perform regulatory functions. The model is designated subfamily rather than equivalog for this reason [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:233333	210	EUKprk	Bacteria:7,Invertebrates:1,Plants:2,Primates:1	TIGR01262, maiA, maleylacetoacetate isomerase.  Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (EC 5.2.1.2) is described as active also on maleylpyruvate, and the example from a Ralstonia sp. catabolic plasmid is described as a maleylpyruvate isomerase involved in gentisate catabolism ...
CDD:233334	353	EUKprk	Bacteria:8,Invertebrates:3,Plants:2	TIGR01263, 4HPPD, 4-hydroxyphenylpyruvate dioxygenase.  This protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic (see PMID:8000039). In some bacterial species, this enzyme has been ...
CDD:233337	624	EUKprk	Bacteria:2,Plants:2	TIGR01273, speA, arginine decarboxylase, biosynthetic.  Two alternative pathways can convert arginine to putrescine. One is decarboxylation by this enzyme followed by removal of the urea moeity by agmatinase. In the other, the ureohydrolase (arginase) acts first, followed by ornithine decarboxylase. This pathway leads to spermidine biosynthesis, hence the gene symbol speA. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not ...
CDD:233341	67	PRK	Bacteria:4	TIGR01280, xseB, exodeoxyribonuclease VII, small subunit.  This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides [DNA metabolism, Degradation of DNA].
CDD:233345	299	EUKprk	Bacteria:6,Plants:1	TIGR01292, TRX_reduct, thioredoxin-disulfide reductase.  This model describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (pfam00070) [Energy metabolism, Electron transport].
CDD:233348	268	EUKprk	Bacteria:12,Invertebrates:1,Plants:1,Primates:1,Rodents:2	TIGR01297, CDF, cation diffusion facilitator family transporter.  This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence [Transport and ...
CDD:130367	97	PRK	Bacteria:4	TIGR01300, CPA3_mnhG_phaG, monovalent cation/proton antiporter, MnhG/PhaG subunit.  This model represents a subfamily of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti, show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons [Transport and binding proteins, Cations and iron carrying compounds].
CDD:233350	450	EUKprk	Bacteria:2,Invertebrates:1,Plants:1	TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase.  This model describes IMP dehydrogenase, an enzyme of GMP biosynthesis. This form contains two CBS domains. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related ...
CDD:130375	55	EUKprk	Bacteria:7,Plants:1	TIGR01308, rpmD_bact, ribosomal protein L30, bacterial/organelle.  This model describes bacterial (and organellar) 50S ribosomal protein L30. Homologous ribosomal proteins of the eukaryotic cytosol and of the archaea differ substantially in architecture, from bacterial L30 and also from each other, and are described by separate models [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:233352	235	EUK	Invertebrates:4,Plants:3,Rodents:1	TIGR01310, L7, 60S ribosomal protein L7, eukaryotic.  This model describes the eukaryotic 60S (cytosolic) ribosomal protein L7 and paralogs that may or may not also be L7. Human, Drosophila, and Arabidopsis all have both a typical L7 and an L7-related paralog. This family is designated subfamily rather than equivalog to reflect these uncharacterized paralogs. Members of this family average ~ 250 residues in length, somewhat longer than the ...
CDD:233353	493	EUKprk	Bacteria:7,Invertebrates:4,Plants:1,Primates:1	TIGR01311, glycerol_kin, glycerol kinase.  This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases [Energy metabolism, Other].
CDD:233354	481	EUKprk	Bacteria:8,Plants:1	TIGR01312, XylB, D-xylulose kinase.  This model describes D-xylulose kinases, a subfamily of the FGGY family of carbohydrate kinases. The member from Klebsiella pneumoniae, designated DalK (see PMID:9324246), was annotated erroneously in GenBank as D-arabinitol kinase but is authentic D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization [Energy metabolism, Sugars].
CDD:233357	445	PRK	Bacteria:8	TIGR01322, scrB_fam, sucrose-6-phosphate hydrolase.  [Energy metabolism, Biosynthesis and degradation of polysaccharides].
CDD:233358	525	PRK	Bacteria:2	TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase.  This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli [Amino acid biosynthesis, Serine family].
CDD:233368	460	EUKprk	Bacteria:10,Invertebrates:1	TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase.  This model describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and ...
CDD:233369	210	EUKprk	Bacteria:7,Environmental:1,Invertebrates:3,Plants:2,Primates:1	TIGR01351, adk, adenylate kinase.  Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a ...
CDD:213607	74	PRK	Bacteria:27,nodiv:1	TIGR01352, tonB_Cterm, TonB family C-terminal domain.  This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these ...
CDD:233370	381	PRK	Bacteria:5	TIGR01353, dGTP_triPase, deoxyguanosinetriphosphate triphosphohydrolase, putative.  dGTP triphosphohydrolase (dgt) releases inorganic triphosphate, an unusual activity reaction product, from GTP. Its activity has been called limited to the Enterobacteriaceae, although homologous sequences are detected elsewhere. This finding casts doubt on whether the activity is shared in other species. In several of these other species, the homologous gene is found in an apparent ...
CDD:233371	127	EUKprk	Bacteria:6,Plants:1,Primates:1	TIGR01354, cyt_deam_tetra, cytidine deaminase, homotetrameric.  This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides].
CDD:233373	409	EUKprk	Bacteria:7,Plants:1	TIGR01356, aroA, 3-phosphoshikimate 1-carboxyvinyltransferase.  This model represents 3-phosphoshikimate-1-carboxyvinyltransferase (aroA), which catalyzes the sixth of seven steps in the shikimate pathway of the biosynthesis of chorimate. Chorismate is last common precursor of all three aromatic amino acids. Sequences scoring between the trusted and noise cutoffs include fragmentary and aberrant sequences in which generally well-conserved motifs are ...
CDD:233374	344	PRK	Bacteria:8	TIGR01357, aroB, 3-dehydroquinate synthase.  This model represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids [Amino acid biosynthesis, Aromatic amino acid family].
CDD:233375	260	PRK	Bacteria:3	TIGR01361, DAHP_synth_Bsub, phospho-2-dehydro-3-deoxyheptonate aldolase.  This model describes one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterized member from Bacillus subtilis, ...
CDD:130431	349	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Plants:1,Primates:1,Synthetic:1	TIGR01364, serC_1, phosphoserine aminotransferase.  This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266) [Amino acid biosynthesis, ...
CDD:233378	358	EUKprk	Bacteria:9,Invertebrates:1,Plants:3,Primates:1	TIGR01368, CPSaseIIsmall, carbamoyl-phosphate synthase, small subunit.  This model represents the whole of the small chain of the glutamine-dependent form (EC 6.3.5.5) of carbamoyl phosphate synthase, CPSase II. The C-terminal domain has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (EC 6.3.4.16). ...
CDD:233379	1050	EUKprk	Bacteria:4,Invertebrates:1,Primates:1	TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large subunit.  Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit ...
CDD:233381	750	EUKprk	Bacteria:3,Plants:1	TIGR01371, met_syn_B12ind, 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase.  This model describes the cobalamin-independent methionine synthase. A family of uncharacterized archaeal proteins is homologous to the C-terminal region of this family. That family is excluded from this model but, along with this family, belongs to Pfam model pfam01717 [Amino acid biosynthesis, Aspartate family].
CDD:233385	27	PRK	Bacteria:9	TIGR01376, POMP_repeat, Chlamydial polymorphic outer membrane protein repeat.  This model represents a repeat region of about 27 residues that appears from twice to over twenty times in Chlamydial polymorphic outer membrane proteins (POMP). Characteristic motifs in the repeat are FXXN and GGAI. Except for a few apparently truncated examples, Chlamydial proteins have this repeat region if and only if they also have the autotransporter beta-domain (pfam03797) at the ...
CDD:233386	205	EUKprk	Bacteria:15,Invertebrates:1,nodiv:1	TIGR01378, thi_PPkinase, thiamine pyrophosphokinase.  This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine ...
CDD:233387	317	PRK	Bacteria:6	TIGR01379, thiL, thiamine-monophosphate kinase.  This model describes thiamine-monophosphate kinase, an enzyme that converts thiamine monophosphate into thiamine pyrophosphate (TPP, coenzyme B1), an enzyme cofactor. Thiamine monophosphate may be derived from de novo synthesis or from unphosphorylated thiamine, known as vitamin B1. Proteins scoring between the trusted and noise cutoff for this model include short forms from the Thermoplasmas (which lack the ...
CDD:213612	179	EUKprk	Bacteria:3,Invertebrates:2,Plants:2,Primates:1	TIGR01383, not_thiJ, DJ-1 family protein.  This model represents the DJ-1 clade of the so-called ThiJ/PfpI family of proteins. PfpI, represented by a distinct model, is a putative intracellular cysteine protease. DJ-1 is described as an oncogene that acts cooperatively with H-Ras. Many members of the DJ-1 clade are annotated (apparently incorrectly) as ThiJ, a protein of thiamine biosynthesis. However, published reports of ThiJ ...
CDD:233391	457	PRK	Bacteria:5	TIGR01386, cztS_silS_copS, heavy metal sensor kinase.  Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.
CDD:233392	415	PRK	Bacteria:11	TIGR01391, dnaG, DNA primase, catalytic core.  Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751) [DNA metabolism, DNA replication, ...
CDD:233393	351	EUKprk	Bacteria:10,Plants:1	TIGR01392, homoserO_Ac_trn, homoserine O-acetyltransferase.  This family describes homoserine-O-acetyltransferase, an enzyme of methionine biosynthesis. This model has been rebuilt to identify sequences more broadly, including a number of sequences suggested to be homoserine O-acetyltransferase based on proximity to other Met biosynthesis genes [Amino acid biosynthesis, Aspartate family].
CDD:130460	595	PRK	Bacteria:5	TIGR01393, lepA, GTP-binding protein LepA.  LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown [Unknown function, General].
CDD:233394	594	EUKprk	Bacteria:6,Plants:1	TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA.  This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown [Regulatory functions, Other, Cellular processes, Adaptations to atypical conditions, Protein synthesis, Translation factors].
CDD:130462	135	PRK	Bacteria:5	TIGR01395, FlgC, flagellar basal-body rod protein FlgC.  This model represents FlgC, one of several components of bacterial flagella that share a domain described by Pfam model pfam00460. FlgC is part of the basal body [Cellular processes, Chemotaxis and motility].
CDD:233395	131	PRK	Bacteria:4,Synthetic:1	TIGR01396, FlgB, flagellar basal-body rod protein FlgB.  This model represents FlgB, one of several components of bacterial flagella that share a domain described by Pfam model pfam00460. FlgB is part of the basal body [Cellular processes, Chemotaxis and motility].
CDD:130464	320	PRK	Bacteria:4	TIGR01397, fliM_switch, flagellar motor switch protein FliM.  Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related ...
CDD:162338	678	PRK	Bacteria:7	TIGR01398, FlhA, flagellar biosynthesis protein FlhA.  This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this ...
CDD:233396	677	PRK	Bacteria:6	TIGR01399, hrcV, type III secretion protein, HrcV family.  Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the ...
CDD:130467	245	PRK	Bacteria:6	TIGR01400, fliR, flagellar biosynthetic protein FliR.  This model recognizes the FliR protein of bacterial flagellar biosynthesis. It distinguishes FliR from the homologous proteins bacterial type III protein secretion systems, known by names such as YopT, EscT, and HrcT [Cellular processes, Chemotaxis and motility].
CDD:130468	253	PRK	Bacteria:7,Synthetic:1	TIGR01401, fliR_like_III, type III secretion protein SpaR/YscT/HrcT.  This model represents members of bacterial type III secretion systems homologous to the flagellar biosynthetic protein FliR (TIGRFAMs:TIGR01400) [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:130469	88	PRK	Bacteria:2	TIGR01402, fliQ, flagellar biosynthetic protein FliQ.  This model describes FliQ, a protein involved in biosynthesis of bacterial flagella. A related family of proteins, excluded from this model, participates in bacterial type III protein secretion systems [Cellular processes, Chemotaxis and motility].
CDD:130471	342	PRK	Bacteria:11	TIGR01404, FlhB_rel_III, type III secretion protein, YscU/HrpY family.  This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs [Protein fate, Protein and peptide ...
CDD:233399	29	PRK	Bacteria:37,nodiv:2	TIGR01409, TAT_signal_seq, Tat (twin-arginine translocation) pathway signal sequence.  Proteins assembled with various cofactors or by means of cytosolic molecular chaperones are poor candidates for translocation across the bacterial inner membrane by the standard general secretory (Sec) pathway. This model describes a family of predicted long, non-Sec signal sequences and signal-anchor sequences (uncleaved signal sequences). All contain an absolutely ...
CDD:130477	80	PRK	Bacteria:5,nodiv:1	TIGR01410, tatB, twin arginine-targeting protein translocase TatB.  This model represents the TatB protein of a Sec-independent system for transporting folded proteins, often with a bound redox cofactor, across the bacterial inner membrane. TatC is the multiple membrane spanning component. TatB, like the related TatA/E proteins, appears to span the membrane one time. The tat system recognizes proteins with an elongated signal sequence containing a conserved ...
CDD:213616	47	EUKprk	Bacteria:9,Plants:1	TIGR01411, tatAE, twin arginine-targeting protein translocase, TatA/E family.  This model distinguishes TatA/E from the related TatB, but does not distinguish TatA from TatE. The Tat (twin-arginine translocation) system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane. Functionally equivalent systems are found in the chloroplast and some in archaeal species. The signal ...
CDD:233401	308	EUKprk	Bacteria:9,Plants:2	TIGR01413, Dyp_perox_fam, Dyp-type peroxidase family.  A defined member of this superfamily is Dyp, a dye-decolorizing peroxidase that lacks a typical heme-binding region. A distinct, uncharacterized branch (TIGR01412) of this superfamily has a typical twin-arginine dependent signal sequence characteristic of exported proteins with bound redox cofactors.
CDD:233402	429	PRK	Bacteria:16,nodiv:1	TIGR01414, autotrans_barl, outer membrane autotransporter barrel domain.  A number of Gram-negative bacterial proteins, mostly found in pathogens and associated with virulence, contain a conserved C-terminal domain that integrates into the outer membrane and enables the N-terminal region to be delivered across the membrane. This C-terminal autotransporter domain is about 400 amino acids in length and includes the aromatic amino acid-rich OMP signal, ...
CDD:233404	174	PRK	Bacteria:11	TIGR01416, Rieske_proteo, ubiquinol-cytochrome c reductase, iron-sulfur subunit.  This model represents the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulfur as found in ubiquinol-cytochrome c reductase. The model excludes the Rieske iron-sulfur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence ...
CDD:233406	343	PRK	Bacteria:4	TIGR01420, pilT_fam, pilus retraction protein PilT.  This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family ...
CDD:188140	253	PRK	Bacteria:3	TIGR01422, phosphonatase, phosphonoacetaldehyde hydrolase.  This enzyme catalyzes the cleavage of the carbon phosphorous bond of a phosphonate. The mechanism depends on the substrate having a carbonyl one carbon away from the cleavage position. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), and contains a modified version of the conserved catalytic motifs of that superfamily: the first motif is ...
CDD:233407	392	PRK	Bacteria:5	TIGR01426, MGT, glycosyltransferase, MGT family.  This model describes the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production [Cellular processes, Toxin production and resistance].
CDD:130495	198	EUKprk	Bacteria:7,Plants:1	TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type II.  Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism ...
CDD:233410	324	EUKprk	Bacteria:2,Mammals:1,Plants:1	TIGR01430, aden_deam, adenosine deaminase.  This family includes the experimentally verified adenosine deaminases of mammals and E. coli. Other members of this family are predicted also to be adenosine deaminase, an enzyme of nucleotide degradation. This family is distantly related to AMP deaminase.
CDD:200102	43	PRK	Bacteria:10	TIGR01439, lp_hng_hel_AbrB, looped-hinge helix DNA binding domain, AbrB family.  This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model ...
CDD:213622	21	PRK	Bacteria:13,Synthetic:1	TIGR01443, intein_Cterm, intein C-terminal splicing region.  This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a ...
CDD:233415	144	EUKprk	Bacteria:12,Plants:1	TIGR01444, fkbM_fam, methyltransferase, FkbM family.  Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of ...
CDD:233416	81	PRK	Bacteria:8,Phages:1	TIGR01445, intein_Nterm, intein N-terminal splicing region.  This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein.
CDD:213625	73	PRK	Bacteria:10,Phages:3	TIGR01446, DnaD_dom, DnaD and phage-associated domain.  This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions].
CDD:233417	586	PRK	Bacteria:4	TIGR01447, recD, exodeoxyribonuclease V, alpha subunit.  This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model [DNA metabolism, DNA ...
CDD:213626	53	PRK	Bacteria:20	TIGR01451, B_ant_repeat, conserved repeat domain.  This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium ...
CDD:233421	214	EUKprk	Bacteria:1,Phages:1,Plants:6,Viruses:1	TIGR01453, grpIintron_endo, group I intron endonuclease.  This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, pfam01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in This model is found in open reading frames of group I ...
CDD:233422	236	EUKprk	Bacteria:5,Invertebrates:2,Plants:3,Primates:1	TIGR01460, HAD-SF-IIA, Haloacid Dehalogenase Superfamily Class (subfamily) IIA.  This model represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a ...
CDD:130529	151	PRK	Bacteria:11	TIGR01462, greA, transcription elongation factor GreA.  The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreA differs functionally in that it releases smaller oligonucleotides. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (TIGR01461) forms a ...
CDD:233423	338	EUKprk	Bacteria:8,Invertebrates:1,Plants:1,Primates:1	TIGR01464, hemE, uroporphyrinogen decarboxylase.  This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:200107	247	PRK	Bacteria:6	TIGR01465, cobM_cbiF, precorrin-4 C11-methyltransferase.  This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:233424	239	PRK	Bacteria:5	TIGR01466, cobJ_cbiH, precorrin-3B C17-methyltransferase.  This model represents precorrin-3B C17-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, EC 2.1.1.133). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. Members of this family may appear as fusion proteins with other enzymes of cobalamin biosynthesis [Biosynthesis of ...
CDD:233425	230	PRK	Bacteria:9	TIGR01467, cobI_cbiL, precorrin-2 C20-methyltransferase.  This model represents precorrin-2 C20-methyltransferase, one of several closely related S-adenosylmethionine-dependent methyltransferases involved in cobalamin (vitamin B12) biosynthesis [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:233426	236	EUKprk	Bacteria:11,Plants:1	TIGR01469, cobA_cysG_Cterm, uroporphyrin-III C-methyltransferase.  This model represents enzymes, or enzyme domains, with uroporphyrin-III C-methyltransferase activity. This enzyme catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). Cobalamin contains cobalt while siroheme contains iron. Siroheme is a cofactor for nitrite and sulfite reductases and therefore plays a role in ...
CDD:233428	280	EUKprk	Bacteria:8,Invertebrates:1,Plants:1,Primates:1,Synthetic:1	TIGR01473, cyoE_ctaB, protoheme IX farnesyltransferase.  This model describes protoheme IX farnesyltransferase, also called heme O synthase, an enzyme that creates an intermediate in the biosynthesis of heme A. Prior to the description of its enzymatic function, this protein was often called a cytochrome o ubiquinol oxidase assembly factor [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, ...
CDD:130539	281	EUKprk	Bacteria:1,Plants:1,Primates:1	TIGR01474, ubiA_proteo, 4-hydroxybenzoate polyprenyl transferase, proteobacterial.  This model represents a family of integral membrane proteins that condenses para-hydroxybenzoate with any of several polyprenyldiphosphates. Heterologous expression studies suggest that for, many but not all members, the activity seen (e.g. octaprenyltransferase in E. coli) reflects available host isoprenyl pools rather than enzyme specificity. A fairly deep ...
CDD:233430	353	EUK	Invertebrates:2	TIGR01477, RIFIN, variant surface antigen, rifin family.  This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a ...
CDD:233431	468	PRK	Bacteria:10,nodiv:1	TIGR01479, GMP_PMI, mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase.  This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present ...
CDD:233434	204	EUKprk	Bacteria:12,Invertebrates:1,Plants:3	TIGR01484, HAD-SF-IIB, HAD-superfamily hydrolase, subfamily IIB.  This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterized by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (TIGR01460) by homology and the predicted secondary ...
CDD:130550	256	PRK	Bacteria:8	TIGR01486, HAD-SF-IIB-MPGP, mannosyl-3-phosphoglycerate phosphatase family.  This small group of proteins is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. Several members of this family from thermophiles (and from Dehalococcoides ethenogenes) are now known to act as mannosyl-3-phosphoglycerate (MPG) phosphatase. In these cases, the enzyme acts after MPG synthase to make the compatible ...
CDD:233435	177	EUKprk	Bacteria:6,Invertebrates:1,Plants:2,Primates:1,Synthetic:1	TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like.  This model represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this ...
CDD:233436	202	PRK	Bacteria:3	TIGR01490, HAD-SF-IB-hyp1, HAD-superfamily subfamily IB hydrolase, TIGR01490.  This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled by This model are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase (TIGR00338). Due to this relationship, several of these sequences have been annotated as "phosphoserine phosphatase ...
CDD:130556	62	EUK	Invertebrates:1	TIGR01492, CPW_WPC, Plasmodium falciparum CPW-WPC domain.  This model represents a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC.
CDD:233438	543	EUKprk	Bacteria:8,Invertebrates:10,Mammals:1,Plants:8,Primates:2,Vertebrates:1	TIGR01494, ATPase_P-type, ATPase, P-type (transporting), HAD superfamily, subfamily IC.  The P-type ATPases are a large family of trans-membrane transporters acting on charged substances. The distinguishing feature of the family is the formation of a phosphorylated intermediate (aspartyl-phosphate) during the course of the reaction. Another common name for these enzymes is the E1-E2 ATPases based on the ...
CDD:130559	85	EUK	Invertebrates:1	TIGR01495, ETRAMP, Plasmodium ring stage membrane protein ETRAMP.  This model describes a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rident parasite Plasmodium yoelii. A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane. Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the ...
CDD:233439	257	PRK	Bacteria:7	TIGR01496, DHPS, dihydropteroate synthase.  This model represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (pfam00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of pfam00809 and COG0294 are ...
CDD:213631	129	EUKprk	Bacteria:12,Plants:1	TIGR01498, folK, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.  This model describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme ...
CDD:233440	398	EUKprk	Bacteria:8,Invertebrates:3	TIGR01499, folC, folylpolyglutamate synthase/dihydrofolate synthase.  This model represents the FolC family of folate pathway proteins. Most examples are bifunctional, active as both folylpolyglutamate synthetase (EC 6.3.2.17) and dihydrofolate synthetase (EC 6.3.2.12). The two activities are similar - ATP + glutamate + dihydropteroate or tetrahydrofolyl-[Glu](n) = ADP + orthophosphate + dihydrofolate or tetrahydrofolyl-[Glu](n+1). A mutation ...
CDD:233443	177	EUKprk	Bacteria:10,Invertebrates:2,Plants:5,Rodents:1	TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED.  This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a ...
CDD:233444	155	PRK	Bacteria:2	TIGR01510, coaD_prev_kdtB, pantetheine-phosphate adenylyltransferase, bacterial.  This model describes pantetheine-phosphate adenylyltransferase, the penultimate enzyme of coenzyme A (CoA) biosynthesis in bacteria. It does not show any strong homology to eukaryotic enzymes of coenzyme A biosynthesis. This protein was previously designated KdtB and postulated (because of cytidyltransferase homology and proximity to kdtA) to be an enzyme of LPS biosynthesis, a ...
CDD:233445	572	EUKprk	Bacteria:8,Mammals:1,Plants:4	TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type ATPase.  This model describes the P-type ATPase primarily responsible for translocating copper ions accross biological membranes. These transporters are found in prokaryotes and eukaryotes. This model encompasses those species which pump copper ions out of cells or organelles (efflux pumps such as CopA of Escherichia coli ) as well as those which pump the ion into cells or ...
CDD:211664	536	EUKprk	Bacteria:10,Plants:1	TIGR01512, ATPase-IB2_Cd, heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase.  This model describes the P-type ATPase primarily responsible for translocating cadmium ions (and other closely-related divalent heavy metals such as cobalt, mercury, lead and zinc) across biological membranes. These transporters are found in prokaryotes and plants. Experimentally characterized members of the seed alignment include: SP|P37617 from E. coli, SP|Q10866 from ...
CDD:233446	443	EUKprk	Bacteria:4,Primates:1	TIGR01513, NAPRTase_put, putative nicotinate phosphoribosyltransferase.  A deep split separates two related families of proteins, one of which includes experimentally characterized examples of nicotinate phosphoribosyltransferase, an the first enzyme of NAD salvage biosynthesis. This model represents the other family. Members have a different (longer) spacing of several key motifs and have an additional C-terminal domain of up to 100 residues. One ...
CDD:233447	556	EUKprk	Bacteria:10,Plants:2,Primates:1	TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase.  This model encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512.
CDD:130592	146	PRK	Bacteria:3	TIGR01529, argR_whole, arginine repressor.  This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif ...
CDD:233453	326	EUKprk	Bacteria:10,Invertebrates:5,Plants:2	TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type I.  This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, ...
CDD:233454	466	EUKprk	Bacteria:5,Invertebrates:1,Primates:1	TIGR01536, asn_synth_AEB, asparagine synthase (glutamine-hydrolyzing).  This model describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the ...
CDD:233455	341	PRK	Bacteria:5,Phages:9	TIGR01537, portal_HK97, phage portal protein, HK97 family.  This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa [Mobile and extrachromosomal element functions, ...
CDD:233461	396	PRK	Bacteria:7,Phages:3	TIGR01547, phage_term_2, phage terminase, large subunit, PBSX family.  This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354 [Mobile and extrachromosomal element functions, Prophage functions].
CDD:233463	162	EUKprk	Bacteria:18,Invertebrates:1,Plants:5,Primates:1,Rodents:1	TIGR01549, HAD-SF-IA-v1, haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E.  This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or ...
CDD:233465	52	PRK	Bacteria:11	TIGR01552, phd_fam, prevent-host-death family protein.  This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists ...
CDD:233467	384	PRK	Bacteria:137,Phages:1,nodiv:2	TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.  This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the ...
CDD:130620	57	EUK	Plants:3,Unassigned:1	TIGR01557, myb_SHAQKYF, myb-like DNA-binding domain, SHAQKYF class.  This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
CDD:233468	116	PRK	Bacteria:2,Phages:4	TIGR01558, sm_term_P27, phage terminase, small subunit, putative, P27 family.  This model describes a distinct family of phage (and integrated prophage) putative terminase small subunit. Members tend to be adjacent to the phage terminase large subunit gene [Mobile and extrachromosomal element functions, Prophage functions].
CDD:130623	91	PRK	Bacteria:5,Phages:2	TIGR01560, put_DNA_pack, uncharacterized phage protein (possible DNA packaging).  This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model [Mobile and extrachromosomal element functions, Prophage functions].
CDD:162421	101	PRK	Bacteria:4,Phages:5,nodiv:1	TIGR01563, gp16_SPP1, phage head-tail adaptor, putative, SPP1 family.  This family describes a small protein of about 100 amino acids found in bacteriophage and in bacterial prophage regions. Examples include gp9 of phage HK022 and gp16 of phage SPP1. This minor structural protein is suggested to be a head-tail adaptor protein (although the source of this annotation was not traced during construction of this model) [Mobile and extrachromosomal ...
CDD:130631	66	EUK	Plants:1	TIGR01568, A_thal_3678, uncharacterized plant-specific domain TIGR01568.  This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
CDD:233473	104	EUK	Invertebrates:1,Plants:1,Primates:1,Rodents:1	TIGR01571, A_thal_Cys_rich, uncharacterized Cys-rich domain.  This model describes an uncharacterized domain of about 100 residues. It is common in plants but found also in Homo sapiens, Dictyostelium, and Leishmania; at least 12 distinct members are found in Arabidopsis. Most members of this family contain more than 10 per cent Cys, but no Cys residue is invariant across the family.
CDD:233475	95	PRK	Bacteria:5	TIGR01573, cas2, CRISPR-associated endoribonuclease Cas2.  This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very ...
CDD:233477	131	PRK	Bacteria:7	TIGR01575, rimI, ribosomal-protein-alanine acetyltransferase.  Members of this model belong to the GCN5-related N-acetyltransferase (GNAT) superfamily. This model covers prokarotes and the archaea. The seed contains a characterized accession for Gram negative E. coli. An untraceable characterized accession (PIR|S66013) for Gram positive B. subtilis scores well (205.0) in the full alignment. Characterized members are lacking in the archaea. Noise cutoff (72.4) was ...
CDD:233480	414	PRK	Bacteria:4	TIGR01579, MiaB-like-C, MiaB-like tRNA modifying enzyme.  This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive ...
CDD:233482	196	PRK	Bacteria:11	TIGR01586, yopT_cys_prot, cysteine protease domain, YopT-type.  The model represents a cysteine protease domain found in proteins of bacteria that include plant pathogens (Pseudomonas syringae), root nodule bacteria, and intracellular pathogens (e.g. Yersinia pestis, Haemophilus ducreyi, Pasteurella multocida, Chlamydia trachomatis) of animal hosts. The domain features a catalytic triad of Cys, His, and Asp. Sequences can be extremely divergent outside of a few ...
CDD:233483	358	PRK	Bacteria:2	TIGR01587, cas3_core, CRISPR-associated helicase Cas3.  This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not ...
CDD:233484	128	PRK	Bacteria:4,Phages:5	TIGR01593, holin_tox_secr, toxin secretion/phage lysis holin.  This model describes one of the many mutally dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species [Protein fate, Protein and peptide secretion and trafficking, Mobile and extrachromosomal element functions, ...
CDD:233487	177	PRK	Bacteria:105	TIGR01596, cas3_HD, CRISPR-associated endonuclease Cas3-HD.  CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This model represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein [Mobile and ...
CDD:233489	190	PRK	Bacteria:5,Phages:1	TIGR01603, maj_tail_phi13, phage major tail protein, phi13 family.  This model describes a set of proteins that share low levels of sequence similarity but similar lengths and similar patterns of charged, hydrophobic, and Gly/Pro residues. All members (except one attributed to mouse embryo cDNA) belong to phage of Gram-positive bacteria. Several are identified as phage major tail proteins. Some members of this family have additional C-terminal regions of ...
CDD:130674	304	PRK	Bacteria:5,Phages:2	TIGR01613, primase_Cterm, phage/plasmid primase, P4 family, C-terminal domain.  This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal ...
CDD:233492	178	EUK	Plants:6	TIGR01614, PME_inhib, pectinesterase inhibitor domain.  This model describes a plant domain of about 200 amino acids, characterized by four conserved Cys residues, shown in a pectinesterase inhibitor from Kiwi to form two disulfide bonds: first to second and third to fourth. Roughly half the members of this family have the region described by This model followed immediately by a pectinesterase domain, pfam01095. This suggests that the pairing of the enzymatic domain ...
CDD:130686	154	PRK	Bacteria:4	TIGR01625, YidE_YbjL_dupl, AspT/YidE/YbjL antiporter duplication domain.  This model represents a domain that is duplicated the aspartate-alanine antiporter AspT, as well as HI0035 of Haemophilus influenzae, YidE and YbjL of E. coli, and a number of other known or putative transporters. Member proteins may have 0, 1, or 2 copies of TrkA potassium uptake domain pfam02080 between the duplications. The domain contains several apparent transmembrane regions and is ...
CDD:233500	140	EUKprk	Bacteria:2,Plants:2	TIGR01632, L11_bact, 50S ribosomal protein L11.  This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:188159	124	PRK	Bacteria:2,Phages:7	TIGR01633, phi3626_gp14_N, putative phage tail component, N-terminal domain.  This model represents the best-conserved region of about 125 amino acids, toward the N-terminus, of a family of proteins from temperate phage of a number of Gram-positive bacteria. These phage proteins range in length from 230 to 525 amino acids [Mobile and extrachromosomal element functions, Prophage functions].
CDD:233501	132	PRK	Bacteria:6,Phages:3	TIGR01637, phage_arpU, phage transcriptional regulator, ArpU family.  This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We ...
CDD:130700	61	EUK	Invertebrates:1	TIGR01639, P_fal_TIGR01639, Plasmodium falciparum uncharacterized domain TIGR01639.  This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized.
CDD:233502	230	EUK	Plants:2	TIGR01640, F_box_assoc_1, F-box protein interaction domain.  This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of ...
CDD:213641	108	PRK	Bacteria:3,Phages:2	TIGR01641, phageSPP1_gp7, phage putative head morphogenesis protein, SPP1 gp7 family.  This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis [Mobile and extrachromosomal element functions, Prophage functions].
CDD:213642	42	EUKprk	Bacteria:11,Invertebrates:1,Primates:1	TIGR01643, YD_repeat_2x, YD repeat (two copies).  This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
CDD:233504	190	PRK	Bacteria:8,Phages:4	TIGR01644, phage_P2_V, phage baseplate assembly protein V.  This model describes a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria ...
CDD:233506	754	EUKprk	Bacteria:1,Invertebrates:2,Plants:6	TIGR01647, ATPase-IIIA_H, plasma-membrane proton-efflux P-type ATPase.  This model describes the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast.
CDD:233509	1057	EUK	Invertebrates:1,Plants:3,Rodents:1	TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase, flippase.  This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes.
CDD:233511	679	PRK	Bacteria:4	TIGR01654, bact_immun_7tm, bacteriocin-associated integral membrane (putative immunity) protein.  This model represents a family of integral membrane proteins, most of which are about 650 residues in size and predicted to span the membrane seven times. Nearly half of the members of this family are found in association with a member of the lactococcin 972 family of bacteriocins (TIGR01653). Others may be associated with uncharacterized proteins that may also act as ...
CDD:233513	1054	EUK	Invertebrates:1,Plants:1,Primates:1	TIGR01657, P-ATPase-V, P-type ATPase of unknown pump specificity (type V).  These P-type ATPases form a distinct clade but the substrate of their pumping activity has yet to be determined. This clade has been designated type V in.
CDD:233517	132	EUKprk	Bacteria:8,Plants:3,Primates:1,Rodents:1,Viruses:1	TIGR01662, HAD-SF-IIIA, HAD-superfamily hydrolase, subfamily IIIA.  This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class III subfamilies are characterized by the lack of any domains located between either between the first and second conserved catalytic motifs (as in the Class I subfamilies, TIGR01493, TIGR01509, TIGR01488 and TIGR01494) or between the second ...
CDD:233518	316	PRK	Bacteria:3,Phages:5	TIGR01665, put_anti_recept, phage minor structural protein, N-terminal region.  This model represents the conserved N-terminal region, typically from about residue 25 to about residue 350, of a family of uncharacterized phage proteins 500 to 1700 residues in length [Mobile and extrachromosomal element functions, Prophage functions].
CDD:233526	128	EUKprk	Bacteria:7,Invertebrates:1,Plants:1,Viruses:4	TIGR01681, HAD-SF-IIIC, HAD-superfamily phosphatase, subfamily IIIC.  This model represents the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. Subfamily III (also including IIIA - TIGR01662 and IIIB - pfam03767) contains sequences which do not contain either of the insert domains (between the 1st and 2nd conserved catalytic motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549, ...
CDD:130743	80	EUKprk	Bacteria:4,Invertebrates:1,Plants:1,Primates:1,nodiv:1	TIGR01682, moaD, molybdopterin converting factor, subunit 1, non-archaeal.  This model describes MoaD. It excludes archaeal homologs, since many Archaea have two MoaD-like proteins, suggesting two different functions. The Pfam model pfam02597 describes both the thiamine biosynthesis protein ThiS and this protein, MoaD, a subunit (together with MoaE, pfam02391) of the molybdopterin converting factor. Both ThiS and MoaD ...
CDD:233527	64	PRK	Bacteria:24	TIGR01683, thiS, thiamine biosynthesis protein ThiS.  This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis [Biosynthesis of cofactors, prosthetic ...
CDD:162489	94	PRK	Bacteria:17	TIGR01690, ICE_RAQPRD, integrative conjugative element protein, RAQPRD family.  This model represents a small family of proteins about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C-terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function is unknown ...
CDD:233534	850	PRK	Bacteria:4	TIGR01693, UTase_glnD, [Protein-PII] uridylyltransferase.  This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family [Central intermediary ...
CDD:233535	241	EUKprk	Bacteria:3,Invertebrates:2	TIGR01694, MTAP, 5'-deoxy-5'-methylthioadenosine phosphorylase.  This model represents the methylthioadenosine phosphorylase found in metazoa, cyanobacteria and a limited number of archaea such as Sulfolobus, Aeropyrum, Pyrobaculum, Pyrococcus, and Thermoplasma. This enzyme is responsible for the first step in the methionine salvage pathway after the transfer of the amino acid moiety from S-adenosylmethionine. The enzyme from human is ...
CDD:233536	502	PRK	Bacteria:4	TIGR01695, mviN, integral membrane protein MviN.  This model represents MviN, a family of integral membrane proteins predicted to have ten or more transmembrane regions. Although frequently listed as a virulence protein, it is not restricted to pathogens and it is an essential protein in Sinorhizobium meliloti. In a number of species its gene is adjacent to that of the uridylyltransferase GlnD , the signal-transducing enzyme that performs the key modification to the ...
CDD:130758	248	EUKprk	Bacteria:3,Invertebrates:2,Plants:1	TIGR01697, PNPH-PUNA-XAPA, inosine/guanosine/xanthosine phosphorylase family.  This model is a subset of the subfamily represented by pfam00896 (phosphorylase family 2). This model excludes the methylthioadenosine phosphorylases (MTAP, TIGR01684) which are believed toplay a specific role in the recycling of methionine from methylthioadenosine. In this subfamily is found three clades of purine phosphorylases based on a neighbor-joining ...
CDD:233540	384	PRK	Bacteria:14	TIGR01709, typeII_sec_gspL, type II secretion system protein L.  This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens [Protein fate, Protein and peptide secretion and trafficking].
CDD:233543	220	PRK	Bacteria:7	TIGR01716, RGG_Cterm, transcriptional activator, Rgg/GadR/MutR family, C-terminal domain.  This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR (GP|2352485) is a positive regulator of a ...
CDD:233545	153	PRK	Bacteria:11,nodiv:1	TIGR01720, NRPS-para261, non-ribosomal peptide synthase domain TIGR01720.  This domain appears to be located immediately downstream from a condensation domain (pfam00668), and is followed primarily by the end of the molecule or another condensation domain (in a few cases it is followed by pfam00501, an AMP-binding module). The converse is not true, pfam00668 domains are not always followed by this domain. This implicates this domain in possible ...
CDD:233546	119	PRK	Bacteria:7,Phages:8	TIGR01725, phge_HK97_gp10, phage protein, HK97 gp10 family.  This model represents an uncharacterized, highly divergent bacteriophage family. The family includes gp10 from HK022 and HK97. It appears related to TIGR01635, a phage morphogenesis family believed to be involved in tail completion [Mobile and extrachromosomal element functions, Prophage functions].
CDD:130787	99	PRK	Bacteria:16	TIGR01726, HEQRo_perm_3TM, amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family.  This model represents one of several classes of multiple membrane spanning regions found immediately N-terminal to the domain described by pfam00528, binding-protein-dependent transport systems inner membrane component. The region covered by This model generally is predicted to contain three transmembrane helices. Substrate specificities attributed to ...
CDD:213647	87	PRK	Bacteria:8	TIGR01727, oligo_HPY, oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain.  This model represents a domain found in the C-terminal regions of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (pfam00005). All characterized members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters ...
CDD:130789	288	PRK	Bacteria:3	TIGR01728, SsuA_fam, ABC transporter, substrate-binding protein, aliphatic sulfonates family.  Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of This model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable ...
CDD:233547	322	PRK	Bacteria:12,nodiv:1	TIGR01730, RND_mfp, RND family efflux transporter, MFP subunit.  This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed ...
CDD:233548	40	PRK	Bacteria:9	TIGR01731, fil_hemag_20aa, adhesin HecA family 20-residue repeat (two copies).  This model represents two copies of a 20-residue repeat found in Bordetella pertussis filamentous hemagglutinin family of adhesins. This family includes extremely long proteins from a number of plant and animal pathogens.
CDD:233550	409	EUKprk	Bacteria:25,Plants:7,nodiv:1	TIGR01733, AA-adenyl-dom, amino acid adenylation domain.  This model represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalyzed is aa + ATP -> aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called "A-domains" in that context (for a review, see ). A-domains are almost invariably followed by ...
CDD:233552	715	PRK	Bacteria:2	TIGR01736, FGAM_synth_II, phosphoribosylformylglycinamidine synthase II.  Phosphoribosylformylglycinamidine synthase is a single, long polypeptide in most Proteobacteria and eukarotes. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis].
CDD:233553	227	PRK	Bacteria:2	TIGR01737, FGAM_synth_I, phosphoribosylformylglycinamidine synthase I.  In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This model describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea [Purines, pyrimidines, nucleosides, and nucleotides, Purine ...
CDD:233554	1202	PRK	Viruses:6	TIGR01739, tegu_FGAM_synt, herpesvirus tegument protein/v-FGAM-synthase.  This model describes a family of large proteins of herpesvirues. The protein is described variably as tegument protein or phosphoribosylformylglycinamidine synthase (FGAM-synthase). Most of the length of the protein shows homology to eukaryotic FGAM-synthase. Functional characterizations were not verified during construction of this model.
CDD:233555	214	EUKprk	Bacteria:6,Invertebrates:2,Plants:2	TIGR01740, pyrF, orotidine 5'-phosphate decarboxylase, subfamily 1.  This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. In many eukaryotes, the region hit by this model is part of a multifunctional protein [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis].
CDD:233557	367	EUKprk	Bacteria:6,Plants:2	TIGR01746, Thioester-redct, thioester reductase domain.  This model includes the terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine , as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG. The mechanism of reduction involves activation of the substrate by adenylation and transfer to a ...
CDD:130811	140	PRK	Bacteria:6	TIGR01750, fabZ, beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ.  This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid ...
CDD:233559	140	PRK	Bacteria:7	TIGR01753, flav_short, flavodoxin, short chain.  Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction [Energy metabolism, Electron transport].
CDD:130820	323	EUKprk	Bacteria:1,Invertebrates:5,Plants:2	TIGR01759, MalateDH-SF1, malate dehydrogenase.  This model represents a family of malate dehydrogenases in bacteria and eukaryotes which utilize either NAD or NADP depending on the species and context. MDH interconverts malate and oxaloacetate and is a part of the citric acid cycle as well as the C4 cycle in certain photosynthetic organisms.
CDD:233560	350	PRK	Bacteria:9,Phages:5	TIGR01760, tape_meas_TP901, phage tail tape measure protein, TP901 family, core region.  This model represents a reasonably well conserved core region of a family of phage tail proteins. The member from phage TP901-1 was characterized as a tail length tape measure protein in that a shortened form of the protein leads to phage with proportionately shorter tails [Mobile and extrachromosomal element functions, Prophage functions].
CDD:200128	49	PRK	Bacteria:16	TIGR01764, excise, DNA binding domain, excisionase family.  An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal ...
CDD:130826	73	PRK	Bacteria:6	TIGR01765, tspaseT_teng_N, transposase, putative, N-terminal domain.  This model represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and This model represents the upstream ORF [Mobile and extrachromosomal element functions, Transposon functions].
CDD:233563	82	PRK	Bacteria:8	TIGR01766, tspaseT_teng_C, transposase, IS605 OrfB family, central region.  This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by Pfam model pfam01385, and other proteins [Mobile and extrachromosomal element functions, Transposon functions].
CDD:233565	468	EUKprk	Bacteria:3,Invertebrates:1,Plants:5	TIGR01770, NDH_I_N, proton-translocating NADH-quinone oxidoreductase, chain N.  This model describes the 14th (based on E. coli) structural gene, N, of bacterial and chloroplast energy-transducing NADH (or NADPH) dehydrogenases. This model does not describe any subunit of the mitochondrial complex I (for which the subunit composition is very different), nor NADH dehydrogenases that are not coupled to ion transport. The Enzyme Commission ...
CDD:233566	299	EUKprk	Bacteria:14,Plants:2,Vertebrates:2	TIGR01771, L-LDH-NAD, L-lactate dehydrogenase.  This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have ...
CDD:233570	291	EUKprk	Bacteria:10,Invertebrates:1,Plants:1,Primates:1	TIGR01777, yfcH, TIGR01777 family protein.  This model represents a clade of proteins of unknown function including the E. coli yfcH protein [Hypothetical proteins, Conserved].
CDD:233574	845	PRK	Bacteria:5	TIGR01782, TonB-Xanth-Caul, TonB-dependent receptor.  This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and ...
CDD:233575	651	PRK	Bacteria:14	TIGR01783, TonB-siderophor, TonB-dependent siderophore receptor.  This subfamily model encompasses a wide variety of TonB-dependent outer membrane siderophore receptors. It has no overlap with TonB receptors known to transport other substances, but is likely incomplete due to lack of characterizations. It is likely that genuine siderophore receptors will be identified which score below the noise cutoff to this model at which point the model should be updated ...
CDD:130844	270	PRK	Bacteria:9	TIGR01784, T_den_put_tspse, conserved hypothetical protein (putative transposase or invertase).  Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The ...
CDD:233576	665	PRK	Bacteria:8,nodiv:1	TIGR01785, TonB-hemin, TonB-dependent heme/hemoglobin receptor family protein.  This model represents the TonB-dependent outer membrane heme/hemoglobin receptor/transporter found in bacteria which live in contact with animals (which contain hemoglobin or other heme-bearing globins) or legumes (which contain leghemoglobin). Some species having hits to this model such as Nostoc, Caulobacter and Chlorobium do not have an obvious source of hemoglobin-like ...
CDD:233577	715	PRK	Bacteria:6	TIGR01786, TonB-hemlactrns, TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein.  This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model ...
CDD:130859	368	PRK	Bacteria:5	TIGR01800, cit_synth_II, 2-methylcitrate synthase/citrate synthase II.  Members of this family are dimeric enzymes with activity as 2-methylcitrate synthase, citrate synthase, or both. Many Gram-negative species have a hexameric citrate synthase, termed citrate synthase I (TIGR01798). Members of this family (TIGR01800) appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesize 2-methylcitrate from ...
CDD:233582	541	PRK	Bacteria:6	TIGR01812, sdhA_frdA_Gneg, succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup.  This model represents the succinate dehydrogenase flavoprotein subunit as found in Gram-negative bacteria, mitochondria, and some Archaea. Mitochondrial forms interact with ubiquinone and are designated EC 1.3.5.1, but can be degraded to 1.3.99.1. Some isozymes in E. coli and other species run primarily in the opposite direction and ...
CDD:233583	439	PRK	Bacteria:4	TIGR01813, flavo_cyto_c, flavocytochrome c.  This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven ...
CDD:233586	435	PRK	Bacteria:5	TIGR01820, TrpE-arch, anthranilate synthase component I, archaeal clade.  This model represents an archaeal clade of anthranilate synthase component I enzymes. This enzyme is responsible for the first step of tryptophan biosynthesis from chorismate. The Sulfolobus enzyme has been reported to be part of a gene cluster for Trp biosynthesis [Amino acid biosynthesis, Aromatic amino acid family].
CDD:211689	310	PRK	Bacteria:6	TIGR01826, CofD_related, conserved hypothetical protein, cofD-related.  This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the Pfam model pfam01933 [Hypothetical proteins, Conserved].
CDD:233589	856	EUKprk	Bacteria:3,Invertebrates:2,Plants:1	TIGR01828, pyru_phos_dikin, pyruvate, phosphate dikinase.  This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes [Energy metabolism, Other].
CDD:233590	239	EUKprk	Bacteria:13,Invertebrates:1,Plants:2	TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein) reductase.  This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis [Fatty acid and phospholipid metabolism, Biosynthesis].
CDD:130900	88	PRK	Bacteria:9	TIGR01841, phasin, phasin family protein.  This model describes a family of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins; the member from Rhodospirillum rubrum is an activator of polyhydroxybutyrate (PHB) degradation. However, the member from Magnetospirillum sp. ...
CDD:130902	423	PRK	Bacteria:4	TIGR01843, type_I_hlyD, type I secretion membrane fusion protein, HlyD family.  Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer ...
CDD:233594	415	PRK	Bacteria:8	TIGR01844, type_I_sec_TolC, type I secretion outer membrane protein, TolC family.  Members of This model are outer membrane proteins from the TolC subfamily within the RND (Resistance-Nodulation-cell Division) efflux systems. These proteins, unlike the NodT subfamily, appear not to be lipoproteins. All are believed to participate in type I protein secretion, an ABC transporter system for protein secretion without cleavage of a signal sequence, although they may, ...
CDD:233595	454	PRK	Bacteria:4	TIGR01845, outer_NodT, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family.  Members of This model comprise a subfamily of the Outer Membrane Factor (TCDB 1.B.17) porins. OMF proteins operate in conjunction with a primary transporter of the RND, MFS, ABC, or PET systems, and a MFP (membrane fusion protein) to tranport substrates across membranes. The complex thus formed allows transport (export) of various solutes (heavy metal cations; drugs, ...
CDD:130906	15	PRK	Bacteria:30,Unassigned:1,nodiv:1	TIGR01847, bacteriocin_sig, bacteriocin-type signal sequence.  Bacteriocins are bacterial peptide products toxic to closely related bacteria. This model represents the N-terminal region up to the GG cleavage motif. Processing to remove this bacteriocin leader peptide occurs together with export by an ABC transporter. Note: because this model is so small (15 amino acids), it may have many spurious high-scoring matches to unrelated proteins, even ...
CDD:233597	346	EUKprk	Bacteria:21,Plants:5	TIGR01850, argC, N-acetyl-gamma-glutamyl-phosphate reductase, common form.  This model represents the more common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step or Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and the gap architecture in a multiple sequence alignment. Bacterial members of this family tend to be found within Arg biosynthesis operons ...
CDD:188173	254	PRK	Bacteria:7	TIGR01852, lipid_A_lpxA, acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase.  This model describes LpxA, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species, but this protein represents the first step (from UDP-N-acetyl-D-glucosamine) and appears to be conserved in function. Proteins ...
CDD:233599	324	PRK	Bacteria:5	TIGR01853, lipid_A_lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase.  This model describes LpxD, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species. This protein represents the third step from UDP-N-acetyl-D-glucosamine. The group added at this step generally is 14:0(3-OH) (myristate) but ...
CDD:233601	196	PRK	Bacteria:2	TIGR01855, IMP_synth_hisH, imidazole glycerol phosphate synthase, glutamine amidotransferase subunit.  This model represents the glutamine amidotransferase subunit (or domain, in eukaryotic systems) of imidazole glycerol phosphate synthase. This subunit catalyzes step 5 of histidine biosynthesis from PRPP. The other subunit, the cyclase, catalyzes step 6 [Amino acid biosynthesis, Histidine family].
CDD:233602	253	PRK	Bacteria:2	TIGR01856, hisJ_fam, histidinol phosphate phosphatase, HisJ family.  This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that ...
CDD:233604	584	PRK	Bacteria:12	TIGR01863, cas_Csd1, CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG.  CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein that tends to be found near CRISPR repeats of the DVULG subtype of CRISPR/Cas locus. We designate this family Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species range for this subtype, so far, is exclusively bacterial and mesophilic, although CRISPR loci in general are particularly common ...
CDD:233605	805	PRK	Bacteria:11	TIGR01865, cas_Csn1, CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI.  CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only [Mobile and extrachromosomal element functions, Other].
CDD:233606	222	PRK	Bacteria:19	TIGR01866, cas_Csn2, CRISPR type II-A/NMEMI-associated protein Csn2.  CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas loci. The species range so far for this subtype is animal pathogens and commensals only. This protein is present in some but not all NMENI CRISPR/Cas loci [Mobile and ...
CDD:233609	97	PRK	Bacteria:12	TIGR01870, cas_TM1810_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2.  These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This model represents the C-terminal domain of a minor family of CRISPR-associated protein from the Mtube subtype of CRISPR/Cas locus. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2 [Mobile and extrachromosomal element functions, Other].
CDD:233612	237	PRK	Bacteria:4	TIGR01875, cas_MJ0381, CRISPR-associated autoregulator DevR family.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This model represents one such family, represented by MJ0381 of Methanococcus jannaschii. This family includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to ...
CDD:233613	199	PRK	Bacteria:32	TIGR01877, cas_cas6, CRISPR-associated endoribonuclease Cas6.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a ...
CDD:233616	127	PRK	Bacteria:8	TIGR01881, cas_Cmr5, CRISPR type III-B/RAMP module-associated protein Cmr5.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species as part of the 6-gene CRISPR RAMP module [Mobile and extrachromosomal ...
CDD:233617	203	PRK	Bacteria:3	TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein.  Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity [Regulatory functions, DNA interactions, Mobile and extrachromosomal element functions, Other].
CDD:130940	401	EUKprk	Bacteria:2,Invertebrates:5,Plants:5	TIGR01885, Orn_aminotrans, ornithine aminotransferase.  This model describes the final step in the biosynthesis of ornithine from glutamate via the non-acetylated pathway. Ornithine amino transferase takes L-glutamate 5-semialdehyde and makes it into ornithine, which is used in the urea cycle, as well as in the biosynthesis of arginine. This model includes low-GC bacteria and eukaryotic species. The genes from two species are annotated as ...
CDD:233618	447	PRK	Bacteria:6	TIGR01887, dipeptidaselike, dipeptidase, putative.  This model represents a clade of probable zinc dipeptidases, closely related to the characterized non-specific dipeptidase, PepV. Many enzymes in this clade have been given names including the terms "Xaa-His" and "carnosinase" due to the early mis-characterization of the Lactobacillus delbrueckii PepV enzyme. These names are likely too specific.
CDD:233619	337	PRK	Bacteria:10	TIGR01888, cas_cmr3, CRISPR type III-B/RAMP module-associated protein Cmr3.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family is found in at least ten different archaeal and bacterial species as part of the CRISPR RAMP modulue but is not a member of the RAMP superfamily itself. A ...
CDD:130944	109	PRK	Bacteria:11	TIGR01889, Staph_reg_Sar, staphylococcal accessory regulator family.  This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by Pfam model pfam01047 [Regulatory functions, DNA interactions].
CDD:233621	363	EUKprk	Bacteria:6,Plants:1	TIGR01891, amidohydrolases, amidohydrolase.  This model represents a subfamily of amidohydrolases which are a subset of those sequences detected by pfam01546. Included within this group are hydrolases of hippurate (N-benzylglycine), indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. These hydrolases are of the carboxypeptidase-type, most likely utilizing a zinc ion in the active site [Protein fate, ...
CDD:233623	153	PRK	Bacteria:10	TIGR01894, cas_TM1795_cmr1, CRISPR type III-B/RAMP module RAMP protein Cmr1.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents the region of stongest conservation, the N-terminal half, of one such family, represented by TM1795 from Thermotoga maritima. This protein is the first of a set ...
CDD:233626	410	PRK	Bacteria:4	TIGR01897, cas_MJ1666, CRISPR-associated protein, MJ1666 family.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a Cas protein about 400 residues in length, found mostly in the Archaea but also in Aquifex [Mobile and extrachromosomal element functions, Other].
CDD:213662	176	PRK	Bacteria:6	TIGR01898, cas_TM1791_cmr6, CRISPR type III-B/RAMP module RAMP protein Cmr6.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded ...
CDD:233627	365	PRK	Bacteria:1	TIGR01899, cas_TM1807_csm5, CRISPR type III-A/MTUBE-associated RAMP protein Csm5.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm5, for CRISPR/cas Subtype Mtube, protein 5 [Mobile and extrachromosomal element ...
CDD:233628	351	PRK	Bacteria:9	TIGR01900, dapE-gram_pos, succinyl-diaminopimelate desuccinylase.  This model represents a clade of succinyl-diaminopimelate desuccinylases from actinobacteria (high-GC gram positives), delta-proteobacteria and aquificales and is based on the characterization of the enzyme from Corynebacterium glutamicum. This enzyme is involved in the biosynthesis of lysine, and is related to the enzyme acetylornithine deacetylase and other amidases and peptidases found within ...
CDD:130956	79	PRK	Bacteria:13	TIGR01901, adhes_NPXG, filamentous hemagglutinin family N-terminal domain.  This model represents a conserved domain found near the N-terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. Members generally have a signal sequence, then an intervening region, then the region described by This model. Following this region, proteins typically have regions rich in repeats but may show no homology between the ...
CDD:233629	297	PRK	Bacteria:3	TIGR01903, cas_TM1808_csm4, CRISPR type III-A/MTUBE-associated RAMP protein Csm4.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4 [Mobile and extrachromosomal element ...
CDD:233630	42	PRK	Bacteria:2	TIGR01904, GSu_C4xC__C2xCH, Geobacter sulfurreducens CxxxxCH...CXXCH domain.  This domain occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches ProSite motif PS00190, the cytochrome c family heme-binding site signature, suggesting.
CDD:213663	41	PRK	Bacteria:2	TIGR01905, paired_CXXCH_1, doubled CXXCH domain.  This model represents a domain of about 41 amino acids that contains, among other motifs, two copies of the motif CXXCH associated with heme binding. Almost every member of this family has at least three copies of this domain (at least six copies of CXXCH) is predicted to be a high molecular weight c-type cytochrome. Members are found mostly in species of Shewanella, Geobacter, and Vibrio.
CDD:233631	207	PRK	Bacteria:7	TIGR01906, integ_TIGR01906, integral membrane protein TIGR01906.  This model represents a family of highly hydrophobic, uncharacterized predicted integral membrane proteins found almost entirely in low-GC Gram-positive bacteria, although a member is also found in the early-branching bacterium Aquifex aeolicus.
CDD:233632	375	PRK	Bacteria:5	TIGR01910, DapE-ArgE, acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase.  This group of sequences contains annotations for both acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase, but does not contain any members with experimental characterization. Bacillus, Staphylococcus and Sulfolobus species contain multiple hits to this subfamily and each may have a separate activity. Determining which is which must await further ...
CDD:233637	261	PRK	Bacteria:1	TIGR01920, Shik_kin_archae, shikimate kinase.  This model represents the shikimate kinase (SK) gene found in archaea which is only distantly related to homoserine kinase (thrB) and not atr all to the bacterial SK enzyme. The SK from M. janaschii has been overexpressed in E. coli and characterized. SK catalyzes the fifth step of the biosynthesis of chorismate from D-erythrose-4-phosphate and phosphoenolpyruvate [Amino acid biosynthesis, Aromatic amino acid family].
CDD:233642	386	EUKprk	Bacteria:9,Invertebrates:1,Plants:4,Rodents:1	TIGR01930, AcCoA-C-Actrans, acetyl-CoA acetyltransferases.  This model represents a large family of enzymes which catalyze the thiolysis of a linear fatty acid CoA (or acetoacetyl-CoA) using a second CoA molecule to produce acetyl-CoA and a CoA-ester product two carbons shorter (or, alternatively, the condensation of two molecules of acetyl-CoA to produce acetoacetyl-CoA and CoA). This enzyme is also known as "thiolase", ...
CDD:233645	223	EUKprk	Bacteria:6,Invertebrates:1	TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis methyltransferases.  This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ...
CDD:233647	251	PRK	Bacteria:10	TIGR01938, nqrC, NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit.  This model represents the NqrC subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump [Transport and binding proteins, Cations and iron carrying compounds].
CDD:233649	435	PRK	Bacteria:5	TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C subunit.  The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase ...
CDD:131001	327	PRK	Bacteria:3	TIGR01946, rnfD, electron transport complex, RnfABCDGE type, D subunit.  The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase ...
CDD:233650	186	PRK	Bacteria:7	TIGR01947, rnfG, electron transport complex, RnfABCDGE type, G subunit.  The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase ...
CDD:233652	129	PRK	Bacteria:98,Synthetic:1	TIGR01951, nusB, transcription antitermination factor NusB.  A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10 [Transcription, Transcription factors].
CDD:233654	341	PRK	Bacteria:3	TIGR01953, NusA, transcription termination factor NusA.  This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model ...
CDD:131009	50	PRK	Bacteria:6	TIGR01954, nusA_Cterm_rpt, transcription termination factor NusA, C-terminal duplication.  NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues ...
CDD:131013	148	PRK	Bacteria:1	TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit.  This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria [Energy metabolism, Electron transport].
CDD:233657	121	PRK	Bacteria:7	TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, subunit C.  This model describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This model excludes the NAD(P)H and ...
CDD:131020	99	PRK	Bacteria:2	TIGR01965, VCBS_repeat, VCBS repeat.  This domain of about 100 residues is found multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion.
CDD:233661	122	EUKprk	Bacteria:5,Plants:1	TIGR01971, NuoI, NADH-quinone oxidoreductase, chain I.  This model represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes ...
CDD:200147	481	PRK	Bacteria:7	TIGR01972, NDH_I_M, proton-translocating NADH-quinone oxidoreductase, chain M.  This model describes the 13th (based on E. coli) structural gene, M, of bacterial NADH dehydrogenase I, as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex [Energy metabolism, Electron transport].
CDD:233662	603	EUKprk	Bacteria:5,Invertebrates:1,Plants:2,Rodents:1	TIGR01973, NuoG, NADH-quinone oxidoreductase, chain G.  This model represents the G subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate ...
CDD:233663	609	PRK	Bacteria:6	TIGR01974, NDH_I_L, proton-translocating NADH-quinone oxidoreductase, chain L.  This model describes the 12th (based on E. coli) structural gene, L, of bacterial NADH dehydrogenase I, as well as chain 5 of the corresponding mitochondrial complex I and subunit 5 (or F) of the chloroplast NAD(P)H-plastoquinone dehydrogenase complex [Energy metabolism, Electron transport].
CDD:233665	243	PRK	Bacteria:10	TIGR01978, sufC, FeS assembly ATPase SufC.  SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PMID:12554644) or associated with the membrane (PMID:11943156). The SUF ...
CDD:131034	403	PRK	Bacteria:9	TIGR01979, sufS, cysteine desulfurases, SufSfamily.  This model represents a subfamily of NifS-related cysteine desulfurases involved in FeS cluster formation needed for nitrogen fixation among other vital functions. Many cysteine desulfurases are also active as selenocysteine lyase and/or cysteine sulfinate desulfinase. This subfamily is associated with the six-gene SUF system described in E. coli and Erwinia as an FeS cluster formation system during oxidative ...
CDD:233666	275	PRK	Bacteria:18,nodiv:1	TIGR01981, sufD, FeS assembly protein SufD.  This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter ...
CDD:233667	437	PRK	Bacteria:5	TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase.  This model represents the enzyme (UbiB) which catalyzes the first hydroxylation step in the ubiquinone biosynthetic pathway in bacteria. It is believed that the reaction is 2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This model finds hits primarily in the proteobacteria. The gene is also known as AarF in certain species [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone].
CDD:233668	224	EUKprk	Bacteria:6,Invertebrates:1,Plants:3,Primates:1	TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase.  This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase [Biosynthesis ...
CDD:233669	382	PRK	Bacteria:4	TIGR01984, UbiH, 2-polyprenyl-6-methoxyphenol 4-hydroxylase.  This model represents the FAD-dependent monoxygenase responsible for the second hydroxylation step in the aerobic ubiquinone bioynthetic pathway. The scope of this model is limited to the proteobacteria. This family is closely related to the UbiF hydroxylase which catalyzes the final hydroxylation step. The enzyme has also been named VisB due to a mutant VISible light sensitive phenotype [Biosynthesis of ...
CDD:131040	112	PRK	Bacteria:5	TIGR01985, phasin_2, phasin.  This model represents a family of granule-associate proteins (phasins) which are part of the polyhydroxyalkanoate synthesis machinery. This family is based on a pair of characterized genes from Methylobacterium extorquens. Members of the seed for this model all contain the rest of the components believed to be essential for this system (see the "polyhydroxyalkanoic acid synthesis" property in the GenPropDB). Members of this family score ...
CDD:233671	387	EUKprk	Bacteria:7,Invertebrates:2,Plants:2,Primates:1	TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family.  This model represents a family of FAD-dependent hydroxylases (monooxygenases) which are all believed to act in the aerobic ubiquinone biosynthesis pathway. A separate set of hydroxylases, as yet undiscovered, are believed to be active under anaerobic conditions. In E. coli three enzyme activities have been described, UbiB (which acts first ...
CDD:213672	185	PRK	Bacteria:7	TIGR01990, bPGM, beta-phosphoglucomutase.  This model represents the beta-phosphoglucomutase enzyme which catalyzes the interconverison of beta-D-glucose-1-phosphate and beta-D-glucose-6-phosphate. The 6-phosphate is capable of non-enzymatic anomerization (alpha <-> beta) while the 1-phosphate is not. A separate enzyme is responsible for the isomerization of the alpha anomers. Beta-D-glucose-1-phosphate results from the phosphorylysis of maltose (2.4.1.8), trehalose ...
CDD:233673	599	PRK	Bacteria:7	TIGR01991, HscA, Fe-S protein assembly chaperone HscA.  The Heat Shock Cognate proteins HscA and HscB act together as chaperones. HscA resembles DnaK but belongs in a separate clade. The apparent function is to aid assembly of iron-sulfur cluster proteins. Homologs from Buchnera and Wolbachia are clearly in the same clade but are highly derived and score lower than some examples of DnaK [Protein fate, Protein folding and stabilization].
CDD:233675	183	EUKprk	Bacteria:3,Plants:3,nodiv:1	TIGR01993, Pyr-5-nucltdase, pyrimidine 5'-nucleotidase.  This family of proteins includes the SDT1/SSM1 gene from yeast which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase. The family spans plants, fungi and a small number of bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily (variant 3, TIGR01509).
CDD:233676	137	PRK	Bacteria:7	TIGR01994, SUF_scaf_2, SUF system FeS assembly protein, NifU family.  Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins ...
CDD:131051	461	PRK	Bacteria:5	TIGR01996, PTS-II-BC-sucr, PTS system, sucrose-specific IIBC component.  This model represents the fused enzyme II B and C components of the sucrose-specific PTS sugar transporter system. Sucrose is converted to sucrose-6-phosphate in the process of translocation into the cell. Some of these transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). The exceptions to this rule are Staphylococci, Streptococci, Lactococci, ...
CDD:233680	243	PRK	Bacteria:7	TIGR02001, gcw_chp, conserved hypothetical protein, proteobacterial.  This model represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis, Ralstonia solanacearum, and Colwellia psychrerythraea, usually as part of a paralogous family. The function is unknown.
CDD:213673	185	PRK	Bacteria:4	TIGR02009, PGMB-YQAB-SF, beta-phosphoglucomutase family hydrolase.  This subfamily model groups together three clades: the characterized beta-phosphoglucomutases (including those from E.coli, B.subtilus and L.lactis, TIGR01990), a clade of putative bPGM's from mycobacteria and a clade including the uncharacterized E.coli and H.influenzae yqaB genes which may prove to be beta-mutases of a related 1-phosphosugar. All of these are members of the larger Haloacid ...
CDD:188194	230	PRK	Bacteria:6	TIGR02018, his_ut_repres, histidine utilization repressor, proteobacterial.  This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional ...
CDD:233691	297	EUKprk	Bacteria:5,Plants:1	TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type.  This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a ...
CDD:233693	295	PRK	Bacteria:4,Environmental:1	TIGR02032, GG-red-SF, geranylgeranyl reductase family.  This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll].
CDD:233695	428	PRK	Bacteria:9,nodiv:1	TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ family.  This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are ...
CDD:233699	287	PRK	Bacteria:2	TIGR02050, gshA_cyan_rel, carboxylate-amine ligase, YbdK family.  This family represents a division of a larger family, the other branch of which is predicted to act as glutamate--cysteine ligase (the first of two enzymes in glutathione biosynthesis) in the cyanobacteria. Species containing this protein, however, are generally not believe to make glutathione, and the function is unknown.
CDD:233703	709	PRK	Bacteria:9	TIGR02063, RNase_R, ribonuclease R.  This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales ...
CDD:213680	251	EUKprk	Bacteria:9,Plants:1	TIGR02067, his_9_HisN, histidinol-phosphatase, inositol monophosphatase family.  This subfamily belongs to the inositol monophosphatase family (pfam00459). The members of this family consist of no more than one per species and are found only in species in which histidine is synthesized de novo but no histidinol phosphatase can be found in either of the two described families (TIGR01261, TIGR01856). In at least one species, the member of this family is ...
CDD:233708	240	PRK	Bacteria:16	TIGR02072, BioC, biotin biosynthesis protein BioC.  This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin].
CDD:233709	727	PRK	Bacteria:8	TIGR02073, PBP_1c, penicillin-binding protein 1C.  This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function [Cell envelope, Biosynthesis and degradation of murein sacculus and ...
CDD:233710	531	PRK	Bacteria:6	TIGR02074, PBP_1a_fam, penicillin-binding protein, 1A family.  Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (TIGR02071). This family also includes related proteins, often designated PBP 1A, ...
CDD:213681	232	PRK	Bacteria:12	TIGR02075, pyrH_bact, uridylate kinase.  This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and ...
CDD:233711	221	PRK	Bacteria:5	TIGR02076, pyrH_arch, uridylate kinase, putative.  This family consists of the archaeal and spirochete proteins most closely related to bacterial uridylate kinases (TIGR02075), an enzyme involved in pyrimidine biosynthesis. Members are likely, but not known, to be functionally equivalent to their bacterial counterparts. However, substantial sequence differences suggest that regulatory mechanisms may be different; the bacterial form is allosterically regulated by GTP ...
CDD:233720	361	EUKprk	Bacteria:11,Plants:1,nodiv:1	TIGR02091, glgC, glucose-1-phosphate adenylyltransferase.  This enzyme, glucose-1-phosphate adenylyltransferase, is also called ADP-glucose pyrophosphorylase. The plant form is an alpha2,beta2 heterodimer, allosterically regulated in plants. Both subunits are homologous and included in this model. In bacteria, both homomeric forms of GlgC and more active heterodimers of GlgC and GlgD have been described. This model describes the GlgC subunit ...
CDD:233722	794	EUKprk	Bacteria:8,Invertebrates:1,Plants:1,Primates:1	TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.  This family consists of phosphorylases. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin ...
CDD:233723	601	PRK	Bacteria:6	TIGR02094, more_P_ylases, alpha-glucan phosphorylases.  This family consists of known phosphorylases, and homologs believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members ...
CDD:233724	473	EUKprk	Bacteria:11,Plants:3,nodiv:1	TIGR02095, glgA, glycogen/starch synthase, ADP-glucose type.  This family consists of glycogen (or starch) synthases that use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose (EC 2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate [Energy metabolism, Biosynthesis and degradation of polysaccharides].
CDD:233725	129	PRK	Bacteria:8	TIGR02096, TIGR02096, conserved hypothetical protein, steroid delta-isomerase-related.  This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
CDD:131152	101	EUKprk	Bacteria:5,Invertebrates:1,Plants:1,Primates:1,nodiv:1	TIGR02097, yccV, hemimethylated DNA binding domain.  This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.
CDD:131153	38	PRK	Bacteria:10	TIGR02098, MJ0042_CXXC, MJ0042 family finger-like domain.  This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
CDD:233726	1260	PRK	Bacteria:7	TIGR02099, TIGR02099, TIGR02099 family protein.  This model describes a family of long proteins, over 1250 amino acids in length and present in the Proteobacteria. The degree of sequence similarity is low between sequences from different genera. Apparent membrane-spanning regions at the N-terminus and C-terminus suggest the protein is inserted into (or exported through) the membrane [Hypothetical proteins, Conserved].
CDD:131155	688	PRK	Bacteria:8	TIGR02100, glgX_debranch, glycogen debranching enzyme GlgX.  This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. In the wide band between the trusted and ...
CDD:233730	605	PRK	Bacteria:10	TIGR02104, pulA_typeI, pullulanase, type I.  Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the subfamilies described in TIGR02102 and TIGR02103 but having a ...
CDD:200158	21	PRK	Bacteria:16	TIGR02107, PQQ_syn_pqqA, coenzyme PQQ precursor peptide PqqA.  This model describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:131170	24	PRK	Bacteria:12	TIGR02115, potass_kdpF, K+-transporting ATPase, KdpF subunit.  This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation [Transport and binding proteins, Cations and iron carrying compounds].
CDD:131171	80	PRK	Bacteria:10	TIGR02116, toxin_Txe_YoeB, toxin-antitoxin system, toxin component, Txe/YoeB family.  The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to models TIGR01552 and/or pfam02604 [Cellular processes, Toxin production and resistance, Mobile and ...
CDD:131173	100	PRK	Bacteria:9	TIGR02118, TIGR02118, conserved hypothetical protein.  This model represents a small family of proteins of unknown function, each about 105 amino acids in length. Conserved sites in the multiple alignment include a pair of aromatic residues, a histidine, and an aspartate [Hypothetical proteins, Conserved].
CDD:233734	399	PRK	Bacteria:8	TIGR02120, GspF, type II secretion system protein F.  This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the"Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the ...
CDD:233736	320	PRK	Bacteria:9	TIGR02122, TRAP_TAXI, TRAP transporter solute receptor, TAXI family.  This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane ...
CDD:233737	613	PRK	Bacteria:6	TIGR02123, TRAP_fused, TRAP transporter, 4TM/12TM fusion protein.  In some species, the 12-transmembrane spanning and 4-transmembrane spanning components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This model describes such transporters, found in the Archaea and in Bacteria [Transport and binding proteins, Unknown substrate].
CDD:233738	320	PRK	Bacteria:11	TIGR02124, hypE, hydrogenase expression/formation protein HypE.  This family contains HypE (or HupE), a protein required for expression of catalytically active hydrogenase in many systems. It appears to be an accessory protein involved in maturation rather than a regulatory protein involved in expression. HypE shows considerable homology to the thiamine-monophosphate kinase ThiL (TIGR01379) and other enzymes.
CDD:131180	211	PRK	Bacteria:10	TIGR02125, CytB-hydogenase, Ni/Fe-hydrogenase, b-type cytochrome subunit.  This model describes a family of cytochrome b proteins which appear to be specific for nickel-iron hydrogenase complexes. Every genome which contains a member of this family posesses a Ni/Fe hydrogenase according to Genome Properties (GenProp0177), and most are gene clustered with other hydrogenase components. Some Ni/Fe hydrogenase-containing species lack a member of this family but contain ...
CDD:233739	136	PRK	Bacteria:9,Phages:3	TIGR02126, phgtail_TP901_1, phage major tail protein, TP901-1 family.  This family includes the members of pfam06199 but is broader. Characterized members are major tail proteins from various phage, including lactococcal temperate bacteriophage TP901-1 [Mobile and extrachromosomal element functions, Prophage functions].
CDD:233740	261	EUKprk	Bacteria:5,Invertebrates:1	TIGR02127, pyrF_sub2, orotidine 5'-phosphate decarboxylase, subfamily 2.  This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. See TIGR01740 for a related but distinct subfamily of the same enzyme [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis].
CDD:233741	308	PRK	Bacteria:3	TIGR02128, G6PI_arch, bifunctional phosphoglucose/phosphomannose isomerase.  This bifunctional isomerase is a member of the larger PGI superfamily and only distantly related to other glucose-6-phosphate isomerases. The family is limited to the archaea.
CDD:233742	212	PRK	Bacteria:15	TIGR02135, phoU_full, phosphate transport system regulatory protein PhoU.  This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function [Regulatory ...
CDD:233743	287	PRK	Bacteria:9	TIGR02136, ptsS_2, phosphate binding protein.  Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975 [Transport and binding proteins, Anions].
CDD:233744	295	PRK	Bacteria:6	TIGR02138, phosphate_pstC, phosphate ABC transporter, permease protein PstC.  The typical operon for the high affinity inorganic phosphate ABC transporter encodes an ATP-binding protein, a phosphate-binding protein, and two permease proteins. This family consists of one of the two permease proteins, PstC, which is homologous to PstA (TIGR00974). In the model bacterium Escherichia coli, this transport system is induced when the concentration of extrallular inorganic ...
CDD:233745	208	PRK	Bacteria:12	TIGR02141, modB_ABC, molybdate ABC transporter, permease protein.  This model describes the permease protein, ModB, of the molybdate ABC transporter. This system has been characterized in E. coli , Staphylococcus carnosus Rhodobacter capsulatus and Azotobacter vinlandii. Molybdate is chemically similar to sulfate, thiosulfate, and selenate. These related substrates, and sometimes molybdate itself, can be transported by the homologous sulfate receptor. Some apparent ...
CDD:233746	171	PRK	Bacteria:1	TIGR02145, Fib_succ_major, Fibrobacter succinogenes major paralogous domain.  This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This ...
CDD:233747	271	PRK	Bacteria:1	TIGR02147, Fsuc_second, TIGR02147 family protein.  This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85 and a smaller number in Bdellovibrio bacteriovorus HD100. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The ...
CDD:233749	158	EUKprk	Bacteria:2,Environmental:1,Plants:3,Primates:1,Rodents:1	TIGR02150, IPP_isom_1, isopentenyl-diphosphate delta-isomerase, type 1.  This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate [Biosynthesis of ...
CDD:233750	333	PRK	Bacteria:12	TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase, type 2.  Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids [Biosynthesis of cofactors, prosthetic ...
CDD:233751	293	EUKprk	Bacteria:9,Invertebrates:1,Primates:1	TIGR02152, D_ribokin_bact, ribokinase.  This model describes ribokinase, an enzyme catalyzing the first step in ribose catabolism. The rbsK gene encoding ribokinase typically is found with ribose transport genes. Ribokinase belongs to the carbohydrate kinase pfkB family (pfam00294). In the wide gulf between the current trusted (360 bit) and noise (100 bit) cutoffs are a number of sequences, few of which are clustered with predicted ...
CDD:233755	487	PRK	Bacteria:15	TIGR02165, cas_GSU0054, CRISPR-associated protein GSU0054/csb2, Dpsyc system.  This model represents a CRISPR-associated protein from the Dpsyc subtype, named for Desulfotalea psychrophila LSv54. CRISPR systems confer resistance in prokaryotes to invasive DNA or RNA, including phage and plasmids. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships ...
CDD:213686	26	PRK	Bacteria:12	TIGR02167, Liste_lipo_26, bacterial surface protein 26-residue repeat.  This model describes a tandem peptide repeat sequence of 25 or 26 residues, found in predicted surface proteins (often lipoproteins) from Listeria monocytogenes, L. innocua, Enterococcus faecalis, Lactobacillus plantarum, Mycoplasma mycoides, Helicobacter hepaticus, and other species.
CDD:233757	1179	PRK	Bacteria:21	TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type.  SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was ...
CDD:233758	1164	PRK	Bacteria:6	TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type.  SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents ...
CDD:233759	209	PRK	Bacteria:10,Phages:2,Viruses:1	TIGR02170, thyX, thymidylate synthase, flavin-dependent.  Two forms of microbial thymidylate synthase are known: ThyA (2.1.1.45) and ThyX (2.1.1.148). This model describes ThyX, a homotetrameric flavoprotein. Both enzymes convert dUMP to dTMP. Under oxygen-limiting conditions, thyX can complement a thyA mutation [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism].
CDD:233762	72	EUKprk	Bacteria:5,Invertebrates:2,Plants:2,Primates:1,Rodents:1,Vertebrates:1	TIGR02174, CXXU_selWTH, selT/selW/selH selenoprotein domain.  This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the ...
CDD:233763	177	PRK	Bacteria:7	TIGR02175, PorC_KorC, 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family.  A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins (H. pylori) used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes the gamma subunit. In Pyrococcus furious, ...
CDD:131234	78	PRK	Bacteria:8	TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family.  A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, ...
CDD:233765	84	EUKprk	Invertebrates:5,Plants:6,Primates:1,Rodents:1,Vertebrates:1,Viruses:2	TIGR02180, GRX_euk, Glutaredoxin.  Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox ...
CDD:233766	79	PRK	Bacteria:17	TIGR02181, GRX_bact, Glutaredoxin, GrxC family.  Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ...
CDD:233768	189	PRK	Bacteria:3	TIGR02185, Trep_Strep, conserved hypothetical integral membrane protein TIGR02185.  This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6 [Cell envelope, Other].
CDD:233770	625	EUKprk	Bacteria:15,Environmental:1,Invertebrates:1,Plants:4,Primates:1	TIGR02188, Ac_CoA_lig_AcsA, acetate--CoA ligase.  This model describes acetate-CoA ligase (EC 6.2.1.1), also called acetyl-CoA synthetase and acetyl-activating enzyme. It catalyzes the reaction ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA and belongs to the family of AMP-binding enzymes described by pfam00501.
CDD:233772	220	PRK	Bacteria:30,nodiv:1	TIGR02191, RNaseIII, ribonuclease III, bacterial.  This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease ...
CDD:233773	319	PRK	Bacteria:12	TIGR02193, heptsyl_trn_I, lipopolysaccharide heptosyltransferase I.  This family consists of examples of ADP-heptose:LPS heptosyltransferase I, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides].
CDD:131251	74	PRK	Bacteria:4,Phages:1	TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family.  This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
CDD:233775	314	PRK	Bacteria:13	TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.  This family consists of examples of ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme involved in biosynthesis of the inner core of lipopolysaccharide (LPS) for Gram-negative bacteria. This enzyme is homologous to UDP-glucose 4-epimerase (TIGR01179) and belongs to the NAD dependent epimerase/dehydratase family (pfam01370) [Cell envelope, Biosynthesis and degradation of surface polysaccharides ...
CDD:233776	315	PRK	Bacteria:18	TIGR02198, rfaE_dom_I, rfaE bifunctional protein, domain I.  RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. The longer, N-terminal domain I (this family) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (TIGR02199) adds ADP to yield ...
CDD:131254	144	PRK	Bacteria:7	TIGR02199, rfaE_dom_II, rfaE bifunctional protein, domain II.  RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. Domain I (TIGR02198) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose [Cell envelope, ...
CDD:131261	222	PRK	Bacteria:8,Environmental:1	TIGR02206, intg_mem_TP0381, conserved hypothetical integral membrane protein TIGR02206.  This model represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc.
CDD:233778	303	PRK	Bacteria:7	TIGR02207, lipid_A_htrB, lipid A biosynthesis lauroyl (or palmitoleoyl) acyltransferase.  This model represents a narrow clade of acyltransferases, nearly all of which transfer a lauroyl group to KDO2-lipid IV-A, a lipid A precursor; these proteins are termed lipid A biosynthesis lauroyl acyltransferase, HtrB. An exception is a closely related paralog of E. coli HtrB, LpxP, which acts in cold shock conditions by transferring a palmitoleoyl rather than lauroyl group ...
CDD:131264	85	PRK	Bacteria:17	TIGR02209, ftsL_broad, cell division protein FtsL.  This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species [Cellular processes, Cell division].
CDD:233780	352	PRK	Bacteria:69	TIGR02210, rodA_shape, rod shape-determining protein RodA.  This protein is a member of the FtsW/RodA/SpoVE family (pfam01098). It is found only in species with rod (or spiral) shapes. In many species, mutation of rodA has been shown to correlate with loss of the normal rod shape. Note that RodA homologs are found, scoring below the cutoffs for this model, in a number of both rod-shaped and coccoid bacteria, including four proteins in Bacillus anthracis, for ...
CDD:233781	411	PRK	Bacteria:7	TIGR02212, lolCE, lipoprotein releasing system, transmembrane protein, LolC/E family.  This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC [Protein fate, Protein and peptide secretion and trafficking].
CDD:233788	295	PRK	Bacteria:34	TIGR02224, recomb_XerC, tyrosine recombinase XerC.  The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome ...
CDD:233789	291	PRK	Bacteria:30	TIGR02225, recomb_XerD, tyrosine recombinase XerD.  The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome ...
CDD:131281	82	PRK	Bacteria:8	TIGR02226, two_anch, N-terminal double-transmembrane domain.  This model represents a prokaryotic N-terminal region of about 80 amino acids. The predicted membrane topology by TMHMM puts the N-terminus outside and spans the membrane twice, with a cytosolic region of about 25 amino acids between the two transmembrane regions. Member proteins tend to be between 600 and 1000 amino acids in length [Hypothetical proteins, Domain].
CDD:233790	163	PRK	Bacteria:18	TIGR02227, sigpep_I_bact, signal peptidase I, bacterial type.  This model represents signal peptidase I from most bacteria. Eukaryotic sequences are likely organellar. Several bacteria have multiple paralogs, but these represent isozymes of signal peptidase I. Virtually all known bacteria may be presumed to A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes [Protein fate, ...
CDD:131283	158	PRK	Bacteria:6	TIGR02228, sigpep_I_arch, signal peptidase I, archaeal type.  This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
CDD:233791	525	EUKprk	Bacteria:5,Invertebrates:1	TIGR02231, TIGR02231, conserved hypothetical protein.  This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
CDD:200169	38	EUKprk	Bacteria:1,Primates:1	TIGR02232, myxo_disulf_rpt, Myxococcus cysteine-rich repeat.  This model represents a sequence region shared between several proteins of Myxococcus xanthus DK 1622 and some eukaryotic proteins that include human pappalysin-1 (SP|Q13219). The region of about 40 amino acids contains several conserved Cys residues presumed to form disulfide bonds. The region appears in up to 13 repeats in Myxococcus.
CDD:233795	140	PRK	Bacteria:7	TIGR02241, TIGR02241, conserved hypothetical phage tail region protein.  This family consists of uncharacterized proteins. All members so far represent bacterial genes found in apparent phage or otherwisely laterally transferred regions of the chromosome. Tentatively identified neighboring proteins tend to be phage tail region proteins. In some species, including Photorhabdus luminescens TTO1, several members of this family may be encoded near each other.
CDD:233798	343	EUKprk	Bacteria:1,Invertebrates:3,Plants:2,Primates:1	TIGR02244, HAD-IG-Ncltidse, HAD superfamily (subfamily IG) hydrolase, 5'-nucleotidase.  This model includes a 5'-nucleotidase specific for purines (IMP and GMP). These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognized by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h" stands for a hydrophobic residue). ...
CDD:233799	128	PRK	Bacteria:12	TIGR02246, TIGR02246, conserved hypothetical protein.  This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
CDD:131304	156	EUK	Invertebrates:2,Plants:7,Vertebrates:1	TIGR02250, FCP1_euk, FCP1-like phosphatase, phosphatase domain.  This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1, ) and closely related phosphatases from eukaryotes including plants, fungi and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by ...
CDD:233801	162	EUK	Invertebrates:2,Plants:4,Primates:1,Rodents:2	TIGR02251, HIF-SF_euk, Dullard-like phosphatase domain.  This model represents the putative phosphatase domain of a family of eukaryotic proteins including "Dullard" , and the NLI interacting factor (NIF)-like phosphatases. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is ...
CDD:200170	203	EUKprk	Bacteria:3,Invertebrates:1,Plants:2,Primates:1,Rodents:1,Vertebrates:1	TIGR02252, DREG-2, REG-2-like, HAD superfamily (subfamily IA) hydrolase.  This family of proteins includes uncharacterized sequences from eukaryotes, cyanobacteria and Leptospira as well as the DREG-2 protein from Drosophila melanogaster which has been identified as a rhythmically (diurnally) regulated gene. This family is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile ...
CDD:233802	179	PRK	Bacteria:18	TIGR02258, 2_5_ligase, 2'-5' RNA ligase.  This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing ...
CDD:131318	179	PRK	Bacteria:1	TIGR02265, Mxa_TIGR02265, Myxococcales-restricted protein, TIGR02265 family.  This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus DK 1622. Members are about 200 amino acids in length. No other homologs are known; the function is unknown.
CDD:233804	96	PRK	Bacteria:1	TIGR02266, gmx_TIGR02266, Myxococcus xanthus paralogous domain TIGR02266.  This domain is related to Type IV pilus assembly protein PilZ (pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
CDD:233805	165	PRK	Bacteria:17	TIGR02273, 16S_RimM, 16S rRNA processing protein RimM.  This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a ...
CDD:233806	179	PRK	Bacteria:9	TIGR02274, dCTP_deam, deoxycytidine triphosphate deaminase.  Members of this family include the Escherichia coli monofunctional deoxycytidine triphosphate deaminase (dCTP deaminase) and a Methanocaldococcus jannaschii bifunctional dCTP deaminase (3.5.4.13)/dUTP diphosphatase (EC 3.6.1.23), which has the EC number 3.5.4.30 for the overall operation [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism].
CDD:213697	42	PRK	Bacteria:11	TIGR02276, beta_rpt_yvtn, 40-residue YVTN family beta-propeller repeat.  This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam ...
CDD:131334	121	PRK	Bacteria:8,nodiv:1	TIGR02281, clan_AA_DTGA, clan AA aspartic protease, TIGR02281 family.  This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are ...
CDD:233810	300	PRK	Bacteria:11	TIGR02283, MltB_2, lytic murein transglycosylase.  Members of this family are closely related to the MltB family lytic murein transglycosylases described by TIGR02282 and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many members of this family (unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (pfam01471), not ...
CDD:233812	587	PRK	Bacteria:9,Environmental:1,nodiv:1	TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family.  The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence ...
CDD:233814	150	PRK	Bacteria:10	TIGR02292, ygfB_yecA, yecA family protein.  This family resembles pfam03695 (version pfam03695.3), uncharacterised protein family Upfam0149, but is broader in scope and includes additional proteins. It includes E. coli proteins YgfB and YecA. The function of this family of proteins is unknown. The crystal structure is known for the member from Haemophilus influenzae (Ygfb, HI0817) [Unknown function, General].
CDD:131368	243	PRK	Bacteria:9	TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding protein.  Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of ...
CDD:131371	376	PRK	Bacteria:5	TIGR02318, phosphono_phnM, phosphonate metabolism protein PhnM.  This family consists of proteins from in the PhnM family. PhnM is a a protein associated with phosphonate utilization in a number of bacterial species. In Pseudomonas stutzeri WM88, a protein that is part of a system for the oxidation of phosphites (another form of reduced phosphorous compound) scores between trusted and noise cutoffs [Energy metabolism, Other].
CDD:233820	285	EUKprk	Bacteria:12,Invertebrates:2	TIGR02320, PEP_mutase, phosphoenolpyruvate phosphomutase.  This family consists of examples of phosphoenolpyruvate phosphomutase, an enzyme that creates a C-P bond as the first step in the biosynthesis of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the ...
CDD:233821	179	PRK	Bacteria:6	TIGR02322, phosphon_PhnN, phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN.  Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PMID:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act ...
CDD:131391	110	PRK	Bacteria:4	TIGR02338, gimC_beta, prefoldin, beta subunit, archaeal.  Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is ...
CDD:233828	524	EUKprk	Bacteria:15,Plants:1	TIGR02348, GroEL, chaperonin GroL.  This family consists of GroEL, the larger subunit of the GroEL/GroES cytosolic chaperonin. It is found in bacteria, organelles derived from bacteria, and occasionally in the Archaea. The bacterial GroEL/GroES group I chaperonin is replaced a group II chaperonin, usually called the thermosome in the Archaeota and CCT (chaperone-containing TCP) in the Eukaryota. GroEL, thermosome subunits, and CCT subunits all fall ...
CDD:233829	354	EUKprk	Bacteria:19,Environmental:1,Plants:1	TIGR02349, DnaJ_bact, chaperone protein DnaJ.  This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
CDD:233830	595	PRK	Bacteria:13	TIGR02350, prok_dnaK, chaperone protein DnaK.  Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to ...
CDD:233831	337	PRK	Bacteria:9	TIGR02352, thiamin_ThiO, glycine oxidase ThiO.  This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine].
CDD:162820	202	PRK	Bacteria:9	TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily.  Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ...
CDD:233835	574	EUKprk	Bacteria:1,Invertebrates:1,Plants:3,Primates:1	TIGR02361, dak_ATP, dihydroxyacetone kinase, ATP-dependent.  This family consists of examples of the form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (2.7.1.29) as the phosphate donor, rather than a phosphoprotein as in E. coli. This form is composed of a single chain with separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in ...
CDD:131417	125	PRK	Bacteria:8	TIGR02364, dha_pts, dihydroxyacetone kinase, phosphotransfer subunit.  In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to.
CDD:233837	194	PRK	Bacteria:11	TIGR02365, dha_L_ycgS, dihydroxyacetone kinase, phosphoprotein-dependent, L subunit.  Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This ...
CDD:131431	105	EUKprk	Bacteria:5,Environmental:1,Plants:3,nodiv:1	TIGR02378, nirD_assim_sml, nitrite reductase [NAD(P)H], small subunit.  This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused [Central intermediary metabolism, Nitrogen metabolism].
CDD:233839	84	PRK	Bacteria:9	TIGR02384, RelB_DinJ, addiction module antitoxin, RelB/DinJ family.  Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the ...
CDD:211740	88	PRK	Bacteria:11	TIGR02385, RelE_StbE, addiction module toxin, RelE/StbE family.  Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed ...
CDD:233844	270	PRK	Bacteria:12	TIGR02392, rpoH_proteo, alternative sigma factor RpoH.  A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be ...
CDD:213709	238	PRK	Bacteria:10	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain.  This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium ...
CDD:233845	429	PRK	Bacteria:13	TIGR02395, rpoN_sigma, RNA polymerase sigma-54 factor.  A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). ...
CDD:233846	185	EUKprk	Bacteria:6,Invertebrates:2,Plants:4	TIGR02396, diverge_rpsU, rpsU-divergently transcribed protein.  This uncharacterized protein is found in a number of Alphaproteobacteria and, with N-terminal regions long enough to be transit peptides, in eukaryotes. This phylogeny suggests mitochondrial derivation. In several Alphaproteobacteria, the gene for this protein is encoded divergently from rpsU, the gene for ribosomal protein S21. S21 is unusual in being encoded outside the ...
CDD:233847	355	EUKprk	Bacteria:25,Plants:2	TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.  This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift ...
CDD:233848	456	EUKprk	Bacteria:9,Plants:3	TIGR02400, trehalose_OtsA, alpha,alpha-trehalose-phosphate synthase [UDP-forming].  This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This model excludes ...
CDD:233849	825	PRK	Bacteria:10	TIGR02401, trehalose_TreY, malto-oligosyltrehalose synthase.  This enzyme, formally named (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase, is the TreY enzyme of the TreYZ pathway of trehalose biosynthesis, an alternative to the OtsAB pathway. Trehalose may be incorporated into more complex compounds but is best known as compatible solute. It is one of the most effective osmoprotectants, and unlike the various betaines does not require nitrogen for its synthesis ...
CDD:233850	544	PRK	Bacteria:11,nodiv:1	TIGR02402, trehalose_TreZ, malto-oligosyltrehalose trehalohydrolase.  Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system [Energy metabolism, Biosynthesis and degradation of polysaccharides].
CDD:233851	543	PRK	Bacteria:9	TIGR02403, trehalose_treC, alpha,alpha-phosphotrehalase.  Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
CDD:233853	412	PRK	Bacteria:13	TIGR02407, ectoine_ectB, diaminobutyrate--2-oxoglutarate aminotransferase.  Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (EC 2.6.1.76) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore ...
CDD:233858	863	EUKprk	Bacteria:10,Invertebrates:1	TIGR02414, pepN_proteo, aminopeptidase N, Escherichia coli type.  The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile (see SP|P04825 for a description of catalytic activity). This family consists of all aminopeptidases closely related to E. ...
CDD:233859	63	PRK	Bacteria:6,Phages:5	TIGR02419, C4_traR_proteo, phage/conjugal plasmid C-4 type zinc finger protein, TraR family.  Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA [Mobile ...
CDD:131473	110	PRK	Bacteria:15,Environmental:2,Synthetic:1	TIGR02420, dksA, RNA polymerase-binding protein DksA.  The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of ...
CDD:233860	366	PRK	Bacteria:7,nodiv:1	TIGR02421, QEGLA, conserved hypothetical protein.  Members of this family include a possible metal-binding motif HEXXXH and, nearby, a perfectly conserved motif QEGLA. All members belong to the Proteobacteria, including Agrobacterium tumefaciens and several species of Vibrio and Pseudomonas, and are found in only one copy per chromosome (Vibrio vulnificus, with two chromosomes, has two). The function is unknown.
CDD:233861	193	PRK	Bacteria:11	TIGR02423, protocat_alph, protocatechuate 3,4-dioxygenase, alpha subunit.  This model represents the alpha chain of protocatechuate 3,4-dioxygenase. The most closely related family outside this family is that of the beta chain (TIGR02422), typically encoded in an adjacent locus. This enzyme acts in the degradation of aromatic compounds by way of p-hydroxybenzoate to succinate and acetyl-CoA [Energy metabolism, Other].
CDD:131480	251	PRK	Bacteria:9	TIGR02427, protocat_pcaD, 3-oxoadipate enol-lactonase.  Members of this family are 3-oxoadipate enol-lactonase. Note that the substrate is known as 3-oxoadipate enol-lactone, 2-oxo-2,3-dihydrofuran-5-acetate, 4,5-Dihydro-5-oxofuran-2-acetate, and 5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the catalyzes the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate ...
CDD:188219	207	PRK	Bacteria:12	TIGR02428, pcaJ_scoB_fam, 3-oxoacid CoA-transferase, B subunit.  Various members of this family are characterized as the B subunits of succinyl-CoA:3-ketoacid-CoA transferase (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase (EC 2.8.3.9). This represents a very distinct clade with strong sequence conservation within the larger family defined by ...
CDD:131484	248	PRK	Bacteria:13,nodiv:1	TIGR02431, pcaR_pcaU, beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family.  Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU [Regulatory functions, DNA interactions].
CDD:233864	189	EUKprk	Bacteria:32,Plants:5	TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase, N-terminal domain.  The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic ...
CDD:233865	47	PRK	Bacteria:18	TIGR02433, lysidine_TilS_C, tRNA(Ile)-lysidine synthetase, C-terminal domain.  TIGRFAMs model TIGR02432 describes the family of the N-terminal domain of tRNA(Ile)-lysidine synthetase. This family (TIGR02433) describes a small C-terminal domain of about 50 residues present in about half the members of family TIGR02432,and in no other protein. Characterized examples of tRNA(Ile)-lysidine synthetase from E. coli and Bacillus subtilis both contain this domain [Protein ...
CDD:233867	108	PRK	Bacteria:90,Environmental:1	TIGR02436, TIGR02436, four helix bundle protein.  This family describes a protein of unknown function whose structure is a bundle of four long alpha helices. Some of the first members of this family were found encoded in the (atypically large) intervening sequence (IVS) of Leptospira 23S RNA, a region often present in the rRNA gene and removed during rRNA processing without re-ligation. However, this location is not conserved, and naming this ...
CDD:233870	633	PRK	Bacteria:11	TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.  Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts early in the biosynthesis (pfam06180). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A number of genomes (actinobacteria, ...
CDD:131500	138	PRK	Bacteria:8	TIGR02447, yiiD_Cterm, thioesterase domain, putative.  This family consists of a broadly distributed uncharacterized domain found often as a standalone protein. The member from Shewanella oneidensis, PDB|1T82_A (Forouhar, et al., unpublished) is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an Acetyltransf_1 domain (pfam00583). The function of this protein is unknown.
CDD:131503	61	PRK	Bacteria:7	TIGR02450, TIGR02450, tryptophan-rich conserved hypothetical protein.  Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
CDD:213711	217	PRK	Bacteria:10	TIGR02453, TIGR02453, TIGR02453 family protein.  Members of this family are widely (though sparsely) distributed bacterial proteins about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown. In several fungi, this model identifies a conserved region of a longer protein. Therefore, it may be incorrect to speculate that all members share a common function.
CDD:233873	198	PRK	Bacteria:17	TIGR02454, CbiQ_TIGR, cobalt ABC transporter, permease protein CbiQ.  This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely ...
CDD:233876	153	EUKprk	Bacteria:6,Invertebrates:1,Phages:1,Plants:1	TIGR02464, ribofla_fusion, conserved hypothetical protein, ribA/ribD-fused.  This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a ...
CDD:233878	204	PRK	Bacteria:17	TIGR02467, CbiE, precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit.  This model recognizes the CbiE methylase which is responsible, in part (along with CbiT), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiT subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin ...
CDD:233880	124	PRK	Bacteria:11	TIGR02469, CbiT, precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit.  This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin ...
CDD:131526	141	PRK	Bacteria:19	TIGR02473, flagell_FliJ, flagellar export protein FliJ.  Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.
CDD:131530	539	EUKprk	Bacteria:5,Invertebrates:2,Plants:2	TIGR02477, PFKA_PPi, diphosphate--fructose-6-phosphate 1-phosphotransferase.  Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyzes the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (EC 2.7.1.90). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes. TIGR02482 ...
CDD:233884	746	EUKprk	Bacteria:1,Invertebrates:3,Mammals:1,Plants:4	TIGR02478, 6PF1K_euk, 6-phosphofructokinase, eukaryotic type.  Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (EC 2.7.1.11) in which two tandem copies of the phosphofructokinase are found. Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal).
CDD:233885	224	PRK	Bacteria:18	TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family.  Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
CDD:131533	77	PRK	Bacteria:13	TIGR02480, fliN, flagellar motor switch protein FliN.  Proteins that consist largely of the domain described by This model for this protein family can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required ...
CDD:233886	126	EUKprk	Bacteria:20,Invertebrates:1	TIGR02481, hemeryth_dom, hemerythrin-like metal-binding domain.  This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most ...
CDD:233887	324	PRK	Bacteria:7	TIGR02483, PFK_mixed, phosphofructokinase.  Members of this family that are characterized, save one, are phosphofructokinases dependent on pyrophosphate (EC 2.7.1.90) rather than ATP (EC 2.7.1.11). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal [Energy metabolism, Glycolysis/gluconeogenesis].
CDD:233890	314	PRK	Bacteria:8,Environmental:1	TIGR02486, RDH, reductive dehalogenase.  This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it ...
CDD:233891	579	PRK	Bacteria:8	TIGR02487, NrdD, anaerobic ribonucleoside-triphosphate reductase.  This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 ...
CDD:131541	259	PRK	Bacteria:11	TIGR02488, flgG_G_neg, flagellar basal-body rod protein FlgG, Gram-negative bacteria.  This family consists of the FlgG protein of the flagellar apparatus in the Proteobacteria and spirochetes [Cellular processes, Chemotaxis and motility].
CDD:233892	89	PRK	Bacteria:31	TIGR02490, flgF, flagellar basal-body rod protein FlgF.  Members of this protein are FlgF, one of several homologous flagellar basal-body rod proteins in bacteria [Cellular processes, Chemotaxis and motility].
CDD:233893	154	PRK	Bacteria:6,Phages:3	TIGR02491, NrdG, anaerobic ribonucleoside-triphosphate reductase activating protein.  This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin ) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer [Purines, pyrimidines, nucleosides, and ...
CDD:233894	324	PRK	Bacteria:15	TIGR02492, flgK_ends, flagellar hook-associated protein FlgK.  The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in ...
CDD:131546	235	EUKprk	Bacteria:7,Plants:1	TIGR02493, PFLA, pyruvate formate-lyase 1-activating enzyme.  An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the ...
CDD:233895	295	PRK	Bacteria:9	TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein family.  This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are ...
CDD:233896	192	PRK	Bacteria:6,Synthetic:1	TIGR02495, NrdG2, anaerobic ribonucleoside-triphosphate reductase activating protein.  This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in ...
CDD:233897	166	PRK	Bacteria:19	TIGR02499, HrpE_YscL_not, type III secretion apparatus protein, HrpE/YscL family.  This model is related to pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108) ...
CDD:233898	410	PRK	Bacteria:12	TIGR02500, type_III_yscD, type III secretion apparatus protein, YscD/HrpQ family.  This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein [Protein fate, Protein and peptide secretion ...
CDD:233899	67	PRK	Bacteria:9	TIGR02501, type_III_yscE, type III secretion system protein, YseE family.  Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized [Cellular processes, Pathogenesis].
CDD:233900	589	PRK	Bacteria:14,Environmental:1,Phages:1	TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent.  This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (Class II RNRs) related to the characterized species from Pyrococcus , Thermoplasma , Corynebacterium and Deinococcus. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA ...
CDD:233902	617	PRK	Bacteria:7,Phages:3,Viruses:7	TIGR02506, NrdE_NrdA, ribonucleoside-diphosphate reductase, alpha subunit.  This model represents the alpha (large) chain of the class I ribonucleotide reductase (RNR). RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Class I RNR's generate the required radical (on tyrosine) via a "non-heme" iron cofactor which resides in the beta (small) ...
CDD:131563	79	PRK	Bacteria:9	TIGR02511, type_III_tyeA, type III secretion effector delivery regulator, TyeA family.  Members of this family include both small proteins, about 90 amino acids, in which this model covers the whole, and longer proteins of about 360 residues which match in the C-terminal region. The longer proteins (HrpJ) have N-terminal regions that match pfam07201. Members of this family belong to bacterial type III secretion systems, and include TyeA from the well-studied Yersinia ...
CDD:233903	374	EUKprk	Bacteria:10,Invertebrates:3,Plants:1	TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A.  This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some ...
CDD:233905	418	PRK	Bacteria:14	TIGR02515, IV_pilus_PilQ, type IV pilus secretin (or competence protein) PilQ.  A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member ...
CDD:233906	462	PRK	Bacteria:9	TIGR02516, type_III_yscC, type III secretion outer membrane pore, YscC/HrcC family.  A number of proteins homologous to the type IV pilus secretin PilQ (TIGR02515) are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). The clade described by this model contains the outer membrane pore proteins of bacterial type III secretion systems, ...
CDD:233907	594	PRK	Bacteria:13	TIGR02517, type_II_gspD, type II secretion system protein D.  In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II ...
CDD:233908	290	PRK	Bacteria:6	TIGR02519, pilus_MshL, pilus (MSHA type) biogenesis protein MshL.  Members of this family are predicted secretins, that is, outer membrane pore proteins associated with delivery of proteins from periplasm to the outside of the cell. Related families include GspD of type II secretion (TIGR02517), the YscC/HrcC family from type III secretion (TIGR02516), and the PilQ secretin of type IV pilus formation (TIGR02515). Members of this family are found in gene clusters ...
CDD:131573	234	PRK	Bacteria:11	TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein PilW.  Members of this family are designated PilF in ref (PMID:8973346) and PilW in ref (PMID:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
CDD:131575	139	PRK	Bacteria:7	TIGR02523, type_IV_pilV, type IV pilus modification protein PilV.  Pilus systems categorized as type IV pilins differ greatly from one another, with some showing greater similarty to type II or type III secretion systems than to each other. Members of this protein family represent the PilV protein of type IV pilus systems as found in Pseudomonas aeruginosa PAO1, Pseudomonas syringae DC3000, Neisseria meningitidis MC58, Xylella fastidiosa 9a5c, etc [Cell envelope, ...
CDD:213719	24	PRK	Bacteria:58	TIGR02532, IV_pilin_GFxxxE, prepilin-type N-terminal cleavage/methylation domain.  This model describes many but not all examples of the N-terminal region of bacterial proteins that resemble type IV pilins at their N-terminus, with a cleavage site G^FxxxE followed by a hydrophobic stretch. The new N-terminal residue, usually Phe, is methylated. Separate domains of the prepilin peptidase appear responsible for cleavage and methylation. Proteins with this N-terminal ...
CDD:213720	24	PRK	Bacteria:16	TIGR02537, arch_flag_Nterm, archaeal flagellin N-terminal-like domain.  This model describes a hydrophobic N-terminal sequence of archaeal flagellins and other archaeal proteins. The sequence is directly analogous to bacterial sequences recognized by TIGR02532, which has cleavage motif resembling G^FxxxE followed by strongly hydrophobic sequence. Such sequences are the recognized for cleavage and methylation, and include pilins and other pilus components and ...
CDD:233914	564	PRK	Bacteria:12	TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.  This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that ...
CDD:213721	43	PRK	Bacteria:9	TIGR02543, List_Bact_rpt, Listeria/Bacterioides repeat.  This model describes a conserved core region, about 43 residues in length, of at least two families of tandem repeats. These include 78-residue repeats from 2 to 15 in number, in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few bacteria ...
CDD:233917	193	PRK	Bacteria:13	TIGR02544, III_secr_YscJ, type III secretion apparatus lipoprotein, YscJ/HrcJ family.  All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related ...
CDD:233918	422	PRK	Bacteria:8	TIGR02546, III_secr_ATP, type III secretion apparatus H+-transporting two-sector ATPase.  [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:233919	503	PRK	Bacteria:12	TIGR02547, casA_cse1, CRISPR type I-E/ECOLI-associated protein CasA/Cse1.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by CT1972 from Chlorobium tepidum, is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It is ...
CDD:233920	159	PRK	Bacteria:16	TIGR02548, casB_cse2, CRISPR type I-E/ECOLI-associated protein CasB/Cse2.  CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It was designated Cse2 originally, and renamed CasB ...
CDD:233921	21	PRK	Bacteria:11	TIGR02549, CRISPR_DxTHG, CRISPR-associated DxTHG motif protein.  This model describes a short region highly conserved between two otherwise substantially different CRISPR-associated (cas) proteins, TIGR02221 and TIGR01987. This region includes the motif [VIL]-D-x-[ST]-H-[GS] [Mobile and extrachromosomal element functions, Other].
CDD:233922	267	PRK	Bacteria:20	TIGR02550, flagell_flgL, flagellar hook-associated protein 3.  This protein family consists of flagellar hook-associated proteins designated FlgL (or HAP3) encoded in bacterial flagellar operons. A N-terminal region of about 150 residues and a C-terminal region of about 85 residues are conserved. Members show considerable length heterogeneity between these two well-conserved terminal regions; the seed alignment 486 columns, while members of this family are from 287 ...
CDD:233923	298	PRK	Bacteria:17,Synthetic:1	TIGR02551, SpaO_YscQ, type III secretion system apparatus protein YscQ/HrcQ.  Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion , while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid , and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae [Protein fate, Protein and peptide secretion ...
CDD:233924	135	PRK	Bacteria:10	TIGR02552, LcrH_SycD, type III secretion low calcium response chaperone LcrH/SycD.  Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory ...
CDD:233933	240	PRK	Bacteria:6	TIGR02568, LcrE, type III secretion regulator YopN/LcrE/InvE/MxiC.  This protein is found in type III secretion operons and, in Yersinia is localized to the cell surface and is involved in the Low-Calicium Response (LCR), possibly by sensing the calcium concentration. In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and interacts with the proteins SipBCD and SicA.//Altered name to reflect regulatory role. ...
CDD:131625	63	PRK	Bacteria:7,Environmental:1	TIGR02574, stabl_TIGR02574, putative addiction module component, TIGR02574 family.  Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this ...
CDD:233935	483	PRK	Bacteria:8	TIGR02577, cas_TM1794_Cmr2, CRISPR-associated protein Cas10/Cmr2, subtype III-B.  This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other ...
CDD:233936	648	PRK	Bacteria:8	TIGR02578, cas_TM1811_Csm1, CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE.  The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats [Mobile and extrachromosomal element functions, Other].
CDD:233937	280	PRK	Bacteria:5	TIGR02580, cas_RAMP_Cmr4, CRISPR type III-B/RAMP module RAMP protein Cmr4.  This model represents a CRISPR-associated protein from the family that includes TM1792 of Thermotoga maritima. This family is part of the broad RAMP superfamily (pfam03787) collection of CRISPR-associated proteins. It is the fourth of a recurring set of six proteins, four of are in the RAMP superfamily, that we designate the CRISPR RAMP module [Mobile and extrachromosomal element functions, Other].
CDD:233939	204	PRK	Bacteria:8	TIGR02582, cas_TM1809, CRISPR type III-A/MTUBE-associated RAMP protein Csm3.  Members of this CRISPR-associated (cas) gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm3, for CRISPR/cas Subtype Mtube, protein 3 [Mobile and extrachromosomal element functions, Other].
CDD:233941	310	PRK	Bacteria:10	TIGR02585, cas_Cst2_DevR, CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP.  CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This clade is a member of the DevR family (TIGR01875) and includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to be regulated through a number ...
CDD:188234	393	PRK	Bacteria:8	TIGR02591, cas_Csh1, CRISPR-associated protein Cas8b/Csh1, subtype I-B/HMARI.  This domain is found in the C-terminal 2/3 of a family of CRISPR associated proteins of the Hmari subtype. Except for the two sequences from halophilic archaea this domain contains a pair of CXXC motifs [Mobile and extrachromosomal element functions, Other].
CDD:213727	42	PRK	Bacteria:44	TIGR02593, CRISPR_cas5, CRISPR-associated protein Cas5, N-terminal domain.  This model represents a shared N-terminal domain, about 43 amino acids in length, common to a number of related protein families each of which is associated with a distinct subtype of CRISPR/cas system, where CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat and Cas is an abbreviation for CRISPR-associated. Members of this family are widely distributed enough ...
CDD:131644	24	PRK	Bacteria:14	TIGR02595, PEP_exosort, PEP-CTERM protein-sorting domain.  This model describes a 25-residue domain that includes a near-invariant Pro-Glu-Pro (PEP) motif, a thirteen residue strongly hydrophobic sequence likely to span the membrane, and a five-residue strongly basic motif that often contains four Arg residues. In nearly every case, this motif is found within nine residues, and usually within five residues, of the extreme C-terminus of the protein. Proteins with ...
CDD:233946	343	PRK	Bacteria:1	TIGR02599, TIGR02599, Verru_Chthon cassette protein C.  This family consists sets of paralogous family of proteins in the Verrucomicrobium spinosum and Chthoniobacter flavus. All members contain the prepilin-type N-terminal cleavage/methylation domain (TIGR02532) at the N-terminus. The mature protein would be about 350 amino acids long. These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation ...
CDD:233947	1265	PRK	Bacteria:1	TIGR02600, Verru_Chthon_A, Verru_Chthon cassette protein A.  In Verrucomicrobium spinosum and Chthoniobacter flavus, a four-gene operon that includes proteins with an N-terminal signal sequence for cleavage and methylation recurs many times. Each operon is likely to encode a membrane complex, the function of which is unknown. This model represents a long protein from this putative membrame complex, with members averaging about 1300 amino acids. The N-terminal ...
CDD:213728	32	PRK	Bacteria:17	TIGR02601, autotrns_rpt, autotransporter-associated beta strand repeat.  This model represent a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (pfam03797, TIGR01414). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most ...
CDD:131652	133	PRK	Bacteria:1	TIGR02603, CxxCH_TIGR02603, putative heme-binding domain, Pirellula/Verrucomicrobium type.  This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino ...
CDD:213729	52	PRK	Bacteria:59	TIGR02605, CxxC_CxxC_SSSS, putative regulatory protein, FmdB family.  This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, PMID:8841393 ). Most members of this family have a C-terminal ...
CDD:233948	69	PRK	Bacteria:13	TIGR02606, antidote_CC2985, putative addiction module antidote protein, CC2985 family.  This bacterial protein family has a very similar seed alignment to that of pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this ...
CDD:233949	78	PRK	Bacteria:16	TIGR02607, antidote_HigA, addiction module antidote protein, HigA family.  Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be ...
CDD:233950	54	PRK	Bacteria:4,Environmental:1	TIGR02608, delta_60_rpt, delta-60 repeat domain.  This domain occurs in tandem repeats, as many as 13, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, and others, many of which are Deltaproteobacteria. The periodicity of the repeat ranges from about 57 to 61 amino acids, and a core region of about 54 is represented by this model and seed alignment.
CDD:213730	74	PRK	Bacteria:9	TIGR02609, doc_partner, putative addiction module antidote.  Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids [Mobile and extrachromosomal element functions, Other].
CDD:233951	356	PRK	Bacteria:34	TIGR02614, ftsW, cell division protein FtsW.  This family consists of FtsW, an integral membrane protein with ten transmembrane segments. In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. All members of the seed alignment for this model are encoded in operons for the biosynthesis of UDP-N-acetylmuramoyl-pentapeptide, a precursor of murein (peptidoglycan). The FtsW designation is ...
CDD:233954	349	PRK	Bacteria:10	TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase.  Members of this protein family are CDP-glucose 4,6-dehydratase from a variety of Gram-negative and Gram-positive bacteria. Members typically are encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate, CDP-D-glucose, used by this enzyme to produce CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis and degradation of surface polysaccharides and ...
CDD:233956	434	EUKprk	Bacteria:14,Plants:1	TIGR02630, xylose_isom_A, xylose isomerase.  Members of this family are the enzyme xylose isomerase (5.3.1.5), which interconverts D-xylose and D-xylulose [Energy metabolism, Sugars].
CDD:233958	336	PRK	Bacteria:8	TIGR02636, galM_Leloir, galactose mutarotase.  Members of this protein family act as galactose mutarotase (D-galactose 1-epimerase) and participate in the Leloir pathway for galactose/glucose interconversion. All members of the seed alignment for this model are found in gene clusters with other enzymes of the Leloir pathway. This enzyme family belongs to the aldose 1-epimerase family, described by Pfam model pfam01263. However, the enzyme described as aldose ...
CDD:233959	730	PRK	Bacteria:9	TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA.  [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:131689	33	PRK	Bacteria:6	TIGR02641, gvpC_cyan_rpt, gas vesicle protein GvpC repeat.  This model describes a 33-amino acid repeated domain in bacterial versions of the gas vesicle protein GvpC, a structural protein less abundant than GvpA [Cellular processes, Other].
CDD:233961	405	PRK	Bacteria:17	TIGR02644, Y_phosphoryl, pyrimidine-nucleoside phosphorylase.  In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the ...
CDD:233963	299	PRK	Bacteria:34	TIGR02651, RNase_Z, ribonuclease Z.  Processing of the 3-prime end of tRNA precursors may be the result of endonuclease or exonuclease activity, and differs in different species. Member of this family are ribonuclease Z, a tRNA 3-prime endonuclease that processes tRNAs to prepare for addition of CCA. In species where all tRNA sequences already have the CCA tail, such as E. coli, the need for such an enzyme is unclear. Protein similar to the E. coli enzyme, matched ...
CDD:233965	365	PRK	Bacteria:13	TIGR02660, nifV_homocitr, homocitrate synthase NifV.  This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase [Biosynthesis of ...
CDD:233966	186	PRK	Bacteria:15,Environmental:1,nodiv:1	TIGR02665, molyb_mobA, molybdopterin-guanine dinucleotide biosynthesis protein A, proteobacterial.  In many molybdopterin-containing enzymes, including nitrate reductase and dimethylsulfoxide reductase, the cofactor is molybdopterin-guanine dinucleotide. The family described here contains MobA, molybdopterin-guanine dinucleotide biosynthesis protein A, from the Proteobacteria only. MobA can reconstitute molybdopterin-guanine dinucleotide ...
CDD:233967	334	PRK	Bacteria:27	TIGR02666, moaA, molybdenum cofactor biosynthesis protein A, bacterial.  The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin].
CDD:233968	302	PRK	Bacteria:11	TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis protein A, archaeal.  This model describes an archaeal family related, and predicted to be functionally equivalent, to molybdenum cofactor biosynthesis protein A (MoaA) of bacteria (see TIGR02666) [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin].
CDD:233969	267	PRK	Bacteria:15	TIGR02669, SpoIID_LytB, SpoIID/LytB domain.  This model describes a domain found typically in two or three proteins per genome in Cyanobacteria and Firmicutes, and sporadically in other genomes. One member is SpoIID of Bacillus subtilis. Another in B. subtilis is the C-terminal half of LytB, encoded immediately upstream of an amidase, the autolysin LytC, to which its N-terminus is homologous. Gene neighborhoods are not well conserved for members of this family, as ...
CDD:131721	214	PRK	Bacteria:9	TIGR02673, FtsE, cell division ATP-binding protein FtsE.  This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein [Cellular processes, Cell division].
CDD:131723	75	PRK	Bacteria:18,Phages:1	TIGR02675, tape_meas_nterm, tape measure domain.  Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are ...
CDD:162974	95	PRK	Bacteria:19	TIGR02683, upstrm_HI1419, putative addiction module killer protein.  Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both ...
CDD:233980	1201	EUKprk	Bacteria:8,Plants:3	TIGR02712, urea_carbox, urea carboxylase.  Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated ...
CDD:233981	561	PRK	Bacteria:11	TIGR02713, allophanate_hyd, allophanate hydrolase.  Allophanate hydrolase catalyzes the second reaction in an ATP-dependent two-step degradation of urea to ammonia and C02, following the action of the biotin-containing urea carboxylase. The yeast enzyme, a fusion of allophanate hydrolase to urea carboxylase, is designated urea amidolyase [Central intermediary metabolism, Nitrogen metabolism].
CDD:131764	447	EUKprk	Bacteria:8,Invertebrates:2	TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP forming), alpha domain.  Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate ...
CDD:233983	256	PRK	Bacteria:7	TIGR02721, ycfN_thiK, thiamine kinase.  Members of this family are the ycfN gene product of Escherichia coli, now identified as the salvage enzyme thiamine kinase (thiK), and additional proteobacterial homologs taken to be orthologs with equivalent function [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine].
CDD:233984	189	PRK	Bacteria:10	TIGR02722, lp_, uncharacterized proteobacterial lipoprotein.  Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby [Cell envelope, Other].
CDD:233985	179	PRK	Bacteria:46,nodiv:1	TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.  This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often ...
CDD:233986	329	PRK	Bacteria:10	TIGR02729, Obg_CgtA, Obg family GTPase CgtA.  This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome ...
CDD:233988	502	PRK	Bacteria:24	TIGR02734, crtI_fam, phytoene desaturase.  Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger Pfam family pfam01593, which also ...
CDD:131785	153	PRK	Bacteria:9	TIGR02738, TrbB, type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB.  This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be ...
CDD:233989	256	PRK	Bacteria:8	TIGR02739, TraF, type-F conjugative transfer system pilin assembly protein TraF.  This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol ...
CDD:233990	271	PRK	Bacteria:8	TIGR02740, TraF-like, TraF-like protein.  This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein.
CDD:131789	130	PRK	Bacteria:8	TIGR02742, TrbC_Ftype, type-F conjugative transfer system pilin assembly protein TrbC.  This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model.
CDD:233991	202	PRK	Bacteria:8	TIGR02743, TraW, type-F conjugative transfer system protein TraW.  This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
CDD:233993	434	PRK	Bacteria:14	TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein FixG.  Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are ...
CDD:233994	797	PRK	Bacteria:10	TIGR02746, TraC-F-type, type-IV secretion system protein TraC.  The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.
CDD:131798	506	PRK	Bacteria:10	TIGR02751, PEPCase_arch, phosphoenolpyruvate carboxylase, archaeal type.  This family is the archaeal-type phosphoenolpyruvate carboxylase, although not every host species is archaeal. These sequences bear little resemblance to the bacterial/eukaryotic type. The members from Sulfolobus solfataricus and Methanothermobacter thermautotrophicus were verified experimentally, while the activity is known to be present in a number of other archaea [Energy metabolism, Other].
CDD:163004	181	PRK	Bacteria:8	TIGR02761, TraE_TIGR, type IV conjugative transfer system protein TraE.  TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
CDD:163005	95	PRK	Bacteria:9	TIGR02762, TraL_TIGR, type IV conjugative transfer system protein TraL.  This protein is part of the type IV secretion system for conjugative plasmid transfer. The function of the TraL protein is unknown [Cellular processes, Conjugation].
CDD:234001	191	PRK	Bacteria:11	TIGR02764, spore_ybaN_pdaB, polysaccharide deacetylase family sporulation protein PdaB.  This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members ...
CDD:234002	429	EUKprk	Bacteria:4,Plants:3,Vertebrates:1	TIGR02765, crypto_DASH, cryptochrome, DASH family.  Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, ...
CDD:234004	258	PRK	Bacteria:13,nodiv:1	TIGR02772, Ku_bact, Ku protein, prokaryotic.  Members of this protein family are Ku proteins of non-homologous end joining (NHEJ) DNA repair in bacteria and in at least one member of the archaea (Archaeoglobus fulgidus). Most members are encoded by a gene adjacent to the gene for the DNA ligase that completes the repair. The NHEJ system is broadly but rather sparsely distributed, being present in about one fifth of the first 250 completed prokarytotic ...
CDD:234007	552	PRK	Bacteria:13	TIGR02776, NHEJ_ligase_prk, DNA ligase D.  Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus ...
CDD:131824	156	PRK	Bacteria:6,nodiv:1	TIGR02777, LigD_PE_dom, DNA ligase D, 3'-phosphoesterase domain.  Most sequences in this family are the 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, involved, along with bacterial Ku protein, in non-homologous end joining, the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences. LigD is variable in architecture, as it lacks this domain in Bacillus subtilis, is permuted in Mycobacterium ...
CDD:234008	245	PRK	Bacteria:5	TIGR02778, ligD_pol, DNA polymerase LigD, polymerase domain.  DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few ...
CDD:234009	298	PRK	Bacteria:3,nodiv:1	TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase domain.  DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis ...
CDD:131827	246	PRK	Bacteria:7,nodiv:1	TIGR02780, TrbJ_Ti, P-type conjugative transfer protein TrbJ.  The TrbJ protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbJ is a homolog of the F-type TraE protein (which is believed to be an inner membrane pore-forming protein, TIGR02761) as well as the vir system VirB5 protein.
CDD:234010	243	PRK	Bacteria:17	TIGR02781, VirB9, P-type conjugative transfer protein VirB9.  The VirB9 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in a type IV secretion system. VirB9 is a homolog of the F-type conjugative transfer system TraK protein (which is believed to be an outer membrane pore-forming secretin, TIGR02756) as well as the Ti system TrbG protein [Cellular processes, Conjugation].
CDD:234012	1135	PRK	Bacteria:8,nodiv:1	TIGR02784, addA_alphas, double-strand break repair helicase AddA, alphaproteobacterial type.  AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the ...
CDD:234013	1230	PRK	Bacteria:9	TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit, Firmicutes type.  AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins ...
CDD:234014	1021	PRK	Bacteria:8,nodiv:1	TIGR02786, addB_alphas, double-strand break repair protein AddB, alphaproteobacterial type.  AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage. More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of the ...
CDD:234015	308	PRK	Bacteria:11	TIGR02788, VirB11, P-type DNA transfer ATPase VirB11.  The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
CDD:234017	346	PRK	Bacteria:34	TIGR02794, tolA_full, TolA protein.  TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed ...
CDD:188247	117	PRK	Bacteria:30,nodiv:1	TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF.  Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. ...
CDD:131843	215	PRK	Bacteria:21	TIGR02796, tolQ, TolQ protein.  TolQ is one of the essential components of the Tol-Pal system. Together with TolR, it harnesses protonmotive force to energize TolA, which spans the periplasm to reach the complex of TolB and Pal at the outer member. The tol-pal system proves to be important for maintaining outer membrane integrity. Gene pairs similar to the TolQ and TolR gene pair often number several per genome, but this model describes specificially TolQ per se, ...
CDD:234018	126	PRK	Bacteria:23,nodiv:1	TIGR02799, thio_ybgC, tol-pal system-associated acyl-CoA thioesterase.  The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert protomotive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer ...
CDD:234019	417	PRK	Bacteria:25,nodiv:1	TIGR02800, propeller_TolB, tol-pal system beta propeller repeat protein TolB.  Members of this protein family are the TolB periplasmic protein of Gram-negative bacteria. TolB is part of the Tol-Pal (peptidoglycan-associated lipoprotein) multiprotein complex, comprising five envelope proteins, TolQ, TolR, TolA, TolB and Pal, which form two complexes. The TolQ, TolR and TolA inner-membrane proteins interact via their transmembrane domains. The ...
CDD:234020	129	PRK	Bacteria:31	TIGR02801, tolR, TolR protein.  The model describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is required to maintain outer membrane integrity, and defects may cause a defect in the import of some organic compounds in addition to the resulting morphologic. While several gene ...
CDD:188250	104	PRK	Bacteria:35	TIGR02802, Pal_lipo, peptidoglycan-associated lipoprotein.  Members of this protein are Pal (also called OprL), the Peptidoglycan-Associated Lipoprotein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly ...
CDD:200213	420	PRK	Bacteria:8,nodiv:1	TIGR02810, agaZ_gatZ, D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit.  Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, ...
CDD:234026	323	PRK	Bacteria:28	TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP family.  This model represents a subfamily of pfam00107 as defined by Pfam, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This subfamily includes proteins studied crystallographically for insight into function: YhdH from Escherichia coli and YhfP from Bacillus subtilis. Members bind NADPH or NAD, ...
CDD:234027	325	PRK	Bacteria:17,nodiv:1	TIGR02824, quinone_pig3, putative NAD(P)H quinone oxidoreductase, PIG3 family.  Members of this family are putative quinone oxidoreductases that belong to the broader superfamily (modeled by Pfam pfam00107) of zinc-dependent alcohol (of medium chain length) dehydrogenases and quinone oxiooreductases. The alignment shows no motif of conserved Cys residues as are found in zinc-binding members of the superfamily, and members are likely to be quinone ...
CDD:234028	147	PRK	Bacteria:10	TIGR02826, RNR_activ_nrdG3, anaerobic ribonucleoside-triphosphate reductase activating protein.  Members of this family represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ...
CDD:234029	186	PRK	Bacteria:12	TIGR02830, spore_III_AG, stage III sporulation protein AG.  CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG [Cellular processes, Sporulation and germination].
CDD:131878	200	PRK	Bacteria:8	TIGR02831, spo_II_M, stage II sporulation protein M.  A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This predicted integral membrane protein is designated stage II sporulation protein M [Cellular processes, Sporulation and germination].
CDD:131879	204	PRK	Bacteria:8	TIGR02832, spo_yunB, sporulation protein YunB.  A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. Mutation of this sigma E-regulated gene, designated yunB, has been shown to cause a sporulation defect [Cellular processes, Sporulation and germination].
CDD:131880	170	PRK	Bacteria:10	TIGR02833, spore_III_AB, stage III sporulation protein AB.  A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB [Cellular processes, Sporulation and germination].
CDD:234030	276	PRK	Bacteria:12	TIGR02834, spo_ytxC, putative sporulation protein YtxC.  This uncharacterized protein is part of a panel of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and nowhere else [Cellular processes, Sporulation and germination].
CDD:234031	206	PRK	Bacteria:12	TIGR02840, spore_YtaF, putative sporulation protein YtaF.  This protein family was identified, at the time of the publication of the Carboxydothermus hydrogenoformans genome, as having a phylogenetic profile that exactly matches the subset of the Firmicutes capable of forming endospores. The species include Bacillus anthracis, Clostridium tetani, Thermoanaerobacter tengcongensis, Geobacillus kaustophilus, etc. This protein, previously named YtaF, is therefore a ...
CDD:131889	180	PRK	Bacteria:13	TIGR02842, CyoC, cytochrome o ubiquinol oxidase, subunit III.  Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is ...
CDD:131894	96	PRK	Bacteria:14	TIGR02847, CyoD, cytochrome o ubiquinol oxidase subunit IV.  Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is ...
CDD:131901	288	PRK	Bacteria:10	TIGR02854, spore_II_GA, sigma-E processing peptidase SpoIIGA.  Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria [Cellular processes, Sporulation and germination].
CDD:234032	283	PRK	Bacteria:11	TIGR02855, spore_yabG, sporulation peptidase YabG.  Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K [Cellular processes, Sporulation and germination].
CDD:131903	85	PRK	Bacteria:10	TIGR02856, spore_yqfC, sporulation protein YqfC.  This small protein, designated YqfC in Bacillus subtilis, is both restricted to and universal in sporulating species of the Firmcutes, such as Bacillus subtilis and Clostridium perfringens. It is part of the sigma(E)-controlled regulon, and its mutation leads to a sporulation defect [Cellular processes, Sporulation and germination].
CDD:234033	529	PRK	Bacteria:16	TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.  The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol ...
CDD:234035	402	PRK	Bacteria:10	TIGR02860, spore_IV_B, stage IV sporulation protein B.  SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else [Cellular processes, Sporulation and germination].
CDD:234036	58	PRK	Bacteria:7	TIGR02861, SASP_H, small acid-soluble spore protein, H-type.  This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of ...
CDD:234038	764	PRK	Bacteria:7	TIGR02865, spore_II_E, stage II sporulation protein E.  Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. ...
CDD:234039	199	PRK	Bacteria:8	TIGR02866, CoxB, cytochrome c oxidase, subunit II.  Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ...
CDD:234040	196	PRK	Bacteria:15	TIGR02867, spore_II_P, stage II sporulation protein P.  Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in ...
CDD:234041	530	PRK	Bacteria:11	TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit.  The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol ...
CDD:234044	341	PRK	Bacteria:9	TIGR02872, spore_ytvI, sporulation integral membrane protein YtvI.  Three lines of evidence show this protein to be involved in sporulation. First, it is under control of a sporulation-specific sigma factor, sigma-E. Second, mutation leads to a sporulation defect. Third, it if found in exactly those genomes whose bacteria are capable of sporulation, except for being absent in Clostridium acetobutylicum ATCC824. This protein has extensive hydrophobic regions and is ...
CDD:234045	382	PRK	Bacteria:9	TIGR02876, spore_yqfD, sporulation protein YqfD.  YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter [Cellular processes, Sporulation and germination].
CDD:234047	189	PRK	Bacteria:13	TIGR02883, spore_cwlD, N-acetylmuramoyl-L-alanine amidase CwlD.  Members of this protein family are the CwlD family of N-acetylmuramoyl-L-alanine amidase. This family has been called the germination-specific N-acetylmuramoyl-L-alanine amidase. CwlD is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in spores. CwlD mutants show a germination defect [Cell envelope, Biosynthesis and ...
CDD:131932	106	PRK	Bacteria:10	TIGR02886, spore_II_AA, anti-sigma F factor antagonist.  The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes [Regulatory functions, Protein interactions, Cellular processes, Sporulation and germination].
CDD:234048	371	PRK	Bacteria:17	TIGR02887, spore_ger_x_C, germination protein, Ger(x)C family.  Members of this protein family are restricted to endospore-forming members of the Firmicutes lineage of bacteria, including the genera Bacillus, Clostridium, Thermoanaerobacter, Carboxydothermus, etc. Members are nearly all predicted lipoproteins and belong to probable transport operons, some of which have been characterized as crucial to germination in response to alanine. Members typically have been ...
CDD:234049	76	PRK	Bacteria:9	TIGR02888, spore_YlmC_YmxH, sporulation protein, YlmC/YmxH family.  Members of this family belong to the broader family of PRC-barrel domain proteins (see pfam05239), but are found only in endospore-forming bacteria of the Firmicutes lineage. Most such species have exactly two members of this family and all have at least one; the function is unknown. One of two members from Bacillus subtilis, YmxH, is strongly induced by the mother cell-specific sigma-E factor ...
CDD:234050	159	PRK	Bacteria:10	TIGR02890, bacill_yteA, regulatory protein, yteA family.  Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence ...
CDD:213748	499	PRK	Bacteria:26	TIGR02891, CtaD_CoxA, cytochrome c oxidase, subunit I.  This large family represents subunit I's (CtaD, CoxA, CaaA) of cytochrome c oxidases of bacterial origin. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits I-III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of ...
CDD:131939	130	PRK	Bacteria:11	TIGR02893, spore_yabQ, spore cortex biosynthesis protein YabQ.  YabQ, a protein predicted to span the membrane several times, is found in exactly those genomes whose species perform sporulation in the style of Bacillus subtilis, Clostridium tetani, and others of the Firmicutes. Mutation of this sigma(E)-dependent gene blocks development of the spore cortex. The length of the C-terminal region, including some hydrophobic regions, is rather variable between members ...
CDD:131942	106	PRK	Bacteria:12	TIGR02896, spore_III_AF, stage III sporulation protein AF.  This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment [Cellular processes, ...
CDD:131944	158	PRK	Bacteria:7	TIGR02898, spore_YhcN_YlaJ, sporulation lipoprotein, YhcN/YlaJ family.  YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the ...
CDD:234052	488	PRK	Bacteria:9	TIGR02900, spore_V_B, stage V sporulation protein B.  SpoVB is the stage V sporulation protein B of the bacterial endopore formation program in Bacillus subtilis and various other Firmcutes. It is nearly universal among endospore-formers. Paralogs with rather high sequence similarity to SpoVB exist, including YkvU in B. subtilis and a number of proteins in the genus Clostridium. Member sequences for the seed alignment were chosen to select those proteins, no more ...
CDD:131952	313	PRK	Bacteria:9	TIGR02906, spore_CotS, spore coat protein, CotS family.  Members of this family include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologs that are more closely related to these two than to the spore coat proteins YutH and YsxE. The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers [Cellular processes, Sporulation and germination].
CDD:131959	39	PRK	Bacteria:8	TIGR02913, HAF_rpt, probable extracellular repeat, HAF family.  The model for this family detects a homology domain of about 40 amino acids. Member proteins always have a least two tandem copies and as many as seven. The spacing between repeats as defined here usually is four residues exactly. This repeat is named for a tripeptide motif HAF found in most members. Some members proteins are found in species with no outer membrane (archaea and Gram-positive bacteria) ...
CDD:234056	174	PRK	Bacteria:21	TIGR02914, EpsI_fam, EpsI family protein.  In Methylobacillus sp strain 12S, EpsI is encoded immediately downstream of the multiple-membrane-spanning putative transporter EpsH, and is predicted to be a periplasmic protein involved in, but not required for, expression of the exopolysaccharide methanolan. In a number of other species, protein homologous to EpsI is encoded either next to EpsH or, more often, combined in a fused gene. We have proposed renaming EpsH, or ...
CDD:234059	899	PRK	Bacteria:7	TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat lipoprotein.  This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of ...
CDD:234060	438	PRK	Bacteria:8	TIGR02919, TIGR02919, accessory Sec system glycosyltransferase GtfB.  Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus [Protein fate, Protein modification and repair].
CDD:234063	365	PRK	Bacteria:9	TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein.  Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other [DNA metabolism, DNA replication, recombination, and repair].
CDD:234064	91	PRK	Bacteria:14	TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific.  Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin [Central intermediary ...
CDD:234065	158	EUKprk	Bacteria:104,Phages:2,Plants:4,nodiv:1	TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family.  This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 ...
CDD:131990	99	PRK	Bacteria:13	TIGR02945, SUF_assoc, FeS assembly SUF system protein.  Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately ...
CDD:234068	446	PRK	Bacteria:10	TIGR02946, acyl_WS_DGAT, acyltransferase, WS/DGAT/MGAT.  This bacteria-specific protein family includes a characterized, homodimeric, broad specificity acyltransferase from Acinetobacter sp. strain ADP1, active as wax ester synthase, as acyl coenzyme A:diacylglycerol acyltransferase, and as acyl-CoA:monoacylglycerol acyltransferase [Unknown function, Enzymes of unknown specificity].
CDD:132002	281	PRK	Bacteria:9	TIGR02957, SigX4, RNA polymerase sigma-70 factor, TIGR02957 family.  This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces ...
CDD:234071	322	EUKprk	Bacteria:8,Plants:3,Primates:1,Vertebrates:2	TIGR02961, allantoicase, allantoicase.  Members of this family are the enzyme allantoicase (EC 3.5.3.4), also called allantoate amidinohydrolase. This enzyme hydrolyzes allantoate to (S)-ureidoglycolate and urea; it can also degrade (R)-ureidoglycolate to glyoxylate and urea. Allantoinase (EC 3.5.2.5) hydrolyzes (S)-allantoin (a xanthine metabolite, via urate) to allantoate. Allantoate can then be degraded either by this enzyme, ...
CDD:200221	112	EUKprk	Bacteria:24,Invertebrates:7,Plants:9,Rodents:1,Vertebrates:1	TIGR02962, hdxy_isourate, hydroxyisourate hydrolase.  Members of this family, hydroxyisourate hydrolase, represent a distinct clade of transthyretin-related proteins. Bacterial members typically are encoded next to ureidoglycolate hydrolase and often near either xanthine dehydrogenase or xanthine/uracil permease genes and have been demonstrated to have hydroxyisourate hydrolase activity. In eukaryotes, a clade ...
CDD:234072	467	EUKprk	Bacteria:15,Invertebrates:1,Vertebrates:1,nodiv:1	TIGR02963, xanthine_xdhA, xanthine dehydrogenase, small subunit.  Members of this protein family are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalization among xanthine dehydrogenases in eukaryotes and ...
CDD:234073	246	PRK	Bacteria:14,nodiv:1	TIGR02964, xanthine_xdhC, xanthine dehydrogenase accessory protein XdhC.  Members of this protein family are the accessory protein XdhC for insertion of the molybdenum cofactor into the xanthine dehydrogenase large chain, XdhB, in bacteria. This protein is not part of the mature xanthine dehydrogenase. Xanthine dehydrogenase is an enzyme for purine catabolism, from other purines to xanthine to urate to further breakdown products [Protein fate, Protein ...
CDD:234074	333	PRK	Bacteria:21,nodiv:1	TIGR02966, phoR_proteo, phosphate regulon sensor kinase PhoR.  Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154) [Signal transduction, Two-component systems].
CDD:132012	401	EUKprk	Bacteria:14,Invertebrates:3,Primates:1	TIGR02967, guan_deamin, guanine deaminase.  This model describes guanine deaminase, which hydrolyzes guanine to xanthine and ammonia. Xanthine can then be converted to urate by xanthine dehydrogenase, and urate subsequently degraded. In some bacteria, the guanine deaminase gene is found near the xdhABC genes for xanthine dehydrogenase. Non-homologous forms of guanine deaminase also exist, as well as distantly related forms outside the ...
CDD:234075	105	PRK	Bacteria:42,nodiv:1	TIGR02968, succ_dehyd_anc, succinate dehydrogenase, hydrophobic membrane anchor protein.  In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhD, the hydrophobic membrane anchor protein. SdhC is apocytochrome b558, which also plays a role in anchoring the complex [Energy metabolism, TCA cycle].
CDD:234076	120	PRK	Bacteria:33	TIGR02970, succ_dehyd_cytB, succinate dehydrogenase, cytochrome b556 subunit.  In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the ...
CDD:234077	329	PRK	Bacteria:17	TIGR02974, phageshock_pspF, psp operon transcriptional activator PspF.  Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH [Regulatory ...
CDD:132021	75	PRK	Bacteria:11	TIGR02976, phageshock_pspB, phage shock protein B.  This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage ...
CDD:213755	219	PRK	Bacteria:16	TIGR02977, phageshock_pspA, phage shock protein A.  Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects [Cellular processes, Adaptations ...
CDD:132023	121	PRK	Bacteria:14	TIGR02978, phageshock_pspC, phage shock protein C.  All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. ...
CDD:234078	227	PRK	Bacteria:14	TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily.  This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
CDD:132027	220	PRK	Bacteria:9	TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit, DevA family.  Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for ...
CDD:132028	162	PRK	Bacteria:4	TIGR02983, SigE-fam_strep, RNA polymerase sigma-70 factor, sigma-E family.  This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
CDD:234079	189	PRK	Bacteria:3	TIGR02984, Sig-70_plancto1, RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1.  This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
CDD:213756	161	PRK	Bacteria:8	TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor, Bacteroides expansion family 1.  This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. ...
CDD:132033	59	PRK	Bacteria:26	TIGR02988, YaaA_near_RecF, S4 domain protein YaaA.  This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not ...
CDD:234081	159	PRK	Bacteria:4	TIGR02989, Sig-70_gvs1, RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family.  This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
CDD:132041	42	PRK	Bacteria:2	TIGR02996, rpt_mate_G_obs, repeat-companion domain TIGR02996.  This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually ...
CDD:234082	298	PRK	Bacteria:12	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family.  This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
CDD:132044	183	PRK	Bacteria:8	TIGR02999, Sig-70_X6, RNA polymerase sigma factor, TIGR02999 family.  This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
CDD:132045	75	PRK	Bacteria:2	TIGR03000, plancto_dom_1, Planctomycetes uncharacterized domain TIGR03000.  Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to six proteins per genome, and may be duplicated within a protein. The function is unknown.
CDD:188267	244	PRK	Bacteria:2	TIGR03001, Sig-70_gmx1, RNA polymerase sigma-70 factor, Myxococcales family 1.  This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
CDD:234083	142	PRK	Bacteria:35,Synthetic:1,nodiv:1	TIGR03002, outer_YhbN_LptA, lipopolysaccharide transport periplasmic protein LptA.  Members of this protein family include LptA (previously called YhbN). It was shown to be an essential protein in E. coli, implicated in cell envelope integrity, and to play a role in the delivery of LPS to the outer leaflet of the outer membrane. It works with LptB (formerly yhbG), a homolog of ABC transporter ATP-binding proteins, encoded by an adjacent gene. ...
CDD:213757	272	PRK	Bacteria:13	TIGR03006, pepcterm_polyde, polysaccharide deacetylase family protein, PEP-CTERM locus subfamily.  Members of this protein family belong to the family of polysaccharide deacetylases (pfam01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff ...
CDD:234084	498	PRK	Bacteria:12	TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant protein, PEP-CTERM locus subfamily.  Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene [Cell envelope, Biosynthesis ...
CDD:200229	116	PRK	Bacteria:18	TIGR03010, sulf_tusC_dsrF, sulfur relay protein TusC/DsrF.  The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for ...
CDD:234085	94	PRK	Bacteria:25,Synthetic:1	TIGR03011, sulf_tusB_dsrH, sulfur relay protein TusB/DsrH.  The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in ...
CDD:234086	127	PRK	Bacteria:12,Synthetic:1	TIGR03012, sulf_tusD_dsrE, sulfur relay protein TusD/DsrE.  The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide ...
CDD:234088	431	PRK	Bacteria:11	TIGR03016, pepcterm_hypo_1, uncharacterized protein, PEP-CTERM system associated.  Members of this protein family are found predominantly in exopolysaccharide biosynthesis operons marked by the presence of the EpsH-family putative exosortase and presence in the genome of the PEP-CTERM protein sorting signal. Members of this family may be distantly related to the EpsL family modeled in TIGR03014.
CDD:132063	207	PRK	Bacteria:12	TIGR03018, pepcterm_TyrKin, exopolysaccharide/PEP-CTERM locus tyrosine autokinase.  Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine ...
CDD:132064	330	PRK	Bacteria:11	TIGR03019, pepcterm_femAB, FemAB-related protein, PEP-CTERM system-associated.  Members of this protein family are found always as part of extended exopolysaccharide biosynthesis loci in bacteria. In nearly every case, these loci contain determinants for the processing of the PEP-CTERM proposed C-terminal protein sorting signal. This family shows remote, local sequence similarity to the FemAB protein family (see pfam02388), whose members [Unknown function, General].
CDD:234090	119	PRK	Bacteria:12	TIGR03021, pilP_fam, type IV pilus biogenesis protein PilP.  Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP [Cell envelope, Surface structures].
CDD:234091	456	PRK	Bacteria:8	TIGR03022, WbaP_sugtrans, Undecaprenyl-phosphate galactose phosphotransferase, WbaP.  The WbaP (formerly RfbP) protein has been characterized as the first enzyme in O-antigen biosynthesis in Salmonella typhimurium. The enzyme transfers galactose from UDP-galactose to a polyprenyl carrier (utilizing the highly conserved C-terminal sugar transferase domain, pfam02397) a reaction which takes place at the cytoplasmic face of the inner membrane. The N-terminal ...
CDD:234092	451	PRK	Bacteria:39	TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose phosphotransferase.  This family of proteins encompasses the E. coli WcaJ protein involved in colanic acid biosynthesis , the Methylobacillus EpsB protein involved in methanolan biosynthesis , as well as the GumD protein involved in the biosynthesis of xanthan. All of these are closely related to the well-characterized WbaP (formerly RfbP) protein which is the first enzyme in O-antigen biosynthesis in ...
CDD:163110	25	PRK	Bacteria:3	TIGR03024, arch_PEF_CTERM, PEF-CTERM protein sorting domain.  This domain, distantly related to the PEP-Cterm domain described in model TIGR02595, is found in Methanosarcina mazei in four different proteins, as well as in other archaea such as Methanococcoides burtonii. Several proteins with this domain have their genes only a short distance from archaeosortase C, a proposed integral membrane transpeptidase. This family should exclude members of the PEFG-CTERM domain ...
CDD:234093	445	PRK	Bacteria:65,nodiv:1	TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase.  Members of this family are generally found near other genes involved in the biosynthesis of a variety of exopolysaccharides. These proteins consist of two fused domains, an N-terminal hydrophobic domain of generally low conservation and a highly conserved C-terminal sugar transferase domain (pfam02397). Characterized and partially characterized members of this ...
CDD:234094	409	PRK	Bacteria:24	TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase.  Enzymes in this family catalyze the NAD-dependent alcohol-to-acid oxidation of nucleotide-linked sugars. Examples include UDP-glucose 6-dehydrogenase (1.1.1.22) , GDP-mannose 6-dehydrogenase (1.1.1.132) , UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136), UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase. These enzymes are most often involved in the ...
CDD:234095	713	PRK	Bacteria:8	TIGR03030, CelA, cellulose synthase catalytic subunit (UDP-forming).  Cellulose synthase catalyzes the beta-1,4 polymerization of glucose residues in the formation of cellulose. In bacteria, the substrate is UDP-glucose. The synthase consists of two subunits (or domains in the frequent cases where it is encoded as a single polypeptide), the catalytic domain modelled here and the regulatory domain (pfam03170). The regulatory domain binds the allosteric activator ...
CDD:200235	153	PRK	Bacteria:7,Viruses:1	TIGR03033, phage_rel_nuc, putative phage-type endonuclease.  Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.
CDD:188272	264	PRK	Bacteria:18	TIGR03036, trp_2_3_diox, tryptophan 2,3-dioxygenase.  Members of this family are tryptophan 2,3-dioxygenase, as confirmed by several experimental characterizations, and by conserved operon structure for many of the other members. This enzyme represents the first of a two-step degradation to L-kynurenine, and a three-step pathway (via kynurenine) to anthranilate plus alanine [Energy metabolism, Amino acids and amines].
CDD:132083	33	EUKprk	Bacteria:13,Plants:15	TIGR03038, PS_II_psbM, photosystem II reaction center protein PsbM.  Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles pfam05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic [Energy metabolism, Photosynthesis].
CDD:213761	321	PRK	Bacteria:10	TIGR03041, PS_antenn_a_b, chlorophyll a/b binding light-harvesting protein.  This model represents a family of proteins from the Cyanobacteria, closely homologous to and yet distinct from PbsC, a chlorophyll a antenna protein of photosystem II. Members are not univerally present in Cyanobacteria, while the family has several members per genome in Prochlorococcus marinus, with seven members in a strain adapted to low light conditions. These antenna proteins may ...
CDD:132086	142	PRK	Bacteria:14	TIGR03042, PS_II_psbQ_bact, photosystem II protein PsbQ.  This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology [Energy metabolism, Photosynthesis].
CDD:200236	58	EUKprk	Bacteria:6,Plants:11	TIGR03043, PS_II_psbZ, photosystem II core protein PsbZ.  PsbZ is a core protein of photosystem II in thylakoid-containing Cyanobacteria and plant chloroplasts. The original Chlamydomonas gene symbol, ycf9, is a synonym. PsbZ controls the interaction of the reaction center core with the light-harvesting antenna [Energy metabolism, Photosynthesis].
CDD:234098	135	PRK	Bacteria:18	TIGR03044, PS_II_psb27, photosystem II protein Psb27.  Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single family models, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences from Arabidopsis are not, at this ...
CDD:132089	159	EUKprk	Bacteria:15,Plants:5	TIGR03045, PS_II_C550, cytochrome c-550.  Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself [Energy metabolism, Photosynthesis].
CDD:213763	109	EUKprk	Bacteria:10,Plants:6	TIGR03047, PS_II_psb28, photosystem II reaction center protein Psb28.  Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family ...
CDD:132093	81	EUKprk	Bacteria:13,Plants:4	TIGR03049, PS_I_psaK, photosystem I reaction center subunit PsaK.  Members of this protein family are the PsaK of the photosystem I reaction center. Photosystems I and II occur together in the same sets of organisms. Photosystem I uses light energy to transfer electrons from plastocyanin to ferredoxin, while photosystem II uses light energy to split water and releases molecular oxygen [Energy metabolism, Photosynthesis].
CDD:132097	29	EUKprk	Bacteria:10,Plants:23	TIGR03053, PS_I_psaM, photosystem I reaction center subunit XII.  Members of this protein family are PsaM, which is subunit XII of the photosystem I reaction center. This protein is found in both the Cyanobacteria and the chloroplasts of plants, but is absent from non-oxygenic photosynthetic bacteria such as Rhodobacter sphaeroides. Species that contain photosystem I also contain photosystem II, which splits water and releases molecular oxygen. The seed ...
CDD:132101	28	PRK	Bacteria:55	TIGR03057, xxxLxxG_by_4, X-X-X-Leu-X-X-Gly heptad repeats.  This model represents a 28-column alignment, comprising four tandem sets of seven residues each, in which the fourth residue tends to be Leu and the seventh tends to be Gly in each set. This heptad periodicity, corresponding to two turns of an alpha helix, suggests alpha-helical structure; in many proteins this 28-region model hits many times in tandem. Arrangement of these sequences on a helical wheel ...
CDD:213765	214	miss	miss	TIGR03060, PS_II_psb29, photosystem II biogenesis protein Psp29.  Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function [Energy metabolism, Photosynthesis].
CDD:132105	164	PRK	Bacteria:5	TIGR03061, pip_yhgE_Nterm, YhgE/Pip N-terminal domain.  This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and ...
CDD:234099	208	PRK	Bacteria:1	TIGR03062, pip_yhgE_Cterm, YhgE/Pip C-terminal domain.  This family contains the C-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03061, represents the conserved N-terminal domain. The domains are separated by regions highly variable in both length and ...
CDD:211782	232	PRK	Bacteria:10	TIGR03064, sortase_srtB, sortase, SrtB family.  Members of this transpeptidase family are, in most cases, designated sortase B, product of the srtB gene. This protein shows only distant similarity to the sortase A family, for which there may be several members in a single bacterial genome. Typical SrtB substrate motifs include NAKTN, NPKSS, etc, and otherwise resemble the LPXTG sorting signals recognized by sortase A proteins [Cell envelope, Other, Protein fate, ...
CDD:132110	111	PRK	Bacteria:1	TIGR03066, Gem_osc_para_1, Gemmata obscuriglobus paralogous family TIGR03066.  This model represents an uncharacterized paralogous family in Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. This family shows sequence similarity to TIGR03067, which is also found in Gemmata obscuriglobus as well as in a few other species [Hypothetical proteins, Conserved].
CDD:234100	107	PRK	Bacteria:1	TIGR03067, Planc_TIGR03067, Planctomycetes uncharacterized domain TIGR03067.  This domain occurs in several species, mostly from the Planctomycetes division of the bacteria. It is expanded into a paralogous family of at least twenty-five members in Gemmata obscuriglobus UQM 2246. This family appears related to TIGR03066, which also is expanded into a large paralogous family in Gemmata obscuriglobus [Unknown function, General].
CDD:132113	257	EUKprk	Bacteria:10,Plants:1	TIGR03069, PS_II_S4, photosystem II S4 domain protein.  Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in ...
CDD:213767	58	PRK	Bacteria:12	TIGR03070, couple_hipB, transcriptional regulator, y4mF family.  Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common ...
CDD:163125	101	PRK	Bacteria:10	TIGR03071, couple_hipA, HipA N-terminal domain.  Although Pfam models pfam07805 and pfam07804 currently are called HipA-like N-terminal domain and HipA-like C-terminal domain, respectively, those models hit the central and C-terminal regions of E. coli HipA but not the N-terminal region. This model hits the N-terminal region of HipA and its homologs, and also identifies proteins that lack match regions for pfam07804 and pfam07805.
CDD:234101	764	PRK	Bacteria:13,nodiv:1	TIGR03074, PQQ_membr_DH, membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family.  This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Members of this family have several predicted transmembrane helices in the N-terminal region, and include the quinoprotein glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli and the quinate/shikimate ...
CDD:234102	526	PRK	Bacteria:17	TIGR03075, PQQ_enz_alc_DH, PQQ-dependent dehydrogenase, methanol/ethanol family.  This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Genes in this family often are found adjacent to the PQQ biosynthesis genes themselves. An unusual, strained disulfide bond between adjacent Cys residues contributes to PQQ-binding, as does a Trp residue that is part of a PQQ enzyme ...
CDD:213773	156	PRK	Bacteria:49,Synthetic:1,nodiv:1	TIGR03082, Gneg_AbrB_dup, membrane protein AbrB duplication.  The model describes a hydrophobic sequence region that is duplicated to form the AbrB protein of Escherichia coli (not to be confused with a Bacillus subtilis protein with the same gene symbol). In some species, notably the Cyanobacteria and Thermus thermophilus, proteins consist of a single copy rather than two copies. The member from Pseudomonas putida, PP_1415, was suggested to be ...
CDD:234103	202	PRK	Bacteria:24	TIGR03083, TIGR03083, uncharacterized Actinobacterial protein TIGR03083.  This protein family pulls together several groups of proteins, each very different from the others. They share in common three conserved regions. The first is a region of about 38 amino acids, nearly always at the N-terminus of a protein. This region has a bulky hydrophobic residue, usually Trp, at position 29, and a His residue at position 37 that is invariant, so far, in over 150 instances. ...
CDD:132128	253	PRK	Bacteria:12	TIGR03084, TIGR03084, TIGR03084 family protein.  This family, like Pfam family pfam07398, belongs to the larger set of probable enzymes modeled by TIGRFAMs family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized [Hypothetical proteins, Conserved].
CDD:132129	199	PRK	Bacteria:3	TIGR03085, TIGR03085, TIGR03085 family protein.  This family, like Pfam family pfam07398 and TIGRFAMs family TIGR03084, belongs to the larger set of probable enzymes defined in family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized [Hypothetical proteins, Conserved].
CDD:234104	180	PRK	Bacteria:4	TIGR03086, TIGR03086, TIGR03086 family protein.  This family, like Pfam family pfam07398 and TIGRFAMs family TIGR030834, belongs to the larger set of probable enzymes defined in family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized.
CDD:234105	397	PRK	Bacteria:9	TIGR03087, stp1, sugar transferase, PEP-CTERM/EpsH1 system associated.  Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of ...
CDD:234106	227	PRK	Bacteria:12	TIGR03089, TIGR03089, TIGR03089 family protein.  This protein family is found, so far, only in the Actinobacteria (Streptomyces, Mycobacterium, Corynebacterium, Nocardia, Propionibacterium, etc.) and never more than one to a genome. Members show twilight-level sequence similarity to family of AMP-binding enzymes described by pfam00501.
CDD:234109	435	PRK	Bacteria:10	TIGR03105, gln_synth_III, glutamine synthetase, type III.  This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur.
CDD:132153	267	PRK	Bacteria:5	TIGR03109, exosortase_1, exosortase A.  The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. We designate this, the most common type so far, exosortase 1. We propose the gene symbol xrtA, analogous to srtA for the most common type of sortase in Gram-positive bacteria.
CDD:132164	312	PRK	Bacteria:2	TIGR03120, one_C_mch, methenyltetrahydromethanopterin cyclohydrolase.  Members of this protein family are the enzyme methenyltetrahydromethanopterin cyclohydrolase, a key enzyme for tetrahydromethanopterin (H4MPT)-linked C1 transfer metabolism [Central intermediary metabolism, One-carbon metabolism].
CDD:234114	556	PRK	Bacteria:12	TIGR03121, one_C_dehyd_A, formylmethanofuran dehydrogenase subunit A.  Members of this largely archaeal protein family are subunit A of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit A. Note that this model does not distinguish tungsten (FwdA) from molybdenum-containing ...
CDD:132166	260	PRK	Bacteria:9	TIGR03122, one_C_dehyd_C, formylmethanofuran dehydrogenase subunit C.  Members of this largely archaeal protein family are subunit C of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdC) from molybdenum-containing ...
CDD:163144	318	PRK	Bacteria:10	TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer pathway protein.  This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in ...
CDD:163145	165	PRK	Bacteria:15	TIGR03124, citrate_citX, holo-ACP synthase CitX.  Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a ...
CDD:132169	275	PRK	Bacteria:11	TIGR03125, citrate_citG, triphosphoribosyl-dephospho-CoA synthase CitG.  Triphosphoribosyl-dephospho-CoA is transferred to, and becomes the prosthetic group of, the respective acyl carrier protein subunits of both citrate lyase and malonate decarboxylase. Members of this protein family are triphosphoribosyl-dephospho-CoA synthases specifically from citrate lyase systems. This protein sometimes occurs as a fusion protein with CitX, the phosphoribosyl-dephospho-CoA ...
CDD:132171	179	PRK	Bacteria:13	TIGR03127, RuMP_HxlB, 6-phospho 3-hexuloisomerase.  Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, ...
CDD:132172	206	PRK	Bacteria:7	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase.  Members of this protein family are 3-hexulose-6-phosphate synthase (HPS), or the HPS domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, ...
CDD:132173	421	PRK	Bacteria:12	TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit B.  Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing ...
CDD:188283	98	PRK	Bacteria:10,Synthetic:1	TIGR03130, malonate_delta, malonate decarboxylase acyl carrier protein.  Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl ...
CDD:132175	295	PRK	Bacteria:11	TIGR03131, malonate_mdcH, malonate decarboxylase, epsilon subunit.  Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on ...
CDD:234115	272	PRK	Bacteria:10	TIGR03132, malonate_mdcB, triphosphoribosyl-dephospho-CoA synthase MdcB.  This protein acts in cofactor biosynthesis, preparing the coenzyme A derivative that becomes attached to the malonate decarboxylase acyl carrier protein (or delta subunit). The closely related protein CitG of citrate lyase produces the same molecule, but the two families are nonetheless readily separated [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:188285	274	PRK	Bacteria:3	TIGR03133, malonate_beta, malonate decarboxylase, beta subunit.  Members of this protein family are the beta subunit of malonate decarboxylase. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase.
CDD:234116	238	PRK	Bacteria:19	TIGR03134, malonate_gamma, malonate decarboxylase, gamma subunit.  Members of this protein family are the gamma subunit of malonate decarboxylase. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase, while the gamma subunit appears either to mediate subunit interaction or to act as a co-decarboxylase with the ...
CDD:234117	202	PRK	Bacteria:23,nodiv:1	TIGR03135, malonate_mdcG, malonate decarboxylase holo-[acyl-carrier-protein] synthase.  Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding ...
CDD:234118	275	PRK	Bacteria:2,Synthetic:1	TIGR03138, QueF, 7-cyano-7-deazaguanine reductase.  This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (preQ0) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the longer, gram-negative version of the enzyme as found in E. coli. The enzymatic step represents the first point at which ...
CDD:213775	115	PRK	Bacteria:3	TIGR03139, QueF-II, 7-cyano-7-deazaguanine reductase.  This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (proQ1) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the shorter, gram-positive version of the enzyme as found in B. subtilis. The enzymatic step represents the first point at which the ...
CDD:213776	45	PRK	Bacteria:32,Synthetic:1	TIGR03141, cytochro_ccmD, heme exporter protein CcmD.  The model for this protein family describes a small, hydrophobic, and only moderately well-conserved protein, tricky to identify accurately for all of these reasons. However, members are found as part of large operons involved in heme export across the inner membrane for assembly of c-type cytochromes in a large number of bacteria. The gray zone between the trusted cutoff (13.0) and noise cutoff ...
CDD:163153	117	PRK	Bacteria:29	TIGR03142, cytochro_ccmI, cytochrome c-type biogenesis protein CcmI.  This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family [Protein fate, Protein folding and stabilization, Energy metabolism, Electron transport].
CDD:234120	243	EUKprk	Bacteria:17,Plants:7	TIGR03144, cytochr_II_ccsB, cytochrome c-type biogenesis protein CcsB.  Members of this protein family represent one of two essential proteins of system II for c-type cytochrome biogenesis. Additional proteins tend to be part of the system but can be replaced by chemical reductants such as dithiothreitol. This protein is designated CcsB in Bordetella pertussis and some other bacteria, resC in Bacillus (where there is additional N-terminal sequence), and ...
CDD:200247	407	PRK	Bacteria:53	TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II.  3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II, FabF) is involved in the condensation step of fatty acid biosynthesis in which the malonyl donor group is decarboxylated and the resulting carbanion used to attack and extend the acyl group attached to the acyl carrier protein. Most genomes encoding fatty acid biosynthesis contain a number of condensing enzymes, often of all three types: 1, 2 and ...
CDD:234123	135	PRK	Bacteria:19	TIGR03153, cytochr_NrfH, cytochrome c nitrate reductase, small subunit.  Members of this protein family are NrfH, a tetraheme cytochrome c. NrfH is the cytochrome c nitrate reductase small subunit, and forms a heterodimer with NrfA, the catalytic subunit. While NrfA can act as a monomer, NrfH can bind to and anchor NrfA in the membrane and enables electron transfer to NrfA from quinones [Energy metabolism, Electron transport].
CDD:234125	351	PRK	Bacteria:58	TIGR03156, GTP_HflX, GTP-binding protein HflX.  This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of ...
CDD:234129	333	PRK	Bacteria:27	TIGR03160, cobT_DBIPRT, nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase.  Members of this family are nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, an enzyme of cobalamin biosynthesis [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin].
CDD:234131	177	PRK	Bacteria:26	TIGR03162, ribazole_cobC, alpha-ribazole phosphatase.  Members of this protein family include the known CobC protein of Salmonella and Eschichia coli species, and homologous proteins found in cobalamin biosynthesis regions in other bacteria. This protein is alpha-ribazole phosphatase (EC 3.1.3.73) and, like many phosphatases, can be closely related in sequence to other phosphatases with different functions. Close homologs excluded from this model include proteins ...
CDD:132208	157	PRK	Bacteria:7	TIGR03164, UHCUDC, OHCU decarboxylase.  Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
CDD:213779	83	PRK	Bacteria:11	TIGR03165, F1F0_chp_2, F1/F0 ATPase, Methanosarcina type, subunit 2.  Members of this protein family are uncharacterized, highly hydrophobic proteins encoded in the middle of apparent F1/F0 ATPase operons. We note, however, that this protein is both broadly and sparsely distributed. It is found in about only about two percent of microbial genomes sequenced, with the first ten examples found coming from the Euryarchaeota, Chlorobia, Betaproteobacteria, ...
CDD:234132	311	PRK	Bacteria:2	TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase.  The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split ...
CDD:234133	303	PRK	Bacteria:30	TIGR03168, 1-PFK, hexose kinase, 1-phosphofructokinase family.  This family consists largely of 1-phosphofructokinases, but also includes tagatose-6-kinases and 6-phosphofructokinases.
CDD:234134	364	PRK	Bacteria:17	TIGR03169, Nterm_to_SelD, pyridine nucleotide-disulfide oxidoreductase family protein.  Members of this protein family include N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD, or selenide,water dikinase, the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium ...
CDD:213781	122	PRK	Bacteria:37	TIGR03170, flgA_cterm, flagella basal body P-ring formation protein FlgA.  This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by pfam08666 [Cellular processes, Chemotaxis and motility].
CDD:234135	210	PRK	Bacteria:19	TIGR03172, TIGR03172, probable selenium-dependent hydroxylase accessory protein YqeC.  This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase ...
CDD:234136	406	PRK	Bacteria:27	TIGR03173, pbuX, xanthine permease.  All the seed members of this model are observed adjacent to genes for either xanthine phosphoribosyltransferase (for the conversion of xanthine to guanine, GenProp0696, ) or genes for the conversion of xanthine to urate and its concomitant catabolism (GenProp0640, GenProp0688, GenProp0686 and GenProp0687). A number of sequences scoring higher than trusted to this model are found in different genomic contexts, and the possibility ...
CDD:234138	261	PRK	Bacteria:36	TIGR03177, pilus_cpaB, Flp pilus assembly protein CpaB.  Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
CDD:213783	341	PRK	Bacteria:34	TIGR03181, PDH_E1_alph_x, pyruvate dehydrogenase E1 component, alpha subunit.  Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc [Energy metabolism, Pyruvate dehydrogenase].
CDD:234139	315	EUKprk	Bacteria:26,Invertebrates:1,Plants:2,Primates:1,Rodents:1,Vertebrates:1	TIGR03182, PDH_E1_alph_y, pyruvate dehydrogenase E1 component, alpha subunit.  Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc [Energy metabolism, Pyruvate dehydrogenase].
CDD:234140	105	PRK	Bacteria:14	TIGR03184, DNA_S_dndE, DNA sulfur modification protein DndE.  This model describes the DndE protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases [DNA metabolism, Restriction/modification].
CDD:234141	650	PRK	Bacteria:7	TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.  This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria [DNA metabolism, ...
CDD:234142	271	PRK	Bacteria:32,Environmental:1	TIGR03187, DGQHR, DGQHR domain.  This highly divergent, uncharacterized domain has several absolutely conserved residues, including a QR pair and FxxxN motif. Its most striking feature, however, is a near invariant pentapeptide motif DGQHR. Several different subfamilies occur specifically as a part of DNA phosphorothioation systems, previously called DND (DNA instability during electrophoresis), while others (e.g. CPS_2936) occur in other contexts ...
CDD:234143	84	EUKprk	Bacteria:52,Plants:6,nodiv:1	TIGR03188, histidine_hisI, phosphoribosyl-ATP pyrophosphohydrolase.  This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model [Amino acid biosynthesis, Histidine family].
CDD:234144	381	PRK	Bacteria:13	TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain.  In Escherichia coli, the protein previously designated YfcK is now identified as the bifunctional enzyme MnmC. It acts, following the action of the heterotetramer of GidA and MnmE, in the modification of U-34 of certain tRNA to 5-methylaminomethyl-2-thiouridine (mnm5s2U). In other bacterial, the corresponding proteins are usually but always found as a ...
CDD:234146	303	PRK	Bacteria:17	TIGR03211, catechol_2_3, catechol 2,3 dioxygenase.  Members of this family all are enzymes active as catechol 2,3 dioxygenase (1.13.11.2), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol (see Mars, et al.). This enzyme is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage), in contrast to the ortho-cleavage (intradiol ring ...
CDD:132259	285	miss	miss	TIGR03215, ac_ald_DH_ac, acetaldehyde dehydrogenase (acetylating).  Members of this protein family are acetaldehyde dehydrogenase (acetylating), EC 1.2.1.10. This enzyme oxidizes acetaldehyde, using NAD(+), and attaches coenzyme A (CoA), yielding acetyl-CoA. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate, etc.
CDD:132261	333	PRK	Bacteria:4	TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase.  Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated ...
CDD:234147	228	PRK	Bacteria:10,nodiv:1	TIGR03223, Phn_opern_protn, putative phosphonate metabolism protein.  This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
CDD:163190	254	PRK	Bacteria:9	TIGR03234, OH-pyruv-isom, hydroxypyruvate isomerase.  This enzyme interconverts tartronate semi-aldehyde (TSA, aka 2-hydroxy 3-oxopropionate) and hydroxypyruvate. The E. coli enzyme has been characterized and found to be specific for TSA, contain no cofactors, and have a rather high Km for hydroxypyruvate of 12.5 mM. The gene is ofter found in association with glyoxalate carboligase (which produces TSA), but has been shown to have no effect on growth on glyoxalate ...
CDD:132287	335	PRK	Bacteria:12	TIGR03243, arg_catab_AOST, arginine and ornithine succinyltransferase subunits.  In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
CDD:213788	179	EUKprk	Bacteria:44,Mammals:1,Plants:1,Rodents:1	TIGR03263, guanyl_kin, guanylate kinase.  Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions].
CDD:234152	353	PRK	Bacteria:9	TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein.  This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely ...
CDD:132319	179	PRK	Bacteria:10	TIGR03276, Phn-HD, phosphonate degradation operons associated HDIG domain protein.  This small clade of proteins are found adjacent to other genes implicated in the catabolism of phosphonates. They are members of the TIGR00277 domain family and contain a series of five invariant histidines (the domain in general has only four).
CDD:132335	174	PRK	Bacteria:11	TIGR03292, PhnH_redo, phosphonate C-P lyase system protein PhnH.  PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
CDD:234159	144	PRK	Bacteria:21,nodiv:1	TIGR03293, PhnG_redo, phosphonate C-P lyase system protein PhnG.  PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam06754.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
CDD:234161	285	EUKprk	Bacteria:22,Plants:3	TIGR03296, M6dom_TIGR03296, M6 family metalloprotease domain.  This model describes a metalloproteinase domain, with a characteristic HExxH motif. Examples of this domain are found in proteins in the family of immune inhibitor A, which cleaves antibacterial peptides, and in other, only distantly related proteases. This model is built to be broader and more inclusive than pfam05547.
CDD:132340	361	PRK	Bacteria:8	TIGR03297, Ppyr-DeCO2ase, phosphonopyruvate decarboxylase.  This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a ...
CDD:211803	278	PRK	Bacteria:4	TIGR03298, argP, transcriptional regulator, ArgP family.  ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242) [Cellular processes, ...
CDD:234162	309	PRK	Bacteria:8	TIGR03299, LGT_TIGR03299, phage/plasmid-like protein TIGR03299.  Members of this uncharacterized protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. The function is unknown [Mobile and extrachromosomal element functions, Other].
CDD:234163	377	PRK	Bacteria:21	TIGR03300, assembly_YfgL, outer membrane assembly lipoprotein YfgL.  Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ [Protein fate, Protein and peptide secretion and trafficking].
CDD:234164	235	PRK	Bacteria:93,nodiv:1	TIGR03302, OM_YfiO, outer membrane assembly lipoprotein YfiO.  Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is ...
CDD:234165	741	PRK	Bacteria:36	TIGR03303, OM_YaeT, outer membrane protein assembly complex, YaeT protein.  Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed ...
CDD:213795	10	EUKprk	Bacteria:197,Plants:1,nodiv:1	TIGR03304, OMP85_target, outer membrane insertion C-terminal signal.  This hidden Markov model detects a 10-residue targeting sequence common to beta-barrel outer membrane proteins (OMP) that rely on Omp85-like proteins for insertion into the outer membrane. Hits should be trusted if they include the last amino acid of a protein sequence that occurs in Gram-negative bacteria. It has been noted that Omp85 target sequences differ somewhat by ...
CDD:234166	188	PRK	Bacteria:11	TIGR03310, matur_ygfJ, molybdenum hydroxylase accessory protein, YgfJ family.  Members of this protein family are probable accessory proteins for the biosynthesis of enzymes related to xanthine dehydrogenase. Comparative genomics suggests a role in the maturation of selenium-dependent molybdenum hydroxylases, although a tenuous alternative hypothesis is a role for this protein (with a requirement for SelD, the selenium donor protein in the selenocysteine and ...
CDD:234167	67	EUKprk	Bacteria:66,Invertebrates:5,Plants:5,Primates:1,nodiv:1	TIGR03317, ygfZ_signature, folate-binding protein YgfZ.  YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are ...
CDD:188306	514	PRK	Bacteria:10	TIGR03319, RNase_Y, ribonuclease Y.  Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA].
CDD:132364	246	PRK	Bacteria:8	TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B.  A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
CDD:234168	193	EUKprk	Bacteria:10,Invertebrates:1,Plants:1,Primates:1	TIGR03328, salvage_mtnB, methylthioribulose-1-phosphate dehydratase.  Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine [Amino acid biosynthesis, Aspartate family].
CDD:132373	112	PRK	Bacteria:14,Synthetic:1	TIGR03330, SAM_DCase_Bsu, S-adenosylmethionine decarboxylase proenzyme, Bacillus form.  Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii, Bacillus subtilis, and a wide range of other species. It differs substantially in architecture from the form as found in Escherichia coli, and lacks any extended homology to the eukaryotic form ...
CDD:132384	190	PRK	Bacteria:15	TIGR03341, YhgI_GntY, IscR-regulated protein YhgI.  IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated ...
CDD:213798	108	PRK	Bacteria:19,Synthetic:1	TIGR03342, dsrC_tusE_dsvC, sulfur relay protein, TusE/DsrC/DsvC family.  Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known ...
CDD:213799	166	PRK	Bacteria:16,Synthetic:1	TIGR03344, VI_effect_Hcp1, type VI secretion system effector, Hcp1 family.  This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of ...
CDD:234172	852	PRK	Bacteria:19,nodiv:1	TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.  Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234173	852	PRK	Bacteria:21	TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB.  Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins [Protein fate, Protein folding and stabilization].
CDD:234174	300	PRK	Bacteria:30	TIGR03347, VI_chp_1, type VI secretion protein, VC_A0111 family.  Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PMID:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234175	1169	PRK	Bacteria:16	TIGR03348, VI_IcmF, type VI secretion protein IcmF.  Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems [Cellular processes, Pathogenesis].
CDD:213800	183	PRK	Bacteria:37,nodiv:1	TIGR03349, IV_VI_DotU, type IV / VI secretion system protein, DotU family.  At least two families of proteins, often encoded by adjacent genes, show sequence similarity due to homology between type IV secretion systems and type VI secretion systems. One is the IcmF family (TIGR03348). The other is the family described by this model. Members include DotU from the Legionella pneumophila type IV secretion system. Many of the members of this protein family from ...
CDD:213801	137	PRK	Bacteria:5	TIGR03350, type_VI_ompA, type VI secretion system OmpA/MotB family protein.  The flagellar motor protein MotB and the Gram-negative bacterial outer membrane protein OmpA share a region of sequence homology. This model describes a domain found fused to type VI secretion system homologs of the type IV system protein DotU (see model TIGR03349), with OmpA/MotB homology [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234177	146	PRK	Bacteria:16	TIGR03352, VI_chp_3, type VI secretion lipoprotein, VC_A0113 family.  Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PMID:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:132396	439	PRK	Bacteria:25	TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family.  Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PMID:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234178	396	PRK	Bacteria:13	TIGR03354, VI_FHA, type VI secretion system FHA domain protein.  Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234179	473	PRK	Bacteria:15	TIGR03355, VI_chp_2, type VI secretion protein, EvpB/VC_A0108 family.  Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PMID:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234180	426	PRK	Bacteria:23,Synthetic:1,nodiv:1	TIGR03356, BGL, beta-galactosidase.  
CDD:234181	133	PRK	Bacteria:27,nodiv:1	TIGR03357, VI_zyme, type VI secretion system lysozyme-like protein.  The description for PFAM family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.
CDD:132401	159	PRK	Bacteria:14,nodiv:1	TIGR03358, VI_chp_5, type VI secretion protein, VC_A0107 family.  Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PMID:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234182	598	PRK	Bacteria:32	TIGR03359, VI_chp_6, type VI secretion protein, VC_A0110 family.  This protein family is associated with type VI secretion in a number of pathogenic bacteria. Mutation is associated with impaired virulence, such as impaired infection of plants by Rhizobium leguminosarum.
CDD:234183	513	PRK	Bacteria:24	TIGR03361, VI_Rhs_Vgr, type VI secretion system Vgr family protein.  Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
CDD:234184	301	PRK	Bacteria:14	TIGR03362, VI_chp_7, type VI secretion-associated protein, VC_A0119 family.  This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812) [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].
CDD:234185	353	PRK	Bacteria:13,Synthetic:1	TIGR03363, VI_chp_8, type VI secretion-associated protein, ImpA family.  This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
CDD:132407	365	PRK	Bacteria:13	TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.  This clade of FAD dependent oxidoreductases (members of the pfam01266 family) is syntenically associated with a family of proposed phosphonatase-like enzymes (TIGR03351) and is also found (less frequently) in association with phosphonate transporter components. A likely role for this enzyme involves the oxidative deamination of an aminophosphonate differring slightly from 2-aminoethylphosphonate, ...
CDD:132408	238	PRK	Bacteria:10	TIGR03365, Bsubt_queE, 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE.  This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine [Protein synthesis, tRNA and rRNA base modification].
CDD:234186	91	PRK	Bacteria:30	TIGR03367, queuosine_QueD, queuosine biosynthesis protein QueD.  Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be ...
CDD:132411	518	PRK	Bacteria:12	TIGR03368, cellulose_yhjU, cellulose synthase operon protein YhjU.  This protein was identified by the partial phylogenetic profiling algorithm (PMID:16930487) as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (PMID:11929533) [Cell envelope, Biosynthesis ...
CDD:234187	322	PRK	Bacteria:11	TIGR03369, cellulose_bcsE, cellulose biosynthesis protein BcsE.  This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm. Members are found in the vicinity of other cellulose biosynthesis genes. The model does not include a much less well-conserved N-terminal region about ...
CDD:132413	25	PRK	Bacteria:3	TIGR03370, VPLPA-CTERM, VPLPA-CTERM protein sorting domain.  A probable protein export sorting signal, PEP-CTERM, was described by Haft, et al. (PMID:16930487). It is predicted to interact with a putative transpeptidase we designate exosortase. This model describes a variant with conserved motif VPLPA, rather than VPEP. It appears to be the recognition sequences for exosortase D (TIGR04152). This variant is found prominently in two members of the Rhodobacterales, ...
CDD:234188	246	PRK	Bacteria:12	TIGR03371, cellulose_yhjQ, cellulose synthase operon protein YhjQ.  Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by ...
CDD:132416	136	PRK	Bacteria:23,nodiv:1	TIGR03373, VI_minor_4, type VI secretion-associated protein, BMA_A0400 family.  Members of this protein family are found exclusively, although not universally, in bacterial species that possess a type VI secretion system. Genes are found in type VI secretion-associated gene clusters. The specific function is unknown. This model represents the rather well-conserved amino-terminal domain of a protein family in which carboxy-terminal regions, when present, ...
CDD:234189	694	PRK	Bacteria:29	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family.  Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is ...
CDD:234190	342	EUK	Invertebrates:2,Plants:6,Vertebrates:1	TIGR03376, glycerol3P_DH, glycerol-3-phosphate dehydrogenase (NAD(+)).  Members of this protein family are the eukaryotic enzyme, glycerol-3-phosphate dehydrogenase (NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8 is defined as sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH. Note the very similar reactions of enzymes defined as EC 1.1.1.94 and 1.1.99.5, assigned to families of proteins in the bacteria.
CDD:234191	516	PRK	Bacteria:6	TIGR03377, glycerol3P_GlpA, glycerol-3-phosphate dehydrogenase, anaerobic, A subunit.  Members of this protein family are the A subunit, product of the glpA gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase [Energy metabolism, Anaerobic].
CDD:213807	419	PRK	Bacteria:1	TIGR03378, glycerol3P_GlpB, glycerol-3-phosphate dehydrogenase, anaerobic, B subunit.  Members of this protein family are the B subunit, product of the glpB gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase [Energy metabolism, Anaerobic].
CDD:132423	357	EUKprk	Bacteria:15,Plants:1	TIGR03380, agmatine_aguA, agmatine deiminase.  Members of this family are agmatine deiminase (3.5.3.12), as characterized in Pseudomonas aeruginosa and plants. Related deiminases include the peptidyl-arginine deiminase (3.5.3.15) as found in Porphyromonas gingivalis [Central intermediary metabolism, Polyamine biosynthesis].
CDD:188311	279	EUKprk	Bacteria:13,Plants:1	TIGR03381, agmatine_aguB, N-carbamoylputrescine amidase.  Members of this family are N-carbamoylputrescine amidase (3.5.1.53). Bacterial genes are designated AguB. The AguAB pathway replaces SpeB for conversion of agmatine to putrescine in two steps rather than one [Central intermediary metabolism, Polyamine biosynthesis].
CDD:213808	27	PRK	Bacteria:5	TIGR03382, GC_trans_RRR, Myxococcales GC_trans_RRR domain.  The domain described here is small (about 30 amino acids), hydrophobic, only moderately conserved, and similar to numerous other transmembrane helix-containing sequence regions from convergent evolution. This domain is found, once per protein but in many proteins per genome in several bacteria of the order Myxococcales. It begins with a signature Gly-Cys motif. Its other features, including a hydrophobic ...
CDD:234192	282	EUKprk	Bacteria:13,Invertebrates:4,Plants:12,Rodents:1,Vertebrates:2	TIGR03383, urate_oxi, urate oxidase.  Members of this protein family are urate oxidase, also called uricase. This protein contains two copies of the domain described by the uricase model pfam01014. In animals, this enzyme has been lost from primates and birds [Central intermediary metabolism, Other].
CDD:132427	189	PRK	Bacteria:5,nodiv:1	TIGR03384, betaine_BetI, transcriptional repressor BetI.  BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet ...
CDD:234195	689	PRK	Bacteria:13	TIGR03396, PC_PLC, phospholipase C, phosphocholine-specific, Pseudomonas-type.  Members of this protein family are bacterial, phosphatidylcholine-hydrolyzing phospholipase C enzymes, with a characteristic domain architecture as found in hemolytyic (PlcH) and nonhemolytic (PlcN) secreted enzymes of Pseudomonas aeruginosa. PlcH hydrolyzes phosphatidylcholine to diacylglycerol and phosphocholine, but unlike PlcN can also hydrolyze sphingomyelin to ceramide ...
CDD:234197	326	EUKprk	Bacteria:7,Invertebrates:1,Primates:1	TIGR03399, RNA_3prim_cycl, RNA 3'-phosphate cyclase.  Members of this protein family are RNA 3'-phosphate cyclase (6.5.1.4), an enzyme whose function is conserved from E. coli to human. The modification this enzyme performs enables certain RNA ligations to occur, although the full biological roll for this enzyme is not fully described. This model separates this enzyme from a related protein, present only in eukaryotes, localized to the ...
CDD:234198	360	EUK	Invertebrates:9,Plants:11,Vertebrates:2	TIGR03400, 18S_RNA_Rcl1p, 18S rRNA biogenesis protein RCL1.  Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only.
CDD:132443	379	PRK	Bacteria:24	TIGR03402, FeS_nifS, cysteine desulfurase NifS.  Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic ...
CDD:132445	367	EUKprk	Bacteria:5,Plants:8,nodiv:1	TIGR03404, bicupin_oxalic, bicupin, oxalate decarboxylase family.  Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
CDD:213809	174	PRK	Bacteria:11	TIGR03406, FeS_long_SufT, probable FeS assembly SUF system protein SufT.  The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely ...
CDD:132448	359	PRK	Bacteria:14	TIGR03407, urea_ABC_UrtA, urea ABC transporter, urea binding protein.  Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine ...
CDD:132449	313	PRK	Bacteria:13	TIGR03408, urea_trans_UrtC, urea ABC transporter, permease protein UrtC.  Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity [Transport and binding proteins, Amino acids, peptides and amines].
CDD:200272	291	PRK	Bacteria:16	TIGR03409, urea_trans_UrtB, urea ABC transporter, permease protein UrtB.  Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity [Transport and binding proteins, Amino acids, peptides and amines].
CDD:234199	230	PRK	Bacteria:30	TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding protein UrtE.  Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity [Transport and binding proteins, Amino acids, peptides and amines].
CDD:234200	242	PRK	Bacteria:23,nodiv:1	TIGR03411, urea_trans_UrtD, urea ABC transporter, ATP-binding protein UrtD.  Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity [Transport and binding proteins, Amino acids, peptides ...
CDD:132453	63	PRK	Bacteria:27	TIGR03412, iscX_yfhJ, FeS assembly protein IscX.  Members of this protein family are YfhJ, a protein of the ISC system for iron-sulfur cluster assembly. Other genes in the system include iscSUA, hscBA, and fdx [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:234201	248	PRK	Bacteria:56	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase.  Members of this protein family are hydroxyacylglutathione hydrolase, a detoxification enzyme known as glyoxalase II. It follows lactoylglutathione lyase, or glyoxalase I, and acts to remove the toxic metabolite methylglyoxal and related compounds. This protein belongs to the broader metallo-beta-lactamase family (pfam00753) [Cellular processes, Detoxification].
CDD:188316	290	PRK	Bacteria:13,nodiv:1	TIGR03414, ABC_choline_bnd, choline ABC transporter, periplasmic binding protein.  Partial phylogenetic profiling (PMID:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and ...
CDD:234203	226	PRK	Bacteria:21,nodiv:1	TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.  Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA metabolism, DNA replication, recombination, and repair].
CDD:163255	102	EUKprk	Bacteria:16,Plants:1,Primates:2,Synthetic:1	TIGR03421, FeS_CyaY, iron donor protein CyaY.  Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. ...
CDD:132463	97	EUK	Invertebrates:6,Plants:18,Primates:2	TIGR03422, mito_frataxin, frataxin.  Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
CDD:234204	592	PRK	Bacteria:66	TIGR03423, pbp2_mrdA, penicillin-binding protein 2.  Members of this protein family are penicillin-binding protein 2 (PBP-2), a protein whose gene (designated pbpA or mrdA) generally is found next to the gene for RodA, a protein required for rod (bacillus) shape in many bacteria. PBP-2 acts as a transpeptidase for cell elongation (hence, rod-shape) [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].
CDD:132465	198	PRK	Bacteria:16	TIGR03424, urea_degr_1, urea carboxylase-associated protein 1.  A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes.
CDD:163257	233	PRK	Bacteria:19	TIGR03425, urea_degr_2, urea carboxylase-associated protein 2.  A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes.
CDD:234205	154	PRK	Bacteria:66	TIGR03426, shape_MreD, rod shape-determining protein MreD.  Members of this protein family are the MreD protein of bacterial cell shape determination. Most rod-shaped bacteria depend on MreB and RodA to achieve either a rod shape or some other non-spherical morphology such as coil or stalk formation. MreD is encoded in an operon with MreB, and often with RodA and PBP-2 as well. It is highly hydrophobic (therefore somewhat low-complexity) and highly divergent, and ...
CDD:234206	404	EUKprk	Bacteria:5,Plants:20	TIGR03429, arom_pren_DMATS, aromatic prenyltransferase, DMATS type.  Members of this protein family are mostly fungal enzymes of secondary metabolite production. Characterized or partially characterized members include several examples of dimethylallyltryptophan synthase, a brevianamide F prenyltransferase, LtxC from lyngbyatoxin biosynthesis, and a probable dimethylallyl tyrosine synthase.
CDD:132472	288	PRK	Bacteria:10	TIGR03431, PhnD, phosphonate ABC transporter, periplasmic phosphonate binding protein.  This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note ...
CDD:163261	100	PRK	Bacteria:3	TIGR03433, padR_acidobact, transcriptional regulator, Acidobacterial, PadR-family.  Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein.
CDD:234207	803	PRK	Bacteria:4	TIGR03434, ADOP, Acidobacterial duplicated orphan permease.  Members of this protein family are found, so far, only in three species of Acidobacteria, namely Acidobacteria bacterium Ellin345, Acidobacterium capsulatum ATCC 51196, and Solibacter usitatus Ellin6076, where they form large paralogous families. Each protein contains two copies of a domain called the efflux ABC transporter permease protein (pfam02687). However, unlike other members of that family ...
CDD:132476	237	PRK	Bacteria:1	TIGR03435, Soli_TIGR03435, soil-associated protein, TIGR03435 family.  Bacterial reference strains encoding members of this protein family are all isolated from soil. These include 39 members from Solibacter usitatus Ellin6076, 27 from Acidobacterium sp. MP5ACTX8 (both Acidobacteria), and four from Pedosphaera parvula Ellin514 (Verrucomicrobia). The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. A few members are fused to ...
CDD:234208	296	PRK	Bacteria:3	TIGR03436, acidobact_VWFA, VWFA-related Acidobacterial domain.  Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
CDD:234209	215	PRK	Bacteria:1	TIGR03437, Soli_cterm, Solibacter uncharacterized C-terminal domain.  This model describes a protein domain found in 90 proteins of Solibacter usitatus Ellin6076, nearly always as the C-terminal domain of a much larger protein. No homologs to this domain are detected outside of S. usitatus, a member of the Acidobacteria.
CDD:132479	301	PRK	Bacteria:30,Environmental:2	TIGR03438, egtD_ergothio, dimethylhistidine N-methyltransferase.  This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs].
CDD:234210	319	EUK	Plants:11	TIGR03439, methyl_EasF, probable methyltransferase domain, EasF family.  This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan ...
CDD:234211	406	PRK	Bacteria:26	TIGR03440, egtB_TIGR03440, ergothioneine biosynthesis protein EgtB.  Members of this family include EgtB, and enzyme of the ergothioneine biosynthesis, as found in numerous Actinobacteria. Characterized homologs to this family include a formylglycine-generating enzyme that serves as a maturase for an aerobic sulfatase (cf. the radical SAM enzymes that serve as anaerobic sulfatase maturases) [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione ...
CDD:132489	292	PRK	Bacteria:11	TIGR03448, mycothiol_MshD, mycothiol synthase.  Members of this family are MshD, the acetyltransferase that catalyzes the final step of mycothiol biosynthesis in various members of the Actinomyctes, Mycothiol replaces glutathione in these species [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs].
CDD:234215	387	PRK	Bacteria:9,nodiv:1	TIGR03453, partition_RepA, plasmid partitioning protein RepA.  Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme ...
CDD:234216	325	PRK	Bacteria:8,nodiv:1	TIGR03454, partition_RepB, plasmid partitioning protein RepB.  Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they ...
CDD:132496	100	EUKprk	Bacteria:13,Plants:4	TIGR03455, HisG_C-term, ATP phosphoribosyltransferase, C-terminal domain.  This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages.
CDD:234217	485	PRK	Bacteria:20	TIGR03458, YgfH_subfam, succinate CoA transferase.  This family of CoA transferases includes enzymes catalyzing at least two related but distinct activities. The E. coli YgfH protein has been characterized as a propionyl-CoA:succinate CoA transferase where it appears to be involved in a pathway for the decarboxylation of succinate to propionate. The Clostridium kluyveri CAT1 protein has been characterized as a acetyl-CoA:succinate CoA transferase and is believed to ...
CDD:132501	261	PRK	Bacteria:11	TIGR03461, pabC_Proteo, aminodeoxychorismate lyase.  Members of this protein family are aminodeoxychorismate lyase (ADC lyase), EC 4.1.3.38, the PabC protein of PABA biosynthesis. PABA (para-aminobenzoate) is a precursor of folate, needed for de novo purine biosynthesis. This enzyme is a pyridoxal-phosphate-binding protein in the class IV aminotransferase family (pfam01063) [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid].
CDD:234219	89	EUKprk	Bacteria:18,Plants:5	TIGR03462, CarR_dom_SF, lycopene cyclase domain.  This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein , where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain ...
CDD:188327	266	PRK	Bacteria:16	TIGR03464, HpnC, squalene synthase HpnC.  This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have ...
CDD:163278	266	PRK	Bacteria:19	TIGR03465, HpnD, squalene synthase HpnD.  The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ...
CDD:163279	328	PRK	Bacteria:14	TIGR03466, HpnA, hopanoid-associated sugar epimerase.  The sequences in this family are members of the pfam01370 superfamily of NAD-dependent epimerases and dehydratases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene and its association with hopene biosynthesis in ...
CDD:234221	411	PRK	Bacteria:14	TIGR03467, HpnE, squalene-associated FAD-dependent desaturase.  The sequences in this family are members of the pfam01593 superfamily of flavin-containing amine oxidases which include the phytoene desaturases. These sequences also include a FAD-dependent oxidoreductase domain, pfam01266. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of squalene, the condensation product of the ...
CDD:234222	212	PRK	Bacteria:10	TIGR03468, HpnG, hopanoid-associated phosphorylase.  The sequences in this family are members of the pfam01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) ...
CDD:213815	384	PRK	Bacteria:9	TIGR03469, HpnB, hopene-associated glycosyltransferase HpnB.  This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. Indeed, the members of ...
CDD:132512	373	PRK	Bacteria:9	TIGR03472, HpnI, hopanoid biosynthesis associated glycosyl transferase protein HpnI.  This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0974) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes ...
CDD:234223	318	PRK	Bacteria:9	TIGR03476, HpnL, putative membrane protein.  This family of hydrophobic proteins is observed in two distinct contexts. It is primarily found in the presence of genes for the biosynthesis and elaboration of hopene where we assign the gene symbol HpnL. In a subset of the genomes containing HpnL a second, often plasmid-encoded, homolog is observed in a context implying the biosynthesis of 2-aminoethylphosphonate head-group containing lipids.
CDD:234224	205	PRK	Bacteria:7	TIGR03477, DMSO_red_II_gam, DMSO reductase family type II enzyme, heme b subunit.  This model represents a heme b-binding subunit, typically called the gamma subunit, of various proteins that also contain a molybdopterin subunit and an iron-sulfur protein. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide ...
CDD:234225	862	PRK	Bacteria:11	TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter like protein HpnN.  The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.
CDD:234226	198	PRK	Bacteria:8	TIGR03481, HpnM, hopanoid biosynthesis associated membrane protein HpnM.  The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here ...
CDD:234230	457	PRK	Bacteria:10	TIGR03491, TIGR03491, RecB family nuclease, putative, TM0106 family.  Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
CDD:234231	396	PRK	Bacteria:14	TIGR03492, TIGR03492, conserved hypothetical protein.  This protein family is restricted to the Cyanobacteria, in one or two copies, save for instances in the genus Deinococcus. This protein shows some sequence similarity, especially toward the C-terminus, to lipid-A-disaccharide synthase (TIGR00215 or pfam02684). The function is unknown.
CDD:132534	135	PRK	Bacteria:6,Phages:3	TIGR03495, phage_LysB, phage lysis regulatory protein, LysB family.  Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.
CDD:213817	411	PRK	Bacteria:59	TIGR03496, FliI_clade1, flagellar protein export ATPase FliI.  Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more ...
CDD:211826	413	PRK	Bacteria:12	TIGR03497, FliI_clade2, flagellar protein export ATPase FliI.  Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more ...
CDD:163293	418	PRK	Bacteria:3	TIGR03498, FliI_clade3, flagellar protein export ATPase FliI.  Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more ...
CDD:234232	283	PRK	Bacteria:35	TIGR03499, FlhF, flagellar biosynthetic protein FlhF.  [Cellular processes, Chemotaxis and motility].
CDD:234233	69	PRK	Bacteria:48	TIGR03500, FliO_TIGR, flagellar biosynthetic protein FliO.  This short protein found in flagellar biosynthesis operons contains a highly hydrophobic N-terminal sequence followed generally by two basic amino acids. This region is reminiscent of but distinct from the twin-arginine translocation signal sequence. Some instances of this gene have been names "FliZ" but phylogenetic tree building supports a single FliO family.
CDD:200280	22	PRK	Bacteria:85	TIGR03501, GlyGly_CTERM, GlyGly-CTERM domain.  This homology domain, GlyGly-CTERM, shares a species distribution with rhombosortase (TIGR03902), a subfamily of rhomboid-like intramembrane serine proteases. It is probably a recognition sequence for protein sorting and then cleavage by rhombosortase. Shewanella species have the largest number of target proteins per genome, up to thirteen. The domain occurs at the extreme carboxyl-terminus of a diverse set of proteins, ...
CDD:234235	374	PRK	Bacteria:10	TIGR03503, TIGR03503, TIGR03503 family protein.  This set of conserved hypothetical protein has a phylogenetic range that closely matches that of TIGR03501, a putative C-terminal protein targeting signal.
CDD:200281	44	PRK	Bacteria:38	TIGR03504, FimV_Cterm, FimV C-terminal domain.  This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
CDD:132544	74	PRK	Bacteria:5	TIGR03505, FimV_core, FimV N-terminal domain.  This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region ...
CDD:234236	231	PRK	Bacteria:31	TIGR03506, FlgEFG_subfam, flagellar hook-basal body protein.  This model encompasses three closely related flagellar proteins usually denoted FlgE, FlgF and FlgG. The names have often been mis-assigned, however. Three equivalog models, TIGR02489, TIGR02490 and TIGR02488, respectively, separate the individual forms into three genome-context consistent groups. The major differences between these genes are architectural, with variable central sections between ...
CDD:234237	659	PRK	Bacteria:8	TIGR03507, decahem_SO1788, decaheme c-type cytochrome, OmcA/MtrC family.  The protein SO_1778 (MtrC) of Shewanella oneidensis MR-1, and its paralog SO_1779 (OmcA), with which it intteracts, are large decaheme proteins, about 900 amino acids in length, involved in the use of manganese [Mn(III/IV)] and iron [Fe(III)] as terminal electron acceptors. This model represents these and similar decaheme proteins, found also in Rhodoferax ferrireducens DSM 15236, Aeromonas ...
CDD:234238	258	PRK	Bacteria:10	TIGR03508, decahem_SO, decaheme c-type cytochrome, DmsE family.  Members of this family are small, decaheme c-type cytochromes, related DmsE of Shewanella oneidensis MR-1, which has been shown to be part of an anaerobic dimethyl sulfoxide reductase.
CDD:234239	649	PRK	Bacteria:7	TIGR03509, OMP_MtrB_PioB, decaheme-associated outer membrane protein, MtrB/PioB family.  Members of this protein family are integral proteins of the bacterial outer membrane, associated with multiheme c-type cytochromes involved in electron transfer. The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decaheme cytochrome MtrA and large, surface-exposed decaheme cytochrome MtrC ...
CDD:132549	49	PRK	Bacteria:38	TIGR03510, XapX, XapX domain.  This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins [Unknown function, General].
CDD:234240	319	PRK	Bacteria:11	TIGR03514, GldB_lipo, gliding motility-associated lipoprotein GldB.  RN RM PMID:10648514 RT Cloning and characterization of the Flavobacterium johnsoniae gliding-motility genes gldB and gldC. RA Hunnicutt DW, McBride MJ RL J Bacteriol. 2000 Feb;182(4):911-8.
CDD:234242	292	PRK	Bacteria:11	TIGR03519, Bac_Flav_fam_1, Bacteroidetes-specific putative membrane protein.  This model describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this motility.
CDD:234244	194	PRK	Bacteria:19	TIGR03527, selenium_YedF, selenium metabolism protein YedF.  Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium ...
CDD:211833	444	EUKprk	Bacteria:2,Invertebrates:4,Plants:1,Primates:1,Vertebrates:1	TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium transferase.  In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein [Protein synthesis, tRNA aminoacylation].
CDD:234247	284	PRK	Bacteria:4	TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific.  Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:234248	251	PRK	Bacteria:48	TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase, release factor-specific.  Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in ...
CDD:234251	34	PRK	Bacteria:74	TIGR03544, DivI1A_domain, DivIVA domain.  This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
CDD:234252	555	PRK	Bacteria:8	TIGR03545, TIGR03545, TIGR03545 family protein.  This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
CDD:200289	154	PRK	Bacteria:9	TIGR03546, TIGR03546, TIGR03546 family protein.  Members of this family are uncharacterized proteins, usually encoded by a gene adjacent to a member of family TIGR03545, which is also uncharacterized.
CDD:234253	346	PRK	Bacteria:5	TIGR03547, muta_rot_YjhT, mutatrotase, YjhT family.  Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein.
CDD:132589	322	PRK	Bacteria:6	TIGR03550, F420_cofG, 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit.  This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a ...
CDD:132590	343	PRK	Bacteria:3	TIGR03551, F420_cofH, 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit.  This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:234254	195	PRK	Bacteria:19	TIGR03552, F420_cofC, 2-phospho-L-lactate guanylyltransferase.  Members of this protein family are the CofC enzyme of coenzyme F420 biosynthesis [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:234256	323	PRK	Bacteria:79,nodiv:1	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1.  The Pfam domain family pfam00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family pfam00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within pfam00296 [Unknown function, Enzymes of unknown specificity].
CDD:234258	227	PRK	Bacteria:11	TIGR03560, F420_Rv1855c, probable F420-dependent oxidoreductase, Rv1855c family.  Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive ...
CDD:234259	134	PRK	Bacteria:49	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily.  pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein Ohr, or organic hydroperoxide resistance protein [Cellular processes, Detoxification].
CDD:234260	135	PRK	Bacteria:37	TIGR03562, osmo_induc_OsmC, peroxiredoxin, OsmC subfamily.  pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress [Cellular processes, Detoxification].
CDD:234261	265	PRK	Bacteria:7	TIGR03564, F420_MSMEG_4879, F420-dependent oxidoreductase, MSMEG_4879 family.  Coenzyme F420 is produced by methanogenic archaea, a number of the Actinomycetes (including Mycobacterium tuberculosis), and rare members of other lineages. The resulting information-rich phylogenetic profile identifies candidate F420-dependent oxidoreductases within the family of luciferase-like enzymes (pfam00296), where the species range for the subfamily encompasses many F420-positive ...
CDD:211840	174	PRK	Bacteria:9,Synthetic:1	TIGR03566, FMN_reduc_MsuE, FMN reductase, MsuE subfamily.  Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model.
CDD:234262	171	PRK	Bacteria:10	TIGR03567, FMN_reduc_SsuE, FMN reductase, SsuE family.  Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566) [Central ...
CDD:234263	365	EUKprk	Bacteria:54,Invertebrates:1	TIGR03568, NeuC_NnaA, UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing.  This family of enzymes catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine. This is in contrast to the related enzyme WecB (TIGR00236) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate.
CDD:234264	329	PRK	Bacteria:34	TIGR03569, NeuB_NnaB, N-acetylneuraminate synthase.  This family is a subset of the pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
CDD:234265	193	PRK	Bacteria:55	TIGR03570, NeuD_NnaD, sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family.  This family of proteins includes the characterized NeuD sialic acid O-acetyltransferase enzymes from E. coli and Streptococcus agalactiae (group B strep). These two are quite closely related to one another, so extension of this annotation to other members of the family in unsupported without additional independent evidence. The neuD gene is often observed in close proximity ...
CDD:234266	298	PRK	Bacteria:17,nodiv:1	TIGR03571, lucif_BA3436, luciferase-type oxidoreductase, BA3436 family.  This family is a distinct subgroup among members of the luciferase monooxygenase domain family. The larger family contains both FMN-binding enzymes (luciferase, alkane monooxygenase) and F420-binding enzymes (methylenetetrahydromethanopterin reductase, secondary alcohol dehydrogenase, glucose-6-phosphate dehydrogenase). Although some members of the domain family bind coenzyme F420 ...
CDD:132611	232	PRK	Bacteria:6	TIGR03572, WbuZ, glycosyl amidation-associated protein WbuZ.  This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is ...
CDD:234267	343	PRK	Bacteria:8	TIGR03573, WbuX, N-acetyl sugar amidotransferase.  This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In ...
CDD:163336	222	PRK	Bacteria:12	TIGR03584, PseF, pseudaminic acid CMP-transferase.  The sequences in this family include the pfam02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to , this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed ...
CDD:132624	156	PRK	Bacteria:6	TIGR03585, PseH, pseudaminic acid biosynthesis N-acetyl transferase.  Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide ...
CDD:163337	327	PRK	Bacteria:12	TIGR03586, PseI, pseudaminic acid synthase.  Members of this family are included within the larger pfam03102 (NeuB) family. NeuB itself (TIGR03569) is involved in the biosynthesis of neuraminic acid by the condensation of phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine. In an analagous reaction, this enzyme, PseI , condenses PEP with 6-deoxy-beta-L-AltNAc4NAc to generate pseudaminic acid.
CDD:234269	380	PRK	Bacteria:15	TIGR03588, PseC, UDP-4-keto-6-deoxy-N-acetylglucosamine 4-aminotransferase.  This family of enzymes are aminotransferases of the pfam01041 family involved in the biosynthesis of pseudaminic acid. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species.
CDD:234270	279	PRK	Bacteria:12	TIGR03590, PseG, pseudaminic acid biosynthesis-associated protein PseG.  This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid , a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores ...
CDD:234271	684	PRK	Bacteria:3	TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.  Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA].
CDD:234272	181	PRK	Bacteria:122,nodiv:1	TIGR03592, yidC_oxa1_cterm, membrane protein insertase, YidC/Oxa1 family, C-terminal domain.  This model describes full-length from some species, and the C-terminal region only from other species, of the YidC/Oxa1 family of proteins. This domain appears to be univeral among bacteria (although absent from Archaea). The well-characterized YidC protein from Escherichia coli and its close homologs contain a large N-terminal periplasmic domain in addition to ...
CDD:234273	366	PRK	Bacteria:14	TIGR03593, yidC_nterm, membrane protein insertase, YidC/Oxa1 family, N-terminal domain.  Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog ...
CDD:234274	429	PRK	Bacteria:26	TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA.  EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability [Protein synthesis, Other].
CDD:188347	69	PRK	Bacteria:8	TIGR03595, Obg_CgtA_exten, Obg family GTPase CgtA, C-terminal extension.  CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
CDD:213833	276	PRK	Bacteria:32	TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein YlqF.  Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other ...
CDD:213834	360	PRK	Bacteria:6	TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH.  This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli [Protein synthesis, Other].
CDD:213835	178	PRK	Bacteria:26	TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein YsxC/EngB.  Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers ...
CDD:234275	530	PRK	Bacteria:44	TIGR03599, YloV, DAK2 domain fusion protein YloV.  This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of ...
CDD:234277	377	PRK	Bacteria:22	TIGR03604, TOMM_cyclo_SagD, thiazole/oxazole-forming peptide maturase, SagD family component.  Members of this protein family include enzymes related to SagD, previously referred to as a scaffold or docking protein involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Newer evidence describes an enzymatic activity, an ATP-dependent cyclodehydration reaction, previously ascribed to the SagC ...
CDD:188352	173	PRK	Bacteria:14	TIGR03605, antibiot_sagB, SagB-type dehydrogenase domain.  SagB of Sterptococcus pyogenes participates in the maturation of streptolysin S from a ribosomally produced precursor polypeptide. Chemically similar systems operate on highly diverse sets of bacteriocin precursors in numerous other bacteria. This model describes a domain within SgaB and homologous regions from other proteins, many of which appear to be involved in biosynthesis of secondary metabolites. ...
CDD:234279	739	PRK	Bacteria:13	TIGR03607, TIGR03607, patatin-related protein.  This bacterial protein family contains an N-terminal patatin domain, where patatins are plant storage proteins capable of phospholipase activity (see pfam01734). Regions of strong sequence conservation are separated by regions of significant sequence and length variability. Members of the family are distributed sporadically among bacteria. The function is unknown [Unknown function, General].
CDD:188353	206	PRK	Bacteria:10	TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC transporter, lactococcin 972 group.  A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins ...
CDD:132648	298	PRK	Bacteria:21	TIGR03609, S_layer_CsaB, polysaccharide pyruvyl transferase CsaB.  The CsaB protein (cell surface anchoring B) of Bacillus anthracis adds a pyruvoyl group to peptidoglycan-associated polysaccharide. This addition is required for proteins with an S-layer homology domain (pfam00395) to bind. Within the larger group of proteins described by pfam04230, this model represents a distinct clade that nearly exactly follows the phylogenetic distribution of the S-layer ...
CDD:234280	117	PRK	Bacteria:15	TIGR03618, Rv1155_F420, PPOX class probable F420-dependent enzyme.  A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was ...
CDD:234281	246	PRK	Bacteria:12	TIGR03619, F420_Rv2161c, probable F420-dependent oxidoreductase, Rv2161c family.  Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive ...
CDD:234282	278	PRK	Bacteria:9	TIGR03620, F420_MSMEG_4141, probable F420-dependent oxidoreductase, MSMEG_4141 family.  Members of this protein family, related to F420-dependent oxidoreductases within the larger family of a bacterial luciferase (an FMN-dependent enzyme), occurs only within the small subset of species that synthesize F420. Most such proteins are from members of the Actinobacteria, but at least one species, Sphingomonas wittichii, belongs to the Alphaproteobacteria [Unknown ...
CDD:200301	295	PRK	Bacteria:11	TIGR03621, F420_MSMEG_2516, probable F420-dependent oxidoreductase, MSMEG_2516 family.  Coenzyme F420 is produced by methanogenic archaea, a number of the Actinomycetes (including Mycobacterium tuberculosis), and rare members of other lineages. The resulting information-rich phylogenetic profile identifies candidate F420-dependent oxidoreductases within the family of luciferase-like enzymes (pfam00296), where the species range for the subfamily encompasses many ...
CDD:234283	874	PRK	Bacteria:13	TIGR03623, TIGR03623, probable DNA repair protein.  Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins.
CDD:234284	346	PRK	Bacteria:14	TIGR03624, TIGR03624, putative hydrolase.  Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown [Unknown function, General].
CDD:234285	202	PRK	Bacteria:34	TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial.  This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to Pfam family pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here.
CDD:234286	330	PRK	Bacteria:1	TIGR03626, L3_arch, archaeal ribosomal protein L3.  This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to Pfam family pfam00297. Eukaryotic proteins are excluded from this model [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:213839	144	PRK	Bacteria:1	TIGR03629, arch_S13P, archaeal ribosomal protein S13P.  This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:132669	102	PRK	Bacteria:14	TIGR03630, arch_S17P, archaeal ribosomal protein S17P.  This model describes exclusively the archaeal ribosomal protein S17P. It excludes the homologous ribosomal protein S17 from bacteria, and is not intended for use on eukaryotic sequences, where some instances of ribosomal proteins S11 score above the trusted cutoff [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:213840	113	PRK	Bacteria:3	TIGR03631, bact_S13, 30S ribosomal protein S13.  This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:188357	108	PRK	Bacteria:2	TIGR03632, bact_S11, 30S ribosomal protein S11.  This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:163366	224	PRK	Bacteria:4	TIGR03633, arc_protsome_A, proteasome endopeptidase complex, archaeal, alpha subunit.  This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:234287	185	PRK	Bacteria:20	TIGR03634, arc_protsome_B, proteasome endopeptidase complex, archaeal, beta subunit.  This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:213841	71	PRK	Bacteria:39	TIGR03635, S17_bact, 30S ribosomal protein S17.  This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17 [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:132675	77	PRK	Bacteria:21	TIGR03636, L23_arch, archaeal ribosomal protein L23.  This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:234288	268	PRK	Bacteria:13	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI.  The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular ...
CDD:234289	278	PRK	Bacteria:18	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI.  The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular ...
CDD:188360	340	PRK	Bacteria:20	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG.  The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular ...
CDD:234290	320	PRK	Bacteria:16	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP.  The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by ...
CDD:132682	72	PRK	Bacteria:19,Synthetic:1	TIGR03643, TIGR03643, TIGR03643 family protein.  This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies [Hypothetical proteins, Conserved].
CDD:132686	77	PRK	Bacteria:32	TIGR03647, Na_symport_sm, putative solute:sodium symporter small subunit.  Members of this family are highly hydrophobic bacterial proteins of about 90 amino acids in length. Members usually are found immediately upstream (sometimes fused to) a member of the solute:sodium symporter family, and therefore are a putative sodium:solute symporter small subunit. Members tend to be found in aquatic species, especially those from marine or other high salt environments ...
CDD:234293	552	PRK	Bacteria:31	TIGR03648, Na_symport_lg, probable sodium:solute symporter, VC_2705 subfamily.  This family belongs to a larger family of transporters of the sodium:solute symporter superfamily, TC 2.A.21. Members of this strictly bacterial protein subfamily are found almost invariably immediately downstream from a member of family TIGR03647. Occasionally, the two genes are fused.
CDD:234294	285	EUK	Plants:8	TIGR03649, ergot_EASG, ergot alkaloid biosynthesis protein, AFUA_2G17970 family.  This family consists of fungal proteins of unknown function associated with secondary metabolite biosynthesis, such as of the ergot alkaloids such as ergovaline. Nomenclature differs because gene order differs - this is EasG in Neotyphodium lolii but is designated ergot alkaloid biosynthetic protein A in several other fungi.
CDD:234295	216	PRK	Bacteria:18	TIGR03652, FeS_repair_RIC, iron-sulfur cluster repair di-iron protein.  Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:234296	170	PRK	Bacteria:4	TIGR03653, arch_L6P, archaeal ribosomal protein L6P.  Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:213843	175	PRK	Bacteria:23	TIGR03654, L6_bact, ribosomal protein L6, bacterial type.  [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:132694	53	PRK	Bacteria:9,Phages:5	TIGR03655, anti_R_Lar, restriction alleviation protein, Lar family.  Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes [Mobile and extrachromosomal element functions, Prophage functions, DNA metabolism, ...
CDD:234298	289	PRK	Bacteria:18	TIGR03659, IsdE, heme ABC transporter, heme-binding protein isdE.  This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron.
CDD:132699	137	PRK	Bacteria:8	TIGR03660, T1SS_rpt_143, T1SS-143 repeat domain.  This model represents a domain of about 143 amino acids that may occur singly or in up to 23 tandem repeats in very large proteins in the genus Vibrio, and in related species such as Legionella pneumophila, Photobacterium profundum, Rhodopseudomonas palustris, Shewanella pealeana, and Aeromonas hydrophila. Proteins with these domains represent a subset of a broader set of proteins with a particular signal for type 1 ...
CDD:234299	89	PRK	Bacteria:11	TIGR03661, T1SS_VCA0849, type I secretion C-terminal target domain (VC_A0849 subclass).  This model represents a C-terminal domain associated with secretion by type 1 secretion systems (T1SS). Members of this subclass do not include the RtxA toxin of Vibrio cholerae and its homologs, although the two classes of proteins share large size, occurrence in genomes with T1SS, regions with long tandem repeats, and regions with the glycine-rich repeat modeled by pfam00353 ...
CDD:234300	723	PRK	Bacteria:7	TIGR03662, Chlor_Arch_YYY, Chlor_Arch_YYY domain.  Members of this highly hydrophobic probable integral membrane family belong to two classes. In one, a single copy of the region modeled by This model represents essentially the full length of a strongly hydrophobic protein of about 700 to 900 residues (variable because of long inserts in some). The domain architecture of the other class consists of an additional N-terminal region, two copies of the region ...
CDD:234302	222	PRK	Bacteria:16	TIGR03664, fut_nucase, futalosine nucleosidase.  This enzyme catalyzes the conversion of futalosine to de-hypoxanthine futalosine in a pathway for the biosynthesis of menaquinone distinct from the pathway observed in E. coli.
CDD:211858	172	PRK	Bacteria:4	TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein.  This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
CDD:234303	132	PRK	Bacteria:11	TIGR03666, Rv2061_F420, PPOX class probable F420-dependent enzyme, Rv2061 family.  A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme ...
CDD:234304	408	PRK	Bacteria:21	TIGR03671, cca_archaeal, CCA-adding enzyme.  
CDD:234305	251	PRK	Bacteria:17	TIGR03672, rpl4p_arch, 50S ribosomal protein L4P.  One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
CDD:234306	338	PRK	Bacteria:23	TIGR03674, fen_arch, flap structure-specific endonuclease.  Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA.
CDD:188365	630	PRK	Bacteria:14	TIGR03675, arCOG00543, arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein.  This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
CDD:234307	357	EUKprk	Bacteria:8,Plants:1	TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and eukaryotic forms.  Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1 [Protein synthesis, Translation factors].
CDD:188368	218	PRK	Bacteria:12	TIGR03679, arCOG00187, arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein.  This protein consists of an N-terminal possible metal-binding domain (pfam04068) followed by a 4Fe-4S cluster binding domain (pfam00037) followed by a C-terminal ABC transporter, ATP-binding domain (pfam00005). This combination of N-terminal domains is observed in the RNase L inhibitor, RLI. This model has the same scope ...
CDD:234308	308	PRK	Bacteria:9	TIGR03682, arCOG04112, diphthamide biosynthesis enzyme Dph2.  Members of this family are the archaeal protein Dph2, members of the universal archaeal protein family designated arCOG04112. The chemical function of this protein is analogous to the radical SAM family (pfam04055), although the sequence is not homologous. The chemistry involves [4Fe-4S]-aided formation of a 3-amino-3-carboxypropyl radical rather than the canonical 5'-deoxyadenosyl radical of the radical ...
CDD:234309	902	PRK	Bacteria:2	TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase.  This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
CDD:234310	150	PRK	Bacteria:3	TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain protein.  This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
CDD:234311	105	PRK	Bacteria:3	TIGR03685, L12P_arch, 50S ribosomal protein L12P.  This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
CDD:211862	171	PRK	Bacteria:4	TIGR03692, ATP_dep_HslV, ATP-dependent protease HslVU, peptidase subunit.  The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:234314	241	PRK	Bacteria:7	TIGR03694, exosort_acyl, N-acyl amino acid synthase, PEP-CTERM/exosortase system-associated.  Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting. PSI-BLAST and CDD reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase, and recent work shows long-chain N-acyl amino acid biosynthesis activity. Several ...
CDD:234315	252	PRK	Bacteria:22	TIGR03695, menH_SHCHC, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase.  This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase [Biosynthesis of cofactors, prosthetic groups, and ...
CDD:234316	76	EUKprk	Bacteria:131,Invertebrates:4,Plants:6,nodiv:1	TIGR03696, Rhs_assc_core, RHS repeat-associated core domain.  This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or ...
CDD:163410	107	PRK	Bacteria:7	TIGR03698, clan_AA_DTGF, clan AA aspartic protease, AF_0612 family.  Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria [Protein fate, Degradation of proteins, peptides, and glycopeptides].
CDD:163411	340	PRK	Bacteria:11	TIGR03699, mena_SCO4550, menaquinone biosynthesis protein, SCO4550 family.  members of this protein family are involved in menaquinone biosynthesis by an alternate pathway via futalosine [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone].
CDD:163413	433	PRK	Bacteria:16	TIGR03701, mena_SCO4490, menaquinone biosynthesis decarboxylase, SCO4490 family.  Members of this protein family are putative decarboxylases involved in a late stage of the alternative pathway for menaquinone, via futalosine, as in Streptomyces coelicolor and Helicobacter pylori [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone].
CDD:234317	799	PRK	Bacteria:7	TIGR03703, plsB, glycerol-3-phosphate O-acyltransferase.  Members of this protein family are PlsB, glycerol-3-phosphate O-acyltransferase, present in E. coli and numerous related species. In many bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system [Fatty acid and phospholipid metabolism, Biosynthesis].
CDD:234319	672	PRK	Bacteria:5	TIGR03705, poly_P_kin, polyphosphate kinase 1.  Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2 [Central intermediary metabolism, ...
CDD:234320	300	PRK	Bacteria:44,nodiv:1	TIGR03706, exo_poly_only, exopolyphosphatase.  It appears that a single enzyme may act as both exopolyphosphatase (Ppx) and guanosine pentaphosphate phosphohydrolase (GppA) in a number of species. Members of the seed alignment use to define this exception-level model are encoded adjacent to a polyphosphate kinase 1 gene, and the trusted cutoff is set high enough (425) that no genome has a second hit. Therefore all members may be presumed to at least share ...
CDD:213852	230	PRK	Bacteria:27	TIGR03707, PPK2_P_aer, polyphosphate kinase 2, PA0141 family.  Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by pfam03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate ...
CDD:234321	493	PRK	Bacteria:11	TIGR03708, poly_P_AMP_trns, polyphosphate:AMP phosphotransferase.  Members of this protein family contain a domain duplication. The characterized member from Acinetobacter johnsonii is polyphosphate:AMP phosphotransferase (PAP), which can transfer the terminal phosphate from poly(P) to AMP, yielding ADP. In the opposite direction, this enzyme can synthesize poly(P). Each domain of this protein family is homologous to polyphosphate kinase, an enzyme that can run in ...
CDD:234322	264	PRK	Bacteria:35	TIGR03709, PPK2_rel_1, polyphosphate:nucleotide phosphotransferase, PPK2 family.  Members of this protein family belong to the polyphosphate kinase 2 (PPK2) family, which is not related in sequence to PPK1. While PPK1 tends to act in the biosynthesis of polyphosphate, or poly(P), members of the PPK2 family tend to use the terminal phosphate of poly(P) to regenerate ATP or GTP from the corresponding nucleoside diphosphate, or ADP from AMP as is the case with ...
CDD:234323	562	PRK	Bacteria:50	TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha subunit.  This family of proteins contains a C-terminal thiamine diphosphate (TPP) binding domain typical of flavodoxin/ferredoxin oxidoreductases (pfam01855) as well as an N-terminal domain similar to the gamma subunit of the same group of oxidoreductases (pfam01558). The genes represented by this model are always found in association with a neighboring gene for a beta subunit (TIGR02177) which also ...
CDD:163423	135	PRK	Bacteria:8	TIGR03711, acc_sec_asp3, accessory Sec system protein Asp3.  This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the ...
CDD:211867	23	PRK	Bacteria:57,nodiv:2	TIGR03715, KxYKxGKxW, KxYKxGKxW signal peptide.  This model describes a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK and PEP-CTERM forms of signal peptide. This domain tends to occur on long, low-complexity (usually Serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C-terminus.
CDD:234326	215	PRK	Bacteria:17	TIGR03716, R_switched_YkoY, integral membrane protein, YkoY family.  Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family often are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains proteins YceF and YkoY from Bacillus subtilis. A ...
CDD:163429	176	PRK	Bacteria:21,nodiv:1	TIGR03717, R_switched_YjbE, integral membrane protein, YjbE family.  Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family commonly are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains protein YjbE from Bacillus subtilis. A ...
CDD:234327	302	PRK	Bacteria:42	TIGR03718, R_switched_Alx, integral membrane protein, TerC family.  Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family often are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains TerC itself from Alcaligenes sp. plasmid IncHI2 pMER610 ...
CDD:163431	552	PRK	Bacteria:2,Synthetic:1	TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.  Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a ...
CDD:234329	322	PRK	Bacteria:19	TIGR03722, arch_KAE1, universal archaeal protein Kae1.  This family represents the archaeal protein Kae1. Its partner Bud32 is fused with it in about half of the known archaeal genomes. The pair, which appears universal in the archaea, corresponds to EKC/KEOPS complex in eukaryotes. A recent characterization of the member from Pyrococcus abyssi, as an iron-binding, atypical DNA-binding protein with an apurinic lyase activity, challenges the common annotation of ...
CDD:234330	314	PRK	Bacteria:48	TIGR03723, T6A_YgjD, tRNA threonylcarbamoyl adenosine modification protein YgjD.  This model represents bacterial members of a protein family that is widely distributed. In a few pathogenic species, the protein is exported in a way that may represent an exceptional secondary function. This model plus companion (archaeal) model TIGR03722 together span the prokaryotic member sequences of TIGR00329, a protein family that appears universal in life, and whose broad ...
CDD:234331	199	PRK	Bacteria:10	TIGR03724, arch_bud32, Kae1-associated kinase Bud32.  Members of this protein family are the Bud32 protein associated with Kae1 (kinase-associated endopeptidase 1) in the Archaea. In many Archaeal genomes, Kae1 and Bud32 are fused. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex, an apparently ancient protein kinase-containing molecular machine [Unknown function, General].
CDD:234332	202	PRK	Bacteria:206,Synthetic:1	TIGR03725, T6A_YeaZ, tRNA threonylcarbamoyl adenosine modification protein YeaZ.  This family describes a protein family, YeaZ, now associated with the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family may occur as fusions with ygjD (previously gcp) or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI [Protein synthesis, tRNA and rRNA base modification].
CDD:211870	34	PRK	Bacteria:9	TIGR03726, strep_RK_lipo, putative cross-wall-targeting lipoprotein signal.  The YSIRK signal domain targets proteins to the cross-wall, or septum, of dividing Gram-positive bacterial. Lipoprotein signal motifs direct a characteristic N-terminal cleavage and lipid modification for membrane anchoring. This Streptococcal-only signal peptide variant appears to be a hybrid between the two, likely directing protein targeting of nascent surface lipoproteins to the ...
CDD:163440	265	PRK	Bacteria:9	TIGR03728, glyco_access_1, glycosyltransferase, SP_1767 family.  Members of this protein family are putative glycosyltransferases. Some members are found close to genes for the accessory secretory (SecA2) system, and are suggested by Partial Phylogenetic Profiling to correlate with SecA2 systems. Glycosylation, therefore, may occur in the cytosol prior to secretion.
CDD:163441	239	PRK	Bacteria:13	TIGR03729, acc_ester, putative phosphoesterase.  Members of this protein family belong to the larger family pfam00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system.
CDD:163442	273	PRK	Bacteria:7	TIGR03730, tungstate_WtpA, tungstate ABC transporter binding protein WtpA.  Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. ...
CDD:234334	48	PRK	Bacteria:14	TIGR03731, lantibio_gallid, lantibiotic, gallidermin/nisin family.  Members of this family are lantibiotic precursors in the family that includes gallidermin, nisin, mutacin, epidermin, and streptin [Cellular processes, Toxin production and resistance].
CDD:234335	241	PRK	Bacteria:11	TIGR03732, lanti_perm_MutE, lantibiotic protection ABC transporter permease subunit, MutE/EpiE family.  Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family is largely restricted to gallidermin-family lantibiotic cassettes, but also include orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. In most species, this subunit is ...
CDD:163445	248	PRK	Bacteria:10	TIGR03733, lanti_perm_MutG, lantibiotic protection ABC transporter permease subunit, MutG family.  Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family is largely restricted to gallidermin-family lantibiotic cassettes, but also include orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. In most species, this subunit is ...
CDD:234336	554	PRK	Bacteria:9	TIGR03734, PRTRC_parB, PRTRC system ParB family protein.  A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
CDD:163447	192	PRK	Bacteria:7	TIGR03735, PRTRC_A, PRTRC system protein A.  A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
CDD:163448	244	PRK	Bacteria:8	TIGR03736, PRTRC_ThiF, PRTRC system ThiF family protein.  A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This family is the PRTRC system ThiF family protein.
CDD:234337	228	PRK	Bacteria:9	TIGR03737, PRTRC_B, PRTRC system protein B.  A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This protein family is designated protein B.
CDD:163453	104	PRK	Bacteria:11	TIGR03741, PRTRC_E, PRTRC system protein E.  A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. This model does not include the low-complexity region.
CDD:234338	342	PRK	Bacteria:9	TIGR03742, PRTRC_F, PRTRC system protein F.  A novel genetic system characterized by seven (usually) major proteins, including a ParB homolog and a ThiF homolog, is commonly found on plasmids or in bacterial chromosomal regions near phage, plasmid, or transposon markers. It is most common among the beta Proteobacteria. We designate the system PRTRC, or ParB-Related,ThiF-Related Cassette. This protein family is designated protein F. It is the most divergent of the families.
CDD:234339	634	PRK	Bacteria:23	TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL subfamily.  Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains [Mobile and extrachromosomal element ...
CDD:234340	893	PRK	Bacteria:12	TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706 family.  Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, ...
CDD:234341	104	PRK	Bacteria:15	TIGR03745, conj_TIGR03745, integrating conjugative element membrane protein, PFL_4702 family.  Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163458	202	PRK	Bacteria:15	TIGR03746, conj_TIGR03746, integrating conjugative element protein, PFL_4703 family.  Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163459	233	PRK	Bacteria:18	TIGR03747, conj_TIGR03747, integrating conjugative element membrane protein, PFL_4697 family.  Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163460	105	PRK	Bacteria:18	TIGR03748, conj_PilL, conjugative transfer region protein, TIGR03748 family.  This model describes the conserved N-terminal region of a variable length protein family associated with laterally transfered regions flanked by markers of conjugative plasmid integration and/or transposition. Most members of the family have the lipoprotein signal peptide motif. A member of the family from a pathogenicity island in Salmonella enterica serovar Dublin strain was designated ...
CDD:163461	257	PRK	Bacteria:21	TIGR03749, conj_TIGR03749, integrating conjugative element protein, PFL_4704 family.  Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163462	111	PRK	Bacteria:24	TIGR03750, conj_TIGR03750, conjugative transfer region protein, TIGR03750 family.  Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:200321	124	PRK	Bacteria:15	TIGR03751, conj_TIGR03751, conjugative transfer region lipoprotein, TIGR03751 family.  Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:234342	472	PRK	Bacteria:19	TIGR03752, conj_TIGR03752, integrating conjugative element protein, PFL_4705 family.  Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:234343	259	PRK	Bacteria:36,Environmental:9	TIGR03753, blh_monoox, beta-carotene 15,15'-monooxygenase, Brp/Blh family.  This integral membrane protein family includes Brp (bacterio-opsin related protein) and Blh (Brp-like protein). Bacteriorhodopsin is a light-driven proton pump with a covalently bound retinal cofactor that appears to be derived beta-carotene. Blh has been shown to cleave beta-carotene to product two all-trans retinal molecules. Mammalian enzymes with similar enzymatic ...
CDD:234345	418	PRK	Bacteria:19	TIGR03755, conj_TIGR03755, integrating conjugative element protein, PFL_4711 family.  Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:234346	297	PRK	Bacteria:17	TIGR03756, conj_TIGR03756, integrating conjugative element protein, PFL_4710 family.  Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163469	113	PRK	Bacteria:15	TIGR03757, conj_TIGR03757, integrating conjugative element protein, PFL_4709 family.  Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163470	65	PRK	Bacteria:12	TIGR03758, conj_TIGR03758, integrating conjugative element protein, PFL_4701 family.  Members of this family of small, hydrophobic proteins are found occasionally on plasmids such as the Pseudomonas putida TOL (toluene catabolic) plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:234347	200	PRK	Bacteria:18	TIGR03759, conj_TIGR03759, integrating conjugative element protein, PFL_4693 family.  Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown [Mobile and extrachromosomal element functions, Plasmid functions].
CDD:163472	218	PRK	Bacteria:11	TIGR03760, ICE_TraI_Pfluor, integrating conjugative element relaxase, PFL_4751 family.  Members of this protein family are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. This model represents the N-terminal domain. Note that no homology is detected to the similarly named TraI relaxase of the F plasmid.
CDD:234348	216	PRK	Bacteria:16	TIGR03761, ICE_PFL4669, integrating conjugative element protein, PFL_4669 family.  Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
CDD:213858	258	PRK	Bacteria:14	TIGR03764, ICE_PFGI_1_parB, integrating conjugative element, PFGI_1 class, ParB family protein.  Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
CDD:234349	105	PRK	Bacteria:33	TIGR03765, ICE_PFL_4695, integrating conjugative element protein, PFL_4695 family.  This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
CDD:234350	483	PRK	Bacteria:14	TIGR03766, TIGR03766, conserved hypothetical integral membrane protein.  Models TIGR03110, TIGR03111, and TIGR03112 describe a three-gene system found in several Gram-positive bacteria, where TIGR03110 (XrtG) is distantly related to a putative transpeptidase, exosortase (TIGR02602). This model describes a small clade that correlates by both gene clustering and phyletic pattern, although imperfectly, to the three gene system. Both this narrow clade, and the larger ...
CDD:211874	41	PRK	Bacteria:14	TIGR03769, P_ac_wall_RPT, actinobacterial surface-anchored protein domain.  This model describes a repeat domain that one to three times in Actinobacterial proteins, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. Where it occurs with duplication in an LPXTG-anchored protein, it tends to be adjacent to the substrate-binding protein of the gene trio of an ABC transporter system, where that ...
CDD:213860	32	PRK	Bacteria:4	TIGR03777, RPE4, Rickettsial palindromic element RPE4 domain.  This model describes protein translations of a family, RPE4, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else.
CDD:213861	24	PRK	Bacteria:1	TIGR03778, VPDSG_CTERM, VPDSG-CTERM protein sorting domain.  Through in silico analysis, we previously described the PEP-CTERM/exosortase system (PMID:16930487). This model describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C-terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif (TIGR02595) of typical exosortase systems and the ...
CDD:234352	410	PRK	Bacteria:6	TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM protein.  Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage [Cellular processes, DNA transformation].
CDD:163492	285	PRK	Bacteria:5	TIGR03780, Bac_Flav_CT_N, Bacteroides conjugative transposon TraN protein.  Members of this family are the TraN protein encoded by transfer region genes of conjugative transposons of Bacteroides. The family is related to conjugative transfer proteins VirB9 and TrbG of Agrobacterium Ti plasmids [Cellular processes, DNA transformation].
CDD:163496	174	PRK	Bacteria:9	TIGR03784, marine_sortase, sortase, marine proteobacterial type.  Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with ...
CDD:188386	63	PRK	Bacteria:11	TIGR03786, strep_pil_rpt, streptococcal pilin isopeptide linkage domain.  This model describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The S. pyogenes major pilin has been shown to undergo isopeptide bond ...
CDD:234353	596	PRK	Bacteria:8	TIGR03788, marine_srt_targ, marine proteobacterial sortase target protein.  Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. ...
CDD:234355	316	PRK	Bacteria:14	TIGR03790, TIGR03790, TIGR03790 family protein.  Despite a broad and sporadic distribution (Cyanobacteria, Verrucomicrobia, Acidobacteria, beta and delta Proteobacteria, and Planctomycetes), this uncharacterized protein family occurs only among the roughly 8 percent of prokarotyic species that carry homologs of the integral membrane protein exosortase (see TIGR02602), a proposed protein-sorting system transpeptidase.
CDD:163504	90	PRK	Bacteria:23	TIGR03792, TIGR03792, uncharacterized cyanobacterial protein, TIGR03792 family.  Members of this family are found, no more than one to a genome, exclusively in (but not universal to) the Cyanobacteria. These proteins are small, 100-150 amino acids. The function is unknown [Unknown function, General].
CDD:234356	77	PRK	Bacteria:6	TIGR03793, TOMM_pelo, NHLP leader peptide domain.  This model represents a domain that is conserved among a large number of putative ribosomal natural products (RNP) precursor, including the thiazole/oxazole-modified microcins (TOMMs). As a leader peptide domain, likely to be removed from the mature product, this domain is unusual in several ways. First, it is longer than most previously described RNP leader peptides. Second, most of the domain is homologous to ...
CDD:163508	710	PRK	Bacteria:14	TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein.  This protein describes a multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows ...
CDD:234357	686	PRK	Bacteria:12	TIGR03797, NHLM_micro_ABC2, NHLM bacteriocin system ABC transporter, ATP-binding protein.  Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal leader sequence cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, members of protein families related to nitrile hydratase alpha ...
CDD:234358	64	PRK	Bacteria:9	TIGR03798, ocin_TIGR03798, nif11-like leader peptide domain.  This model describes a conserved, fairly long (about 65 residue) leader peptide region for a family of putative ribosomal natural products (RNP) of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain [Cellular processes, Biosynthesis of ...
CDD:163513	521	PRK	Bacteria:2	TIGR03801, asp_4_decarbox, aspartate 4-decarboxylase.  This enzyme, aspartate 4-decarboxylase (EC 4.1.1.12), removes the side-chain carboxylate from L-aspartate, converting it to L-alanine plus carbon dioxide. It is a PLP-dependent enzyme, homologous to aspartate aminotransferase (EC 2.6.1.1) [Energy metabolism, Amino acids and amines].
CDD:234359	562	PRK	Bacteria:10	TIGR03802, Asp_Ala_antiprt, aspartate-alanine antiporter.  All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
CDD:213862	34	PRK	Bacteria:3	TIGR03803, Gloeo_Verruco, Gloeo_Verruco repeat.  This model describes a rare protein repeat, found so far in two species of Verrucomicrobia (Chthoniobacter flavus and Verrucomicrobium spinosum) and in four different proteins of Gloeobacter violaceus PCC7421. In the Verrucomicrobial species, the repeat region is followed by a PEP-CTERM protein-sorting signal, suggesting an extracellular location.
CDD:234360	44	PRK	Bacteria:13	TIGR03804, para_beta_helix, parallel beta-helix repeat (two copies).  This model represents a tandem pair of an approximately 22-amino acid (each) repeat homologous to the beta-strand repeats that stack in a right-handed parallel beta-helix in the periplasmic C-5 mannuronan epimerase, AlgA, of Pseudomonas aeruginosa. A homology domain consisting of a longer tandem array of these repeats is described in the SMART database as CASH (SM00722), and is found in many ...
CDD:163517	314	PRK	Bacteria:8	TIGR03805, beta_helix_1, parallel beta-helix repeat-containing protein.  Members of this protein family contain a tandem pair of beta-helix repeats (see TIGR03804). Each repeat is expected to consist of three beta strands that form a single turn as they form a right-handed helix of stacked beta-structure. Member proteinsa occur regularly in two-gene pairs along with another uncharacterized protein family; both protein families exhibit either lipoprotein or regular ...
CDD:163518	317	PRK	Bacteria:8	TIGR03806, chp_HNE_0200, conserved hypothetical protein, HNE_0200 family.  The model TIGR03805 describes an uncharacterized protein family that contains repeats associated with the formation of a right-handed helical stack of parallel beta strands, homologous to those found in a number of carbohydrate-binding proteins and sugar hydrolases. This model describes another uncharacterized protein family, found in the same species as TIGR03805 member proteins, usually as ...
CDD:234362	300	PRK	Bacteria:24	TIGR03814, Gln_ase, glutaminase A.  This family describes the enzyme glutaminase, from a larger family that includes serine-dependent beta-lactamases and penicillin-binding proteins. Many bacteria have two isozymes. This model is based on selected known glutaminases and their homologs within prokaryotes, with the exclusion of highly-derived (long branch) and architecturally varied homologs, so as to achieve conservative assignments. A sharp drop in scores occurs ...
CDD:234363	322	PRK	Bacteria:15	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein.  Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PMID:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer ...
CDD:234364	109	PRK	Bacteria:15	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein.  Members of this small, highly hydrophobic protein family occur in a pilus/secretion-like region that usually is next to an uncharacterized DEAH-box helicase, in Actinobacteria. Members show sequence similarity to the TadE-like family described by pfam07811. The function is unknown [Unknown function, General].
CDD:213866	282	PRK	Bacteria:24	TIGR03818, MotA1, flagellar motor stator protein MotA.  The MotA protein, along with its partner MotB, comprise the stator complex of the bacterial flagellar motor. MotAB span the cytoplasmic membrane and undergo conformational changes powered by the translocation of protons. These conformational changes in turn are communicated to the rotor assembly, producing torque. This model represents one family of MotA proteins which are often not identified by the ...
CDD:200328	340	PRK	Bacteria:14	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.  Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.
CDD:163533	321	PRK	Bacteria:14	TIGR03821, AblA_like_1, lysine-2,3-aminomutase-like protein.  Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in E. coli, Buchnera, Yersinia, etc.
CDD:213867	96	PRK	Bacteria:61	TIGR03824, FlgM_jcvi, flagellar biosynthesis anti-sigma factor FlgM.  FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain.
CDD:163538	137	PRK	Bacteria:10	TIGR03826, YvyF, flagellar operon protein TIGR03826.  This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
CDD:163539	266	PRK	Bacteria:17	TIGR03827, GNAT_ablB, putative beta-lysine N-acetyltransferase.  Members of this protein family are GNAT family acetyltransferases, based on a seed alignment in which every member is associated with a lysine 2,3-aminomutase family protein, usually as the adjacent gene. This family includes AblB, the enzyme beta-lysine acetyltransferase that completes the two-step synthesis of the osmolyte (compatible solute) N-epsilon-acetyl-beta-lysine; all members of the family ...
CDD:234367	304	miss	miss	TIGR03828, pfkB, 1-phosphofructokinase.  This enzyme acts in concert with the fructose-specific phosphotransferase system (PTS) which imports fructose as fructose-1-phosphate. The action of 1-phosphofructokinase results in beta-D-fructose-1,6-bisphosphate and is an entry point into glycolysis (GenProp0688).
CDD:163542	127	PRK	Bacteria:39	TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix protein, YgiT family.  This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted ...
CDD:163543	46	PRK	Bacteria:54,Environmental:3	TIGR03831, YgiT_finger, YgiT-type zinc finger domain.  This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
CDD:163545	62	PRK	Bacteria:20	TIGR03833, TIGR03833, conserved hypothetical protein.  A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the ...
CDD:213869	28	PRK	Bacteria:10	TIGR03834, EAGR_box, EAGR box.  The EAGR box (Enriched in Aromatic and Glycine Residues) is found in three different proteins of the Mycoplasma genitalium terminal organelle, which acts in both cytadherence and gliding motility. The presence of this domain in a genome predicts the Mycoplasma-type terminal organelle structure, gliding motility, and cytadherence. The EAGR box may occur from one to nine times in a protein.
CDD:234369	371	PRK	Bacteria:30	TIGR03837, efp_adjacent_2, conserved hypothetical protein, PP_1857 family.  This model describes a conserved hypothetical protein that typically is encoded next to the gene efp for translation elongation factor P. The function is unknown.
CDD:234370	271	PRK	Bacteria:24	TIGR03838, queuosine_YadB, glutamyl-queuosine tRNA(Asp) synthetase.  This protein resembles a shortened glutamyl-tRNA ligase, but its purpose is to modify tRNA(Asp) at a queuosine position in the anticodon rather than to charge a tRNA with its cognate amino acid [Protein synthesis, tRNA and rRNA base modification].
CDD:213871	213	PRK	Bacteria:31	TIGR03840, TMPT_Se_Te, thiopurine S-methyltransferase, Se/Te detoxification family.  Members of this family are thiopurine S-methyltransferase from a branch in which at least some member proteins can perform selenium methylation as a means to detoxify selenium, or perform a related detoxification of tellurium. Note that the EC number definition does not specify a particular thiopurine, but rather represents a class of activity.
CDD:234372	253	PRK	Bacteria:35	TIGR03843, TIGR03843, conserved hypothetical protein.  This model represents a protein family largely restricted to the Actinobacteria (high-GC Gram-positives), although it is also found in the Chloroflexi. Distant similarity to the phosphatidylinositol 3- and 4-kinase is suggested by the matching of some members to pfam00454.
CDD:163557	157	PRK	Bacteria:14	TIGR03845, sulfopyru_alph, sulfopyruvate decarboxylase, alpha subunit.  This model represents the alpha subunit, or the N-terminal region, of sulfopyruvate decarboxylase, an enzyme of coenzyme M biosynthesis. Coenzyme M is found almost exclusively in the methanogenic archaea. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA ...
CDD:234373	181	PRK	Bacteria:7	TIGR03846, sulfopy_beta, sulfopyruvate decarboxylase, beta subunit.  Nearly every member of this protein family is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see PMID:19581363).
CDD:213872	177	PRK	Bacteria:14	TIGR03847, TIGR03847, conserved hypothetical protein.  The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
CDD:163560	204	PRK	Bacteria:15	TIGR03848, MSMEG_4193, probable phosphomutase, MSMEG_4193 family.  A three-gene system broadly conserved among the Actinobacteria includes MSMEG_4193 and homologs, a subgroup among the larger phosphoglycerate mutase family protein (pfam00300). Another member of the trio is a probable kinase, related to phosphatidylinositol kinases; that context supports the hypothesis that this protein acts as a phosphomutase.
CDD:163562	437	PRK	Bacteria:12	TIGR03850, bind_CPR_0540, carbohydrate ABC transporter substrate-binding protein, CPR_0540 family.  Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include ...
CDD:163563	450	PRK	Bacteria:8	TIGR03851, chitin_NgcE, carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein.  Members of this protein family are the substrate-binding protein, a lipid-anchored protein of Gram-positive bacteria in all examples found so far, that include NgcE of the chitin-degrader, Streptomyces olivaceoviridis, and close homologs from other species likely to share the same function. NgcE binds both N-acetylglucosamine and the chitin dimer, ...
CDD:163565	77	PRK	Bacteria:38	TIGR03853, matur_matur, probable metal-binding protein.  This model describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic ...
CDD:234374	337	PRK	Bacteria:22,nodiv:1	TIGR03858, LLM_2I7G, probable oxidoreductase, LLM family.  This model describes a highly conserved, somewhat broadly distributed family withing the luciferase-like monooxygenase (LLM) superfamily. Most members are from species incapable of synthesizing coenzyme F420, bound by some members of the LLM superfamily. Members, therefore, are more likely to use FMN as a cofactor.
CDD:163571	81	PRK	Bacteria:8	TIGR03859, PQQ_PqqD, coenzyme PQQ biosynthesis protein PqqD.  This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ [Biosynthesis of cofactors, prosthetic groups, and carriers, Other].
CDD:234375	422	PRK	Bacteria:49	TIGR03860, FMN_nitrolo, FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family.  This model represents a distinctive clade, in which all characterized members are FMN-binding, within the larger family of luciferase-like monooxygenases (LLM), among which there are both FMN- and F420-binding enzymes. A well-characterized member is nitrilotriacetate monooxygenase from Aminobacter aminovorans (Chelatobacter heintzii), where nitrilotriacetate is a ...
CDD:234376	347	PRK	Bacteria:16	TIGR03863, PQQ_ABC_bind, ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system.  Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U [Transport and binding proteins, Carbohydrates, organic ...
CDD:188394	236	PRK	Bacteria:15	TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system.  Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols ...
CDD:188395	162	PRK	Bacteria:11	TIGR03865, PQQ_CXXCW, PQQ-dependent catabolism-associated CXXCW motif protein.  Members of this protein family have a CXXXCW motif, consistent with a possible role in redox cofactor binding. This protein family shows strong relationships by phylogenetic profiling and conserved gene neighborhoods with a transport system for alcohols metabolized by PQQ-dependent enzymes.
CDD:163583	232	PRK	Bacteria:18	TIGR03871, ABC_peri_MoxJ_2, quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein.  This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC ...
CDD:163587	206	miss	miss	TIGR03875, RNA_lig_partner, RNA ligase partner, MJ_0950 family.  This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also ...
CDD:188398	164	PRK	Bacteria:29	TIGR03882, cyclo_dehyd_2, bacteriocin biosynthesis cyclodehydratase domain.  This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
CDD:234380	346	PRK	Bacteria:14	TIGR03883, DUF2342_F420, uncharacterized protein, coenzyme F420 biosynthesis associated.  A phylogenetic tree of the DUF2342 family (TIGR03624) consists of two major branches. One of these branches, modeled here, is observed almost entirely to be found in coenzyme F420 biosynthesizing species of the Actinobacterial, Chloroflexi and Archaeal lineages. The few organisms having genes within this family and lacking F420 biosynthesis may either have an undiscovered F420 ...
CDD:234381	223	PRK	Bacteria:9	TIGR03888, nitrile_beta, nitrile hydratase, beta subunit.  Members of this protein family are the beta subunit of nitrile hydratase. The alpha subunit is represented by model TIGR01323. While nitrile hydratase is given the specific EC number 4.2.1.84, nitriles are a class of compounds, and one genome may carry more than one nitrile hydratase. The enzyme occurs in both non-heme iron and non-corrin cobalt forms [Energy metabolism, Amino acids and amines].
CDD:234382	263	PRK	Bacteria:28	TIGR03891, thiopep_ocin, thiopeptide-type bacteriocin biosynthesis domain.  This domain occurs within longer proteins that contain lantibiotic dehydratase domains (see pfam04737 and pfam04738), and as single-domain proteins in bacteriocin biosynthesis genomic contexts. Three named genes in this family, SioK in Streptomyces sioyaensis, TsrD in Streptomyces laurentii, and NosD in Streptomyces actuosus, all occur in regions associated with thiopeptide biosynthesis ...
CDD:200334	43	PRK	Bacteria:14	TIGR03892, thiopep_precurs, thiazolylpeptide-type bacteriocin precursor.  Members of this protein family are the precursors of a family of small bacteriocins (i.e. microcins) with thiopeptide type modifications, a highly modified subclass of heterocycle-containing peptide antibiotics. Members tend to be found clustered in genomes with proteins recognized by TIGR03891 and proteins/domains annotated as lantibiotic dehydratase (pfam04737, pfam04738), and with a ...
CDD:188408	61	PRK	Bacteria:10	TIGR03893, lant_SP_1948, type 2 lantibiotic, SP_1948 family.  This model recognizes a number of type 2 lantibiotic-type bacteriocins, related to but distinct from the family that includes lichenicidin and mersacidin. Sequence similarity among members consists largely of a 20-residue block of conserved sequence that covers most of the leader peptide region, absent from the mature lantibiotic. This is followed by a region with characteristic composition for ...
CDD:234385	931	PRK	Bacteria:37,nodiv:1	TIGR03897, lanti_2_LanM, type 2 lantibiotic biosynthesis protein LanM.  Members of this family are known generally as LanM, a multifunctional enzyme of lantibiotic biosynthesis. This catalysis by LanM distinguishes the type 2 lantibiotics, such as mersacidin, cinnamycin, and lichenicidin, from LanBC-produced type 1 lantibiotics such as nisin and subtilin. The N-terminal domain contains regions associated with Ser and Thr dehydration. The C-terminal region ...
CDD:188413	44	PRK	Bacteria:10	TIGR03898, lanti_MRSA_kill, type 2 lantibiotic, mersacidin/lichenicidin family.  This model recognizes a number of type 2 lantibiotic-type bacteriocins, including mersacidin and lichenicidin. Members often are found as gene pairs encoding two-chain bacteriocins. Maturation is accomplished, at least in part, by a LanM-type enzyme (TIGR03897). This model describes only the leader peptide region [Cellular processes, Toxin production and resistance].
CDD:188414	250	PRK	Bacteria:20	TIGR03899, TIGR03899, TIGR03899 family protein.  Members of this protein family are conserved hypothetical proteins with a limited species distribution within the Gammaproteobacteria. It is common in the genera Vibrio and Shewanella, and in this resembles the C-terminal domain and putative protein sorting motif TIGR03501. This model, but design, does not extend to all homologs,but rather represents a particular clade.
CDD:234387	31	PRK	Bacteria:8	TIGR03901, MYXO-CTERM, MYXO-CTERM domain.  This model describes MYXO-CTERM, a C-terminal putative protein sorting domain, analogous to LPXTG (TIGR01167) and PEP-CTERM (TIGR02595). It is restricted to the Myxococcales, a division of the Deltaproteobacteria, with over 60 members occurring in Plesiocystis pacifica SIR-1. An example protein is TraA, involved in outer membrane exchange (lipids and proteins) through which one strain of Myxococcus can repair a mobility ...
CDD:234388	154	PRK	Bacteria:62	TIGR03902, rhom_GG_sort, rhomboid family GlyGly-CTERM serine protease.  This model describes a rhomboid-like intramembrane serine protease. Its species distribution closely matches model TIGR03501, GlyGly-CTERM, which describes a protein targeting domain analogous to LPXTG and PEP-CTERM. In a number of species (Ralstonia eutropha ,R. metallidurans, R. solanacearum, Marinobacter aquaeolei, etc) with just one GlyGly-CTERM protein (i.e., a dedicated system), the ...
CDD:234390	559	PRK	Bacteria:60	TIGR03904, SAM_YgiQ, uncharacterized radical SAM protein YgiQ.  Members of this family are fairly widespread uncharacterized radical SAM family proteins, many of which are designated YgiQ [Unknown function, Enzymes of unknown specificity].
CDD:234393	230	PRK	Bacteria:18	TIGR03914, UDG_fam_dom, uracil-DNA glycosylase family domain.  This model represents a clade within the uracil-DNA glycosylase superfamily. Among characterized proteins, it most closely resembles the Thermus thermophilus uracil-DNA glycosylase TTUDGA, which acts uracil (deamidated cytosine) in both single-stranded DNA and U/G pairs of double-stranded DNA. This domain may occur either as a stand-alone protein or as the C-terminal domain of a fusion with another ...
CDD:234394	242	PRK	Bacteria:75	TIGR03915, SAM_7_link_chp, probable DNA metabolism protein.  This model represents a conserved hypothetical protein that almost invariably pairs with an uncharacterized radical SAM protein. The pair occurs in about twenty percent of completed prokaryotic genomes. About forty percent of the members of this family occur as fusion proteins, where the C-terminal domain belongs to the uracil-DNA glycosylase family, a DNA repair family (because uracil in DNA is ...
CDD:188431	415	PRK	Bacteria:15	TIGR03916, rSAM_link_UDG, putative DNA modification/repair radical SAM protein.  This uncharacterized protein of about 400 amino acids in length contains a radical SAM protein in the N-terminal half. Members are present in about twenty percent of prokaryotic genomes, always paired with a member of the conserved hypothetical protein TIGR03915. Roughly forty percent of the members of that family exist as fusions with a uracil-DNA glycosylase-like region, TIGR03914. ...
CDD:188432	40	PRK	Bacteria:4	TIGR03917, Frankia_40_dom, Frankia-40 domain.  This model describes a paralogous domain of length 40, restricted to smaller proteins of the genus Frankia, a member of the Actinobacteria. The function is unknown.
CDD:234395	391	PRK	Bacteria:54	TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase HydF.  This model describes the family of the [Fe] hydrogenase maturation protein HypF as characterized in Chlamydomonas reinhardtii and found, in an operon with radical SAM proteins HydE and HydG, in numerous bacteria. It has GTPase activity, can bind an 4Fe-4S cluster, and is essential for hydrogenase activity [Protein fate, Protein modification and repair].
CDD:234396	456	PRK	Bacteria:22	TIGR03919, T7SS_EccB, type VII secretion protein EccB, Actinobacterial.  This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccB1, EccB2, etc. This model does not identify functionally related proteins in the Firmicutes such as Staphylococcus aureus and Bacillus anthracis [Protein fate, Protein and ...
CDD:234397	431	PRK	Bacteria:7	TIGR03920, T7SS_EccD, type VII secretion integral membrane protein EccD.  Members of this family are EccD, a component of actinobacterial type VII secretion systems (T7SS) with ten to eleven predicted transmembrane helix regions [Protein fate, Protein and peptide secretion and trafficking].
CDD:234398	350	PRK	Bacteria:9	TIGR03921, T7SS_mycosin, type VII secretion-associated serine protease mycosin.  Members of this family are subtilisin-related serine proteases, found strictly in the Actinobacteria and associated with type VII secretion operons. The designation mycosin is used for members from Mycobacterium [Protein fate, Protein and peptide secretion and trafficking, Protein fate, Protein modification and repair].
CDD:234399	341	PRK	Bacteria:16	TIGR03923, T7SS_EccE, type VII secretion protein EccE.  This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccE1, EccE2, etc. This model represents a conserved core region, and many members have 200 or more additional C-terminal residues [Protein fate, Protein and peptide secretion and trafficking].
CDD:234400	661	PRK	Bacteria:21	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa.  This model represents the N-terminal domain or EccCa subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes [Protein fate, Protein and peptide secretion and trafficking].
CDD:234401	566	PRK	Bacteria:6	TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb.  This model represents the C-terminal domain or EccCb subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes [Protein fate, Protein and peptide secretion and trafficking].
CDD:188441	377	PRK	Bacteria:12	TIGR03926, T7_EssB, type VII secretion protein EssB.  Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This protein is designated YukC in Bacillus subtilis and EssB is Staphylococcus aureus [Protein fate, Protein and peptide secretion and trafficking].
CDD:200340	150	PRK	Bacteria:14	TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA.  Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and ...
CDD:234402	1296	PRK	Bacteria:12	TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC, C-terminal domain.  This model describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria [Protein fate, Protein and peptide secretion and trafficking].
CDD:188444	193	PRK	Bacteria:9	TIGR03929, T7_esaA_Nterm, type VII secretion protein EsaA, N-terminal domain.  Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This model represents the conserved N-terminal domain.
CDD:234403	90	PRK	Bacteria:57,Synthetic:1	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target.  Members of this protein family include secretion targets for the two main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from pfam06013. The best characterized member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length ...
CDD:234404	172	PRK	Bacteria:13	TIGR03931, T7SS_Rv3446c, type VII secretion-associated protein, Rv3446c family, C-terminal domain.  Members of this protein family occur as part of the ESX-4 cluster of type VII secretion system (T7SS) proteins in Mycobacterium tuberculosis and in similar T7SS clusters in other Actinobacteria genera, including Corynebacterium, Nocardia, Rhodococcus, and Saccharopolyspora. This model describes the better-conserved C-terminal region [Protein fate, Protein and peptide ...
CDD:188449	42	PRK	Bacteria:19	TIGR03934, TQXA_dom, TQXA domain.  This model describes a domain of about 40 residues with an invariant TQ dipeptide in an almost invariant TQxA[VI]W motif. This domain occurs in surface-expressed proteins of Gram-positive bacteria, many of which are anchored by LPXTG-containing sortase target domains. Numerous members of this family have domains pfam05738 (Cna protein B-type domain) and pfam08341 (fibronectin-binding protein signal sequence).
CDD:234405	209	PRK	Bacteria:85,Environmental:1	TIGR03936, sam_1_link_chp, radical SAM-linked protein.  This model describes an uncharacterized protein encoded adjacent to, or as a fusion protein with, an uncharacterized radical SAM protein.
CDD:188452	407	PRK	Bacteria:17	TIGR03937, PgaC_IcaA, poly-beta-1,6 N-acetyl-D-glucosamine synthase.  Members of this protein family are biofilm-forming enzymes that polymerize N-acetyl-D-glucosamine residues in beta(1,6) linkage. One named members is IcaA (intercellular adhesin protein A), an enzyme that acts (with aid of subunit IcaD) in Polysaccharide Intercellular Adhesin (PIA) biosynthesis in Staphylococcus epidermis). The homologous member in E. coli is designated PgaC. Members are often ...
CDD:188453	619	PRK	Bacteria:24	TIGR03938, deacetyl_PgaB, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB.  Two well-characterized systems produce polysaccharide based on N-acetyl-D-glucosamine in straight chains with beta-1,6 linkages. These are encoded by the icaADBC operon in Staphylococcus species, where the system is designated polysaccharide intercellular adhesin (PIA), and the pgaABCD operon in Gram-negative bacteria such as E. coli. Both systems include a putative polysaccharide ...
CDD:234406	800	PRK	Bacteria:15	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA.  Members of this protein family are the poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin PgaA of Gram-negative bacteria. There is no counterpart in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis systems of Gram-positive bacteria such as Staphylococcus epidermidis. The PGA polysaccharide adhesin is a critical determinant of biofilm formation. The conserved C-terminal domain ...
CDD:188455	141	PRK	Bacteria:10	TIGR03940, PGA_PgaD, poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD.  Members of this protein family are PgaD, essential to the production of poly-beta-1,6-N-acetyl-D-glucosamine (PGA). This cytoplasmic membrane protein appears to be an auxiliary subunit to the PGA synthase, PgaC (TIGR03937) [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides].
CDD:234407	154	PRK	Bacteria:33	TIGR03941, tRNA_deam_assoc, putative tRNA adenosine deaminase-associated protein.  This model describes a protein family about 200 amino acids in length with only five invariant residues, including an Arg, a Ser-Asp pair, and two Gly residues. Members always are found exclusively in Actinobacteria, and always adjacent to homologs of TadA, a tRNA-specific adenosine deaminase from Escherichia coli. Homology, phyletic pattern, and gene neighborhood together suggest a ...
CDD:188457	363	PRK	Bacteria:15	TIGR03942, sulfatase_rSAM, anaerobic sulfatase-maturating enzyme.  Members of this protein family are radical SAM family enzymes, maturases that prepare the oxygen-sensitive radical required in the active site of anaerobic sulfatases. This maturase role has led to many misleading legacy annotations suggesting that this enzyme maturase is instead a sulfatase regulatory protein. All members of the seed alignment are radical SAM enzymes encoded next to or near an ...
CDD:234408	220	PRK	Bacteria:52	TIGR03943, TIGR03943, TIGR03943 family protein.  Members of this occur in gene pairs with members of pfam03773. The N-terminal region contains several predicted transmembrane helix regions while the few invariant residues (G, CxxD, and W) occur in the C-terminal region.
CDD:188459	327	PRK	Bacteria:23	TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis protein SbnB.  Members of this protein family are probable NAD-dependent dehydrogenases related to the alanine dehydrogenase of Archaeoglobus fulgidus (see TIGR02371, PDB structure 1OMO and PMID:15313611) and more distantly to ornithine cyclodeaminase. Members include the staphylobactin biosynthesis protein SbnB and tend to occur in contexts suggesting non-ribosomal peptide synthesis, always adjacent to ...
CDD:234409	304	PRK	Bacteria:23	TIGR03945, PLP_SbnA_fam, 2,3-diaminopropionate biosynthesis protein SbnA.  Members of this family include SbnA, a protein of the staphyloferrin B biosynthesis operon of Staphylococcus aureus. SbnA and SbnB together appear to synthesize 2,3-diaminopropionate, a precursor of certain siderophores and other secondary metabolites. SbnA is a pyridoxal phosphate-dependent enzyme [Cellular processes, Biosynthesis of natural products].
CDD:234410	45	PRK	Bacteria:8	TIGR03949, bact_IIb_cerein, class IIb bacteriocin, lactobin A/cerein 7B family.  Members of this protein family are described variably as bacteriocins per se, one chain of a two-chain bacteriocin, or bacteriocin enhancer proteins. All members of the seed alignment occur in paired gene contexts with another member of the same protein family. This family includes bacteriocins that appear not to undergo post-translational modification, other than cleavage at a Gly-Gly ...
CDD:234411	223	PRK	Bacteria:21	TIGR03950, sidero_Fe_reduc, siderophore ferric iron reductase, AHA_1954 family.  Members of this protein family are 2Fe-2S cluster binding proteins, found regularly in the context of siderophore transporters. Members are distantly related to FhuF from E. coli, a ferric iron reductase linked to removal of iron from hydroxamate-type siderophores (PMID:14756576) [Energy metabolism, Electron transport, Transport and binding proteins, Cations and iron carrying compounds].
CDD:234412	182	PRK	Bacteria:10	TIGR03951, Fe_III_red_FhuF, siderophore-iron reductase FhuF.  Members of this protein family, including FhuF of E. coli, are siderophore ferric iron reductases that appear to play a role in iron removal from certain hydroxamate-type siderophores, including coprogen, ferrichrome, ferrioxamine B, and aerobactin. Genes occur in regularly in siderophore transport and/or biosynthesis clusters. The C-terminus includes four Cys residues in a C-C-10(X)-C-X-X-C motif that ...
CDD:234414	188	PRK	Bacteria:25	TIGR03953, rplD_bact, 50S ribosomal protein L4, bacterial/organelle.  Members of this protein family are ribosomal protein L4. This model recognizes bacterial and most organellar forms, but excludes homologs from the eukaryotic cytoplasm and from archaea [Protein synthesis, Ribosomal proteins: synthesis and modification].
CDD:188469	85	PRK	Bacteria:81	TIGR03954, integ_memb_HG, integral membrane protein.  This model describes a strictly bacterial integral membrane domain of about 85 residues in length. It occurs in proteins that on rare occasions are fused to transporter domains such as the major facilitator superfamily domain. Of three invariant residues, two occur as a His-Gly dipeptide in the middle of three predicted transmembrane helices [Unknown function, General].
CDD:234416	340	PRK	Bacteria:38	TIGR03956, rSAM_HydE, [FeFe] hydrogenase H-cluster radical SAM maturase HydE.  This model describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [Fe] hydrogenase in Chlamydomonas reinhardtii and numerous bacteria [Protein fate, Protein modification and repair].
CDD:188474	76	PRK	Bacteria:49	TIGR03959, hyd_TM1266, putative iron-only hydrogenase system regulator.  Members of this protein family occur as part of a system for producing iron-only hydrogenases, dependent on radical SAM proteins HydE and HydG and GTPase HydF. One member of this family, TM_1266 from Thermotoga maritima, has a known crystal structure. The small size, about 80 residues, and a distant relationship to the nickel regulator NikR of the CopG transcriptional regulator family suggest a ...
CDD:188475	605	PRK	Bacteria:19	TIGR03960, rSAM_fuse_unch, radical SAM family uncharacterized protein.  This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification [Unknown function, Enzymes of unknown specificity].
CDD:234420	81	PRK	Bacteria:14	TIGR03967, mycofact_MftB, putative mycofactocin binding protein MftB.  Families TIGR03969 and TIGR03962 describe, respectively, the putative mycofactocin precursor and its cognate radical SAM peptide maturase. This small protein family appears in the same sporadically distributed cassette and may serve as a scaffolding protein during mycofactocin maturation or as a carrier protein for the mature product, a putative novel redox carrier. A feature of ...
CDD:188483	190	PRK	Bacteria:13	TIGR03968, mycofact_TetR, mycofactocin system transcriptional regulator.  Members of this family are TetR family putative transcriptional regulators that occur in genome contexts near proteins of the mycofactocin system. These include the precursor peptide (TIGR03969), a radical SAM peptide maturase (TIGR03962), and a putative carrier protein (TIGR03967).
CDD:234423	297	PRK	Bacteria:5	TIGR03972, rSAM_TYW1, wyosine biosynthesis protein TYW1.  Members of this protein family are the archaeal protein TWY1, a radical SAM protein that catalyzes the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification [Protein synthesis, tRNA and rRNA base modification].
CDD:234424	43	PRK	Bacteria:29	TIGR03973, six_Cys_in_45, six-cysteine peptide SCIFF.  Members of this protein family are essentially universal in the class Clostidia and therefore highly abundant in the human gut microbiome. This short peptide is designated SCIFF, for Six Cysteines in Forty-Five residues. It is a presumed ribosomal natural product precursor, always found associated with a yet-uncharacterized radical SAM protein, family TIGR03974, that resembles other peptide modification radical ...
CDD:234425	451	PRK	Bacteria:29	TIGR03974, rSAM_six_Cys, SCIFF radical SAM maturase.  Members of this protein family are predicted radical SAM enzymes universally associated with Six Cysteines in Forty-Five protein, or SCIFF (family TIGR03973), a predicted ribosomal natural product precursor that is nearly universal in the class Clostridia. Similarity of this family to radical SAM maturases (PqqE and subtilosin A maturase) found in the vicinity of other peptide precursors suggests this protein is ...
CDD:234426	606	PRK	Bacteria:12	TIGR03975, rSAM_ocin_1, bacteriocin maturation radical SAM protein 1.  Models TIGR03793 and TIGR03798 describe bacteriocin precursor families to occur often in large paralogous families and are subject to various modifications, including by LanM family lantibiotic synthases and by cyclodehydratases. This model represents a radical SAM protein family that regularly occurs in the context of these bacteriocins, and may occur where other familiar peptide modification ...
CDD:234427	89	PRK	Bacteria:23	TIGR03976, chp_LLNDYxLRE, His-Xaa-Ser system protein HsxD.  This rare conserved hypothetical protein of small size occurs exclusively, and perhaps universally, in the context of a pair of (uncharacterized) radical SAM proteins, TIGR03977 and TIGR03978. Many members of this family have invariant motifs LYW and LLNDYxLRE, but PSI-BLAST starting from family members well below 20 % pairwise sequence identity to this group eventually brings in the entire family as ...
CDD:188492	292	PRK	Bacteria:20	TIGR03977, rSAM_pair_HxsC, His-Xaa-Ser system radical SAM maturase HxsC.  This model describes the downstream member, HxsC, of a pair of uncharacterized radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme appears to be part of a peptide modification system.
CDD:188493	466	PRK	Bacteria:18	TIGR03978, rSAM_paired_1, His-Xaa-Ser system radical SAM maturase HxsB.  This model describes the upstream member, HxsB, of a pair of uncharacterized radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme appears to be part of a peptide modification system.
CDD:188495	58	PRK	Bacteria:73	TIGR03980, prismane_assoc, hybrid cluster protein-associated redox disulfide domain.  Members of this protein family resemble the domain of unknown function DUF1858 described by pfam08984, but all members contain an apparent redox-active disulfide. In at least one member protein, a cysteine in the CXXC motif is substituted by a selenocysteine. Most member proteins consist of this domain only, but a few members are fused to or adjacent to members of the ...
CDD:234429	147	PRK	Bacteria:14	TIGR03984, TIGR03984, CRISPR-associated protein, TIGR03984 family.  Members of this protein family are found exclusively in CRISPR-containing organisms, in operon contexts with RAMP (repeat-associated mystery protein) proteins also linked to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats).
CDD:188500	249	PRK	Bacteria:8	TIGR03985, TIGR03985, CRISPR-associated protein, TIGR03985 family.  Members of this protein family belong to CRISPR-associated (Cas) gene clusters. The majority of members are Cyanobacterial.
CDD:234430	562	PRK	Bacteria:22	TIGR03986, TIGR03986, CRISPR-associated protein.  Members of this protein family, part of the larger RAMP family, are found exclusively in species with CRISPR systems, in local contexts containing other RAMP (Repeat-Associated Mystery Proteins).
CDD:188502	120	PRK	Bacteria:17	TIGR03987, TIGR03987, TIGR03987 family protein.  Conserved hypothetical protein.
CDD:188503	77	PRK	Bacteria:18	TIGR03988, antisig_RsrA, mycothiol system anti-sigma-R factor.  Members of this family are the anti-sigma-R factor RsrA, which contains a CXXC motif as a thiol-disulphide redox switch. It interacts with sigma-R. It regulates and is regulated by the mycothiol system, which occurs in many actinomycetes [Transcription, Transcription factors].
CDD:188504	369	PRK	Bacteria:9	TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family.  This model describes a clade within the family pfam00107 of zinc-binding dehydrogenases. The family pfam00107 contains class III alcohol dehydrogenases, including enzymes designated S-(hydroxymethyl)glutathione dehydrogenase and NAD/mycothiol-dependent formaldehyde dehydrogenase. Members of the current family occur only in species that contain the very small protein mycofactocin (TIGR03969), a possible ...
CDD:234431	443	PRK	Bacteria:45	TIGR03990, Arch_GlmM, phosphoglucosamine mutase.  The MMP1680 protein from Methanococcus maripaludis has been characterized as the archaeal protein responsible for the second step of UDP-GlcNAc biosynthesis. This GlmM protein catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. The first-characterized bacterial GlmM protein is modeled by TIGR01455. These two families are members of the larger phosphoglucomutase/phosphomannomutase family ...
CDD:234432	337	PRK	Bacteria:15	TIGR03991, alt_bact_glmU, UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase.  The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis. Homologs of this enzyme are identified in a number of bacterial organisms and modeled here. A number of these are observed in proximity to the GlmS and GlmM genes, and phylogenetic profiling by PPP ...
CDD:234433	393	PRK	Bacteria:19	TIGR03992, Arch_glmU, UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase.  The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis. Many of the genes identified by this model are in proximity to the GlmS and GlmM genes and are also presumed to be GlmU. However, some archaeal genomes contain multiple closely-related homologs from this family ...
CDD:234434	143	PRK	Bacteria:20	TIGR03993, hydrog_HybE, [NiFe] hydrogenase assembly chaperone, HybE family.  Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain.
CDD:234435	401	PRK	Bacteria:22	TIGR03994, rSAM_HemZ, coproporphyrinogen dehydrogenase HemZ.  Members of this radical SAM protein family are HemZ, a protein involved in coproporphyrinogen III decarboxylation. Alternative names for this enzyme (EC 1.3.99.22) include coproporphyrinogen dehydrogenase and oxygen-independent coproporphyrinogen III oxidase. The family is related to, but distinct from HemN, and in Bacillus subtilis was shown to be connected to peroxide stress and catalase formation ...
CDD:234437	528	PRK	Bacteria:19	TIGR03998, thiol_BshC, bacillithiol biosynthesis cysteine-adding enzyme BshC.  Members of this protein family are BshC, an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs].
CDD:234438	374	PRK	Bacteria:20	TIGR03999, thiol_BshA, N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA.  Members of this protein family are BshA, a glycosyltransferase required for bacillithiol biosynthesis. This enzyme combines UDP-GlcNAc and L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate synthase. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes [Biosynthesis of cofactors, prosthetic groups, and carriers, ...
CDD:234439	226	PRK	Bacteria:16	TIGR04001, thiol_BshB1, bacillithiol biosynthesis deacetylase BshB1.  Members of this protein family are BshB1 (YpjG), an enzyme of bacillithiol biosynthesis; either BshB1 or BshB2 (YojG) must be present, and often both are present. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs].
CDD:188527	366	PRK	Bacteria:11	TIGR04012, poly_gGlu_PgsB, poly-gamma-glutamate synthase PgsB/CapB.  Of four genes commonly found to be involved in biosynthesis and export of poly-gamma-glutamate, pgsB(capB) and pgsC(capC) are found to be involved in the synthesis per se. Members of this family are designated PgsB, a nomeclature that covers both cases in which the poly-gamma-glutamate is secreted and those in which it is retained to form capsular material.PgsB has been shown to have ...
CDD:234440	382	PRK	Bacteria:22	TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain protein, MJ_1487 family.  Members of this family have both a B12 binding homology domain (pfam02310) and a radical SAM domain (pfam04055), and occur only once per genome. Some species with members of this family have a related protein with similar domain architecture. This protein is occurs largely in archaeal methanogens but also in a few bacteria, including Thermotoga maritima and Myxococcus ...
CDD:188533	316	PRK	Bacteria:29,Environmental:1	TIGR04018, Bthiol_YpdA, putative bacillithiol system oxidoreductase, YpdA family.  Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete [Unknown function, Enzymes of unknown specificity].
CDD:188534	105	PRK	Bacteria:40	TIGR04019, B_thiol_YtxJ, bacillithiol system protein YtxJ.  Members of this protein family, including YtxJ from Bacillus subtilis, occur in species that encode proteins for synthesizing bacillithiol. The protein is described as thioredoxin-like, while another bacillithiol-associated protein, YpdA (TIGR04018), is described as thioredoxin reductase-like [Unknown function, Enzymes of unknown specificity].
CDD:188535	341	PRK	Bacteria:14	TIGR04020, seco_metab_LLM, natural product biosynthesis luciferase-like monooxygenase domain.  This model describes a subfamily within the bacterial luciferase-like monooxygenase (LLM) family that regularly occurs within large non-ribosomal protein synthases/polyketide synthases, but also as small proteins. The LLM family includes members that bind either FMN or F420, and FMN is more likely in this case because many members are from species that lack F420 ...
CDD:188537	391	PRK	Bacteria:16	TIGR04022, sulfur_SfnB, sulfur acquisition oxidoreductase, SfnB family.  Members of this protein family belong to the greater family of acyl-CoA dehydrogenases. This family includes the sulfate starvation induced protein SfnB of Pseudomonas putida strain DS1, which is both encoded nearby to and phylogenetically closely correlated with the dimethyl sulphone monooxygenase SfnG. This family shows considerable sequence similarity to the Rhodococcus dibenzothiophene ...
CDD:188538	115	PRK	Bacteria:13	TIGR04023, PPOX_MSMEG_5819, PPOX class probable F420-dependent enzyme, MSMEG_5819 family.  A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. This subfamily within the PPOX family occurs in at least 19 distinct species of F420 producers and is likely to bind F420 rather than FMN [Unknown function, Enzymes ...
CDD:188540	197	PRK	Bacteria:70	TIGR04025, PPOX_FMN_DR2398, PPOX class probable FMN-dependent enzyme, DR_2398 family.  Members of the PPOX family (see pfam01243) may contain either FMN or F420 as cofactor. This subfamily consists of proteins mostly from species that lack the capability to synthesize F420, and therefore most likely all bind FMN.
CDD:188541	185	PRK	Bacteria:20	TIGR04026, PPOX_FMN_cyano, PPOX class probable FMN-dependent enzyme, alr4036 family.  Members of the PPOX family (see pfam01243) may contain either FMN or F420 as cofactor. This subfamily described here is widespread in Cyanobacteria and plants, and is named for alr4036 from Nostoc sp. PCC 7120. The family consists mostly of proteins from species that lack the capability to synthesize F420, so it is probable that all members bind FMN rather than F420 [Unknown ...
CDD:188547	172	PRK	Bacteria:12	TIGR04032, toxin_SdpC, antimicrobial peptide, SdpC family.  This protein family contains the antimicrobial peptide SdpC, used in cannibalistic killing by Bacillus subtilis, and related sequences in species as distant as Myxococcus xanthus from the Deltaproteobacteria. A conserved gene neighborhood includes proteins associated with immunity.
CDD:234444	62	PRK	Bacteria:13	TIGR04035, glucan_65_rpt, glucan-binding repeat.  This model describes a region of about 63 amino acids that is composed of three repeats of a more broadly distributed family of shorter repeats modeled by pfam01473. While the shorter repeats are often associated with choline binding (and therefore with cell wall binding), the longer repeat described here represents a subgroup of repeat sequences associated with glucan binding, as found in a number ...
CDD:234445	199	PRK	Bacteria:22	TIGR04037, LLM_duo_CE1759, LLM-partnered FMN reductase, CE1759 family.  This family represents a distinct clade within pfam03358. That family includes enzymes such as the NADH-dependent FMN reductase MsuE. Members of the present family regularly co-occur in genomes, typically as gene pairs, with members of TIGR04036, a probable FMN-dependent member of the bacterial luciferase-like monooxygenase (LLM) family. At least one member, RF|YP_001509627.1 from Frankia sp. ...
CDD:188553	191	PRK	Bacteria:17,Environmental:1	TIGR04038, tatD_link_rSAM, radical SAM protein, TatD family-associated.  Members of this family are radical SAM proteins found in about 5 percent of microbial genomes. A portion occur as gene fusions with, or adjacent to, members of the TatD family of hydrolases (pfam01026). The TatD family may have several paralogs per genome, including TatD itself from E. coli (a soluble protein not actually part of the twin-arginine translocation complex), which ...
CDD:188554	336	PRK	Bacteria:10	TIGR04039, MXAN_0977_Heme2, di-heme enzyme, MXAN_0977 family.  This model describes a subfamily of di-heme proteins related to the di-heme cytochrome c peroxidase and to MauG (methylamine utilization G), an enzyme that performs a tryptophan tryptophylquinone modification to the methylamine dehydrogenase light chain.
CDD:188555	497	PRK	Bacteria:1	TIGR04040, glycyl_YjjI, glycine radical enzyme, YjjI family.  Members of this family are homologs to enzymes known to undergo activation by a radical SAM protein to create an active site glycyl radical. This family appears to be activated by the YjjW radical SAM protein, usually encoded by an adjacent gene [Unknown function, Enzymes of unknown specificity].
CDD:188556	276	PRK	Bacteria:19	TIGR04041, activase_YjjW, glycine radical enzyme activase, YjjW family.  Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme [Protein fate, Protein ...
CDD:188557	90	PRK	Bacteria:30	TIGR04042, MSMEG_0570_fam, MSMEG_0570 family protein.  This small protein, about 90 residues long, has no detectable homologs outside the set included about trusted cutoff for This model. Member proteins serve as markers for an eight-gene region whose overall function is unknown. One member of the cluster is a radical SAM protein with some similarity to enzymes of cofactor biosynthesis, another a glycosyltransferase, several hydrolases or oxidoreductases, and several unknown.
CDD:234446	354	PRK	Bacteria:14	TIGR04043, rSAM_MSMEG_0568, radical SAM protein, MSMEG_0568 family.  Members of this protein family are radical SAM proteins related to MSMEG_0568 from Mycobacterium smegmatis. Members occur within 8-gene operons in species as diverse as M. smegmatis, Rhizobium leguminosarum, Synechococcus elongatus, and Sorangium cellulosum. The function of the operon is unknown, but similarity of MSMEG_0568 to some cofactor biosynthesis radical SAM proteins suggests a similar ...
CDD:188560	153	PRK	Bacteria:14	TIGR04045, MSMEG_0567_GNAT, putative N-acetyltransferase, MSMEG_0567 N-terminal domain family.  Members of this family belong to the GNAT family (pfam00583), in which numerous characterized examples, though not all, are are shown to be N-acetyltransferases or to interact with acetyl-CoA. This family occurs in a sparsely distributed biosynthetic cluster that occurs in Actinobacteria, Cyanobacteria, and Proteobacteria.
CDD:234448	373	PRK	Bacteria:11	TIGR04047, MSMEG_0565_glyc, glycosyltransferase, MSMEG_0565 family.  A conserved gene cluster found sporadically from Actinobacteria to Proteobacteria to Cyanobacteria features a radical SAM protein, an N-acetyltransferase, an oxidoreductase, and two additional proteins whose functional classes are unclear. The metabolic role of the cluster is probably biosynthetic. This glycosyltransferase, named from member MSMEG_0565 from Mycobacterium smegmatis, occurs in most ...
CDD:188564	316	PRK	Bacteria:12	TIGR04049, AIR_rel_sll0787, AIR synthase-related protein, sll0787 family.  Members of this family include sll0787 from Synechocystis sp. PCC 6803 and resemble the C-terminal region of MSMEG_0567 from Mycobacterium smegmatis, where the N-terminal is a GNAT family N-acetyltransferase. The conserved cluster is found broadly (Cyanobacteria, Proteobacteria, Actinobacteria) in about 8 percent of genomes and appears to be biosynthetic. The product is unkown [Unknown ...
CDD:188567	206	PRK	Bacteria:9	TIGR04052, AZL_007920_fam, AZL_007920/MXAN_0976 family protein.  Members of this rare protein family regularly occur next to a member of the MXAN_0977 subfamily (TIGR04039) of the di-heme cytochrome c peroxidase/MauG family (pfam03150). MauG itself (TIGR03791) is a protein modification enzyme responsible for the tryptophan tryptophylquinone (TTQ) modification involved in methylamine dehydrogenase activation. All members of this family have a motif of four spaced ...
CDD:234449	365	PRK	Bacteria:14	TIGR04053, sam_11, radical SAM protein, BA_1875 family.  Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse [Unknown function, Enzymes of unknown specificity].
CDD:188570	325	PRK	Bacteria:13	TIGR04055, rSAM_NirJ2, putative heme d1 biosynthesis radical SAM protein NirJ2.  Members of this radical SAM protein subfamily, designated NirJ2, occur in genomic contexts with a paralog NirJ1 and with other nitrite reductase operon genes associated with heme d1 biosynthesis, as in Heliobacillus mobilis and Heliophilum fasciatum. NirJ2 is presumed by bioinformatics analysis (Xiong, et al.) to be a heme d1 biosynthesis protein by context.
CDD:234450	982	PRK	Bacteria:4	TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein, SusC/RagA family.  This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this ...
CDD:213888	31	PRK	Bacteria:23	TIGR04057, SusC_RagA_signa, TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region.  This model describes a 31-residue signature region of the SusC/RagA family of outer membrane proteins from the Bacteriodetes. While many TonB-dependent outer membrane receptors are associated with siderophore import, this family seems to include generalized nutrient receptors that may convey fairly large oligomers of protein or carbohydrate. This family occurs ...
CDD:234451	267	PRK	Bacteria:14	TIGR04060, formate_focA, formate transporter FocA.  FocA (formate channel A) forms a pentameric formate-selective channel through the plasma membrane. The focA gene is largely restricted to Proteobacteria and occurs adjacent to genes for pyruvate formate lyase (PFL) and the PFL activase, a radical SAM protein. FocA is homologous to a nitrite transport protein, NirC [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].
CDD:188577	151	PRK	Bacteria:11	TIGR04062, dnd_assoc_4, dnd system-associated protein 4.  A DNA sulfur modification system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. Members of this protein fam ily are strictly limited to species with the dnd operon, and are found close to the dnd operon on the chromosomes of species such as Nostoc sp. PCC 7120, Geobacter uraniireducens Rf4, and Roseobacter denitrificans OCh 114 [DNA metabolism, ...
CDD:234452	397	PRK	Bacteria:20	TIGR04063, stp3, PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family.  PEP-CTERM/exosortase is a protein-sorting system associated with exopolysaccharide production. Members of this protein family are group 1 glycosyltransferases (see pfam00534) in which the overwhelming majority occur in species with the EpsH1 form of exosortase (see TIGR03109), and usually co-clustered with the exosortase. A typical member is Daro_2409 from Dechloromonas aromatica RCB.
CDD:234454	361	PRK	Bacteria:11	TIGR04066, nat_prod_clost, peptide maturation system protein, TIGR04066 family.  Members of this protein family occur in various Clostridial genomes, always in the context of a short peptide and a radical SAM protein predicted to modify the short peptide. PSI-BLAST analysis suggests a sequence relationship to archaeal proteins designated as subunits of an H+-transporting two-sector ATPase. The modified peptide is likely to be a bacteriocin, and this protein is a ...
CDD:234455	462	PRK	Bacteria:10	TIGR04068, rSAM_ocin_clost, Cys-rich peptide radical SAM maturase CcpM.  Members of this family are radical SAM enzymes that occur next to clostridial Cys-rich predicted bacteriocin (or other class of ribosomal natural product) precursors (see families TIGR04065 and TIGR04067). They include a TIGR04085 C-terminal additional 4Fe4S cluster-binding domain that is associated with peptide modification by radical SAM enzymes, and they are proposed to be ribosomal natural ...
CDD:188584	77	PRK	Bacteria:8	TIGR04069, ocin_ACP_rel, peptide maturation system acyl carrier-related protein.  Both PSI-BLAST and large numbers of noise-level HMM hits show a relationship between this family and the phosphopantetheine attachment site domain modeled by pfam00550. That domain includes acyl carrier proteins (ACP) and features an essentially invariant serine residue that is the attachment site for the phosphopantetheine prosthetic group. In this family, the corresponding residue is ...
CDD:213890	338	PRK	Bacteria:16	TIGR04070, photo_TT_lyase, spore photoproduct lyase.  DNA damage to bacterial spores from ultraviolet light accumulates in the form of 5-thyminyl-5,6-dihydrothymine, spore photoproduct. The damage is repaired by spore photoproduct lyase, a member of the radical SAM family of enzymes. The score of this model is set to restrict itself to spore-forming members of the Firmicutes, but additional homologs scoring below the trusted cutoff tend to occur in radioresistant ...
CDD:188588	75	PRK	Bacteria:20,Environmental:1	TIGR04073, exo_TIGR04073, putative exosortase-associated protein, TIGR04073 family.  Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. The N-terminal signal sequence is divergent and not included in ...
CDD:234456	462	PRK	Bacteria:18	TIGR04074, bacter_Hen1, 3' terminal RNA ribose 2'-O-methyltransferase Hen1.  Members of this protein family are bacterial Hen1, a 3' terminal RNA ribose 2'-O-methyltransferase that acts in bacterial RNA repair. All members of the seed alignment belong to a cassette with the RNA repair enzyme polynucleotide kinase-phosphatase (Pnkp). Chemically similar Hen1 in eukaryotes acts instead on small regulatory RNAs [Transcription, RNA processing, Protein synthesis, tRNA ...
CDD:234457	851	PRK	Bacteria:17	TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase.  Members of this protein family are the bacterial polynucleotide kinase-phosphatase (Pnkp) whose genes occur paired with genes for the 3' terminal RNA ribose 2'-O-methyltransferase Hen1. All members of the seed alignment belong to a cassette with the Hen1. The pair acts in bacterial RNA repair. This enzyme performs end-healing reactions on broken RNA, preparing from the RNA ligase to close the break. The ...
CDD:234458	89	PRK	Bacteria:52	TIGR04076, TIGR04076, TIGR04076 family protein.  Members of this protein family are uncharacterized. The only invariant residue, and one of three other residues better than 90 percent conserved are both Cys. Phylogenetic profiling results and occasional fusion genes suggest a role for members of this family in redox reactions or iron cluster metabolism. Species occasionally have two or three copies.
CDD:234459	516	PRK	Bacteria:9	TIGR04082, rSAM_for_selen, selenobiotic family peptide radical SAM maturase.  Members of this protein family are radical SAM (rSAM) enzymes similar in sequence to others with known or postulated roles in peptide modification, and regularly found adjacent to members of the GSU_1558 peptide family described by model TIGR04081. GSU_1558 and several other members of that family appear to be selenoproteins, hence the term selenobiotic.
CDD:234461	94	PRK	Bacteria:200	TIGR04085, rSAM_more_4Fe4S, radical SAM additional 4Fe4S-binding SPASM domain.  This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, ...
CDD:234462	115	PRK	Bacteria:90	TIGR04086, TIGR04086_membr, putative membrane protein, TIGR04086 family.  Members of this family of strongly hydrophobic putative transmembrane protein average about 125 amino acids in length and occur mostly, but not exclusively, in the Firmicutes. Members are quite diverse in sequence. The function is unknown.
CDD:213891	34	PRK	Bacteria:51	TIGR04088, cognate_SipW, SipW-cognate class signal peptide.  This model describes a protein N-terminal domain found regularly in proteins encoded near a variant form of signal peptidase I such as the SipW protein of Bacillus subtilis. Many though not all members are homologs of camelysin (a casein-cleaving metalloprotease) and TasA (CotN), a metalloprotease that is secreted, along with extracellular polysaccharide (EPS), to be the major protein constituent of the ...
CDD:234463	179	PRK	Bacteria:8	TIGR04089, exp_by_SipW_III, alternate signal-mediated exported protein, RER_14450 family.  Members of this Actinobacterial protein family contain the cognate signal peptide domain, modeled by TIGR04088, for the variant SipW form of the signal peptidase I family. The remainder of this protein, however, differs from families such as Peptidase_M73 (pfam12389) and YqxM (TIGR04087) that share the same signal peptide domain. Some additional homologs to this family lack ...
CDD:188606	380	PRK	Bacteria:39	TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis protein DltB.  Members of this protein family are DltB, part of a four-gene operon for D-alanyl-lipoteichoic acid biosynthesis that is present in the vast majority of low-GC Gram-positive organisms. This protein may be involved in transport of D-alanine across the plasma membrane [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].
CDD:234465	383	PRK	Bacteria:42	TIGR04092, LTA_DltD, D-alanyl-lipoteichoic acid biosynthesis protein DltD.  Members of this protein family are DltD, part of the DltABCD system widely distributed in the Firmicutes for D-alanylation of lipoteichoic acids. The most common form of LTA, as in Staphylococcus aureus, has a backbone of polyglycerolphosphate.
CDD:234468	451	PRK	Bacteria:10	TIGR04095, dnd_restrict_1, DNA phosphorothioation system restriction enzyme.  The DNA phosphorothioate modification system dnd (DNA instability during electrophoresis) recently has been shown to provide a modification essential to a restriction system. This protein family was detected by Partial Phylogenetic Profiling as linked to dnd, and its members usually are clustered with the dndABCDE genes.
CDD:188611	478	PRK	Bacteria:13	TIGR04096, dnd_rel_methyl, DNA phosphorothioation-associated putative methyltransferase.  Members of this protein family show distant local sequence similarity to a number of S-adenosyl-methionine-dependent methyltransferases. The family is identified by Partial Phylogenetic Profiling as closely tied to the DNA phosphorothioation system (dnd), and members are found adjacent to dnd genes in at least 13 species (Streptomyces lividans TK24, Shewanella frigidimarina ...
CDD:234469	270	PRK	Bacteria:21	TIGR04098, biosyn_clust_1, biosynthesis cluster domain.  Radical SAM family TIGR04043 is a marker for a widespread eight-gene probable biosynthetic cluster of unknown function. This protein family describes a domain that occurs as an additional protein for some of those clusters, but also as the N-terminal domain of large, multidomain polyketide synthases and in other contexts.
CDD:234470	259	PRK	Bacteria:3	TIGR04099, biosn_Pnap_2097, probable biosynthetic protein, Pnap_2097 family.  Radical SAM family TIGR04043 is a marker for a widespread eight-gene probable biosynthetic cluster of unknown function. This protein family occurs only in the context of TIGR04043 member-containing biosynthetic clusters, although in a minority of such clusters. This protein family belongs to the TIGR04098 domain family, which also includes N-terminal domains of several probable polyketide ...
CDD:200353	108	PRK	Bacteria:18	TIGR04102, SWIM_PBPRA1643, SWIM/SEC-C metal-binding motif protein, PBPRA1643 family.  Members of this protein family have a SWIM, or SEC-C, domain (see pfam02810), a 21-amino acid putative Zn-binding domain that is shared with SecA, plant MuDR transposases, etc. This small protein family of unknown function occurs primarily in marine bacteria.
CDD:234471	94	PRK	Bacteria:18	TIGR04104, cxxc_20_cxxc, cxxc_20_cxxc protein.  This small, uncommon, poorly conserved protein is found primarily in the Firmicutes. It features are pair of CxxC motifs separated by about 20 amino acids, followed by a highly hydrophobic region of about 45 amino acids. It has no conserved gene neighborhood, and its function is unknown.
CDD:234472	462	PRK	Bacteria:43	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3.  See PMID:20395274 for descriptions of different groups.
CDD:234473	420	PRK	Bacteria:14	TIGR04107, rSAM_HutW, putative heme utilization radical SAM enzyme HutW.  HutW is a radical SAM enzyme closely related to HemN, the heme biosynthetic oxygen-independent coproporphyrinogen oxidase. It belongs to operons associated with heme uptake and utilization in Vibrio cholerae and related species, but neither it not HutX has been shown to be needed, as is HutZ, for heme utilization. HutW failed to complement a Salmonella enterica hemN mutant (PMID:15205415), ...
CDD:211904	153	PRK	Bacteria:23	TIGR04108, HutX, putative heme utilization carrier protein HutX.  Members of this protein family are HutX, found paired with HutW in some heme utilization loci although not shown directly to be necessary for heme utilization. This protein is homologous to the heme carrier protein HemS, while its partner HutW is homologous to (but does not complement) HemN, the radical SAM enzyme oxygen-independent coproporphyrinogen III oxidase involved in heme biosynthesis.
CDD:200362	55	PRK	Bacteria:31	TIGR04111, BcepMu_gp16, phage-associated protein, BcepMu gp16 family.  Members of this protein family occur in Burkholderia phage BcepMu, Pseudomonas phage B3, and Burkholderia phage KS10, and many bacterial putative prophage regions. The member from Burkholderia phage BcepMu is named gp16. Homology suggests DNA-binding activity [Mobile and extrachromosomal element functions, Prophage functions].
CDD:200363	337	PRK	Bacteria:31	TIGR04112, seleno_YedE, putative selenium metabolism protein, YedE family.  For 79 of the first 80 reference genomes in which a member of this protein family, YedE, is found, a selenium utilization system is found, spread over a broad taxonomic range (Firmicutes, spirochetes, delta-proteobacteria, Fusobacteria, Bacteriodes, etc. This family is less widespread than YedF, also involved in selenium metabolism.
CDD:234474	704	PRK	Bacteria:9	TIGR04113, cas_csx17, CRISPR-associated protein Csx17, subtype Dpsyc.  Members of this protein family are found exclusively in CRISPR-associated (cas) type I system gene clusters of the Dpsyc subtype. Markers for that type include a variant form of cas3 (model TIGR02621) and the GSU0054-like protein family (model TIGR02165). This family occurs in less than half of known Dpsyc clusters.
CDD:234475	18	PRK	Bacteria:8	TIGR04114, tSAM_targ_Cxxx, modification target Cys-rich repeat.  This model describes a cysteine-rich repeat found in a number of bacterial putative radical-SAM modified natural product precursors. A substantial fraction of members of this family have been missed during gene-finding. A true hit to the model must exceed both TC on the whole and trusted cutoff 2 for at least one domain, to avoid false-positives from African swine fever virus proteins.
CDD:234476	90	PRK	Bacteria:9	TIGR04116, CXXX_rpt_assoc, CXXX repeat peptide modification system protein.  Members of this protein family occur strictly in the presence of a peptide modification radical SAM enzyme described by model TIGR04115 and some small peptide in which, for a stretch, every fourth amino acid is Cys. Cysteine residues usually are flanked by residues with sterically small side chains, as with many radical SAM-modified peptides. Many of the latter are recognized by model TIGR04114.
CDD:200370	210	PRK	Bacteria:9	TIGR04119, CXXX_matur, CXXX repeat peptide maturase.  This model describes a peptide maturase that works with, usually fused to, a radical SAM enzyme in a system that modifies peptides with multiple tandem repeats of CXXX sequences. This protein includes an iron-sulfur cluster binding region associated with peptide modification as described in domain model TIGR04085.
CDD:234477	526	PRK	Bacteria:11	TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent, PP_1105 family.  This model describes a family of ATP-dependent DNA ligases present in about 12 % of prokaryotic genomes. It occurs as part of a four-gene system with an exonuclease, a helicase and a phosphoesterase, with all four genes clustered or at least the first two and last two paired. This family resembles DNA ligase I (see TIGR00574 and pfam01068), and its presumed function may be in DNA repair, ...
CDD:234478	803	PRK	Bacteria:39	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated.  Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H.
CDD:200373	326	PRK	Bacteria:34	TIGR04122, Xnuc_lig_assoc, putative exonuclease, DNA ligase-associated.  Members of this protein family frequently are found annotated as a putative exonuclease involved in mRNA processing. This protein is found, exclusively in bacteria, associated with three other proteins: an ATP-dependent DNA ligase, a helicase, and putative phosphoesterase.
CDD:234479	208	PRK	Bacteria:57	TIGR04123, P_estr_lig_assc, metallophosphoesterase, DNA ligase-associated.  Members of this protein family are an uncharacterized putative metallophosphoesterase associated with a DNA ligase, a helicase, and a putative exonuclease. It may play a role in DNA repair. Its system is present in about 12 % of prokaryotic reference genomes.
CDD:200376	262	PRK	Bacteria:15	TIGR04125, exosort_PGF_TRM, archaeosortase A, PGF-CTERM-specific.  This family is an archaeal variant of the (normally bacterial) putative protein-sorting integral membrane protein exosortase, hence archaeosortase. In species a member of this family, its PGF-CTERM cognate sequence (TIGR04126) occurs at the C-termini of from two to over fifty proteins per genome. Those target proteins may not share homology to each other in regions N-terminal to the PGF-CTERM region.
CDD:200377	28	PRK	Bacteria:22	TIGR04126, PGF_CTERM, PGF-CTERM archaeal protein-sorting signal.  This model describes a strictly archaeal putative protein-sorting motif, PGF-CTERM. It is the (predicted) recognition sequence for an exosortase homolog, archaeosortase (TIGR04125). In some archaea, up to fifty proteins have this domain as their C-terminal region, usually preceded by a Thr-rich region likely to be heavily glycosylated. The removal of this sorting signal may be associated with a ...
CDD:200378	136	PRK	Bacteria:11	TIGR04127, flavo_near_exo, exosortase F-associated protein.  Members of this protein family are always found next to an exosortase/archaeosortase-like protein, and occur so far only in the flavobacteria, within the Bacteroidetes. Members do not have an obvious PEP-CTERM-like C-terminal protein sorting domain.
CDD:200379	174	PRK	Bacteria:9	TIGR04128, exoso_Fjoh_1448, exosortase family protein XrtF.  Members of this protein family are exosortase-related proteins found always in association with a member of family TIGR04127, a small, hydrophobic, uncharacterized protein limited to the Bacteriodetes. Exosortases are proposed transpeptidases with a cysteine active site (3.4.22.-), but usually are associated with specific C-terminal target motifs (PEP-CTERM, PEF-CTERM, PGF-CTERM, etc).
CDD:200380	49	PRK	Bacteria:20	TIGR04129, CxxH_BA5709, CxxH/CxxC protein, BA_5709 family.  Members of this protein family occur exclusively in the Firmicutes, in at least 50 different species. Members average about 55 residues in length, and four of the five invariant or nearly invariant residues occur in motifs CxxH and CxxC. The function is unknown.
CDD:234480	85	PRK	Bacteria:16,Environmental:1	TIGR04131, Bac_Flav_CTERM, gliding motility-associated C-terminal domain.  This model describes a protein homology domain unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this ...
CDD:200385	150	PRK	Bacteria:11	TIGR04134, lipo_with_rSAM, putative lipoprotein, rSAM/lipoprotein system.  Members of this family are Bacteroidetes lineage putative lipoproteins that always occur in pairs with a radical SAM enzyme, TIGR04133, from a branch of the radical SAM superfamily in which many members perform peptide or protein modifications. In some members, the region distal to the Cys of the putative lipoprotein cleavage motif is duplicated.
CDD:200388	50	PRK	Bacteria:22	TIGR04137, Chlam_Ver_rRNA, Chlam_Verruc_Plancto small basic protein.  Members of this protein family are commonly found next to markers of rRNA processing such as YbeY. They are extremely lineage-restricted, in the Planctomycetes and Chlamydiae/Verrucomicrobia group. Since classification is based on rRNA molecular phylogeny, this provides additional support for a role in rRNA metabolism. This small protein, about 50 amino acids in length, is rich in basic residues, ...
CDD:200389	122	PRK	Bacteria:19,Environmental:1	TIGR04138, Plancto_Ver_chp, Verruc_Plancto-restricted protein.  Members of this protein family are extremely lineage-restricted, occurring exclusively in the Planctomycetes and Chlamydiae/Verrucomicrobia group, although not in Chlamydia itself. The function is unknown; the lack of invariant residues other than a single Phe suggests an ancient, conserved, non-enzymatic role.
CDD:234481	516	PRK	Bacteria:31	TIGR04141, TIGR04141, sporadically distributed protein, TIGR04141 family.  This model describes a sporadically distributed conserved hypothetical protein in which complete members average over 500 amino acids in length, although matching sequences frequently are truncated or broken into tandem ORFs. Regular co-clustering with known markers of mobility (integrases, transposases, phage proteins, restriction enzymes, etc.) suggests this family also is part of the ...
CDD:200396	45	PRK	Bacteria:12	TIGR04145, Firmicu_CTERM, Firmicu-CTERM domain.  This C-terminal domain is found only in the Firmicutes, where its presence is sporadically distributed. Proteins with this domain are most conserved in the C-terminal region, where the pattern of ending with a transmembrane domain resembles both the LPXTG (sortase target) and PEP-CTERM (exosortase target) domain structures. However, members occur exclusively in the presence of an exosortase-like protein XrtG ...
CDD:234482	43	PRK	Bacteria:17	TIGR04149, GG_sam_targ_CFB, natural product precursor, GG-Bacteroidales family.  Sequences in this protein domain family include a leader peptide region, up to and including a Gly-Gly cleavage motif, and about 15 additional residues, usually Cys-rich, from a family of predicted ribosomal natural product precursors. Many of these are associated with peptide-modifying radical SAM enzymes. The core region, up through the diglycine motif, resembles and contains some ...
CDD:234483	407	PRK	Bacteria:9	TIGR04150, pseudo_rSAM_GG, pseudo-rSAM protein, GG-Bacteroidales system.  Many peptide-modifying radical SAM enzymes have two 4Fe4S-binding regions, an N-terminal one recognized by Pfam radical SAM domain-defining model pfam04055 and a C-terminal one recognized by TIGR04085. Members of this protein family occur in cassettes with such a radical SAM family (TIGR04148) and with a peptide modification target (TIGR04149). Surprisingly, members of this family show ...
CDD:200403	486	PRK	Bacteria:9	TIGR04152, exosort_VPLPA, exosortase D, VPLPA-CTERM-specific.  This model describes a variant sub class, exosortase D, of protein sorting enzyme (see parent exosortase model TIGR02602), specific for the VPLPA-CTERM variant (TIGR03370) of the PEP-CTERM protein sorting signal [Protein fate, Protein and peptide secretion and trafficking].
CDD:234484	186	PRK	Bacteria:11	TIGR04153, cyanosort_assoc, cyanosortase-associated protein.  Members of this protein family are found exclusively in the Cyanobacteria, usually next to and in at least one case fused to a protein that is a strictly cyanobacterial version of exosortase (TIGR03763).
CDD:234485	815	PRK	Bacteria:23	TIGR04154, archaeo_STT3, oligosaccharyl transferase, archaeosortase A system-associated.  Members of this protein family occur, one to three members per genome, in the same species of Euryarchaeota as contain the predicted protein-sorting enzyme archaeosortase (TIGR04125) and its cognate protein-sorting signal PGF-CTERM (TIGR04126).
CDD:200406	25	PRK	Bacteria:15	TIGR04155, cyano_PEP, PEP-CTERM protein sorting domain, cyanobacterial subclass.  This domain model describes a subclass with family TIGR02595 of PEP-CTERM protein sorting signals associated with bacterial exosortases. This subclass is restricted to Cyanobacteria, including the genera Cyanothece, Nostoc, Trichodesmium, Lyngbya, Arthospira, etc. This PEP-CTERM subclass features strongly conserved residues within the transmembrane region, including a Gx4GxG motif. ...
CDD:234487	406	PRK	Bacteria:6	TIGR04157, glyco_rSAM_CFB, glycosyltransferase, GG-Bacteroidales peptide system.  Members of this protein family are predicted glycosyltransferases that occur in conserved gene neighborhoods in various members of the Bacteroidales. These neighborhoods feature a radical SAM enzyme predicted to act in peptide modification (family TIGR04148), peptides from family TIGR04149 with a characteristic GG cleavage motif, and several other proteins.
CDD:200417	95	PRK	Bacteria:3	TIGR04166, methano_MtrB, tetrahydromethanopterin S-methyltransferase, subunit B.  Members of this protein family are the MtrB protein of the tetrahydromethanopterin S-methyltransferase complex. This system is universal in archaeal methanogens [Energy metabolism, Methanogenesis].
CDD:234488	303	PRK	Bacteria:63	TIGR04167, rSAM_SeCys, radical SAM/Cys-rich domain protein.  Members of this protein family have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam12345 domain. The C-terminal region has several conserved Cys residues, one of which is replaced by selenocysteine in at least five bacterial reference genomes.
CDD:200419	269	PRK	Bacteria:24	TIGR04168, TIGR04168, TIGR04168 family protein.  Members of this uncharacterized protein family are restricted, in 49 of 50 genomes, to organisms with a family TIGR04167 radical SAM protein, which occasionally is a selenoprotein.
CDD:213892	313	PRK	Bacteria:32,nodiv:1	TIGR04171, RNR_1b_NrdF, ribonucleoside-diphosphate reductase, class 1b, beta subunit.  Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism].
CDD:234490	27	EUKprk	Bacteria:11,Plants:1	TIGR04174, IPTL_CTERM, IPTL-CTERM protein sorting domain.  This model describes a variant form of the PEP-CTERM C-terminal protein-sorting domain, with a consensus motif IPTL replacing the more typical VPEP. A majority of these sequences have a WG (Trp-Gly) motif at positions 7-8 of the domain. Species with multiple (up to 15) copies of this domain include Acidovorax citrulli, Acidovorax delafieldii 2AN, Delftia acidovorans SPH-1, and gamma proteobacterium NOR5-3.
CDD:200429	97	PRK	Bacteria:248,Environmental:6	TIGR04178, exo_archaeo, exosortase/archaeosortase family protein.  This model represents the most conserved region of the multitransmembrane protein family of exosortases and archaeosortases. The region includes nearly invariant motifs at the ends of three predicted transmembrane helices on the extracytoplasmic face: a Cys (often Cys-Xaa-Gly), Asn-Xaa-Xaa-Arg, and His. This model is much broader than the bacterial exosortase model (TIGR02602), and ...
CDD:200431	297	PRK	Bacteria:20	TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family.  This clade within the NAD dependent epimerase/dehydratase superfamily (pfam01370) is characterized by inclusion of its members within a cassette of seven distinctive enzymes. These include four genes homologous to the elements of the neuraminic (sialic) acid biosynthesis cluster (NeuABCD), an aminotransferase and a nucleotidyltransferase in addition to the epimerase/dehydratase. ...
CDD:200432	359	PRK	Bacteria:40	TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.  This clade of aminotransferases is a member of the pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family is named after the instance in Leptospira interrogans serovar Lai, str. 56601, where it is the 31st gene in the 91-gene lipopolysaccharide biosynthesis locus. Members of this family are generally found within a subcluster of seven or more genes including an epimerase/dehydratase, four genes ...
CDD:200433	293	PRK	Bacteria:13	TIGR04182, glyco_TIGR04182, glycosyltransferase, TIGR04182 family.  Members of this family are glycosyltransferases restricted to the archaea. All but two members are from species with the PGF-CTERM/archaeosortase A system, a proposed maturation system for exported, glycosylated proteins as are found often in S-layers.
CDD:234491	71	PRK	Bacteria:59,Environmental:1	TIGR04183, Por_Secre_tail, Por secretion system C-terminal sorting domain.  Species that include Porphyromonas gingivalis, Fibrobacter succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella forsetii, Prevotella intermedia, and Salinibacter ruber average twenty or more copies of a C-terminal domain, modeled by This model, associated with sorting to the outer membrane and covalent modification.
CDD:211909	72	PRK	Bacteria:19	TIGR04186, GRASP_targ, putative ATP-grasp target RiPP.  A RiPP is a ribosomally produced, post-translationally modified peptide. This family regularly occurs next to ATP-grasp enzymes related to those of microviridin maturation and next to a methyltransferase.
CDD:211910	312	PRK	Bacteria:11	TIGR04187, GRASP_SAV_5884, ATP-grasp ribosomal peptide maturase, SAV_5884 family.  Members of this protein family are ATP-grasp ligase family enzymes that regularly occur in a contexts with a methyltransferase and a putative ribosomally translated post-translationally modified peptide precursor. Because of this conserved gene neighborhood and close sequence similarity to ATP-grasp enzymes from microviridin/marinostatin biosynthesis cassettes, this enzyme is ...
CDD:234492	363	PRK	Bacteria:13	TIGR04188, methyltr_grsp, methyltransferase, ATP-grasp peptide maturase system.  Members of this protein family are predicted SAM-dependent methyltransferases that regularly occur in the context of a putative peptide modification ATP-grasp enzyme (TIGR04187, related to enzymes of microviridin maturation) and a putative ribosomal peptide modification target (TIGR04186).
CDD:234493	2315	PRK	Bacteria:15	TIGR04189, surface_SprA, cell surface protein SprA.  SprA is a cell surface protein widely distributed in the Bacteroidetes lineage. In Flavobacterium johnsoniae, a species that shows gliding motility, mutation disrupts gliding.
CDD:234494	136	PRK	Bacteria:34,Environmental:1	TIGR04191, YphP_YqiW, bacillithiol system oxidoreductase, YphP/YqiW family.  This protein family is one of several observed in species that express bacillithiol, an analog of glutathione and mycothiol. Rather than being involved in bacillithiol biosynthesis, members are likely to act in bacillithiol-dependent processes.
CDD:211920	85	PRK	Bacteria:29	TIGR04197, T7SS_SACOL2603, type VII secretion effector, SACOL2603 family.  Members of this protein family are similar in length and sequence (although remotely) to the WXG100 family of type VII secretion system (T7SS) targets, described by family TIGR03930. Phylogenetic profiling shows that members of this family are similarly restricted to species with T7SS, marking this family as a related set of T7SS effectors. Members include SACOL2603 from Staphylococcus aureus ...
CDD:234496	893	PRK	Viruses:35	TIGR04198, paramyx_RNAcap, mRNA capping enzyme, paramyxovirus family.  This model represents a common C-terminal region shared by paramyxovirus-like RNA-dependent RNA polymerases (see model pfam00946). Polymerase proteins described by these two models are often called L protein (large polymerase protein). Capping of mRNA requires RNA triphosphatase and guanylyl transferase activities, demonstrated for the rinderpest virus L protein and at least partially localized ...
CDD:234498	22	PRK	Bacteria:4	TIGR04201, Myxo_Cys_RPT, Cys-rich repeat, Myxococcales-type.  This repeat is restricted to the Myxococcales, a division of the deltaproteobacteria. It occurs in several surface proteins, and may form a stalk region. The repeat averages about 21 amino acids in length with four or five Cys, three of which are nearly invariant.
CDD:211925	61	PRK	Viruses:29	TIGR04202, capSnatchArena, RNA endonuclease, cap-snatching, arenavirus family.  This model describes a shared signature region from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses. This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself.
CDD:234499	38	PRK	Bacteria:14	TIGR04203, RPT_S_cricet, Streptococcal surface-anchored protein repeat, S. criceti family.  This model describes a repeat sequence that occurs primarily LPXTG-anchored Streptococcus surface proteins, although it does occur elsewhere. It can comprise a major fraction of the length of repeat proteins taht exceed 2000 in length.
CDD:234500	139	PRK	Bacteria:8	TIGR04206, near_ArtA, TIGR04206 family protein.  Members of this integral membrane protein family are found exclusively in halophilic archaea. In at least three species (Haloarcula marismortui, Haloquadratum walsbyi, and Haloferax volcanii), members are found in the gene neighborhood of archaeosortase A, suggesting a role in protein sorting.
CDD:211930	30	PRK	Bacteria:9	TIGR04207, halo_sig_pep, surface glycoprotein signal peptide.  This N-terminal homology domain appears to be a specialized class of signal peptide. It occurs mostly in the halophilic archaea, primarily on proteins with the C-terminal PGF-CTERM domain, including the S-layer-forming major surface glycoprotein of several species. The PGF-CTERM domain is the putative archaeosortase A recognition sequence. However, this N-terminal domain occurs also in several archaeal ...
CDD:211932	144	PRK	Bacteria:7	TIGR04209, sarcinarray, sarcinarray family protein.  Members of this protein family are exclusive to archaea, probably all of which have S-layer surface protein arrays. All member proteins have an N-terminal signal sequence. The majority of known members belong to codirectional tandem arrays in the genus Methanosarcina (nine in M. barkeri str. Fusaro). Nearly all members have an additional 50 residues, (trimmed from the seed alignment for This model), consisting of ...
CDD:211933	173	PRK	Viruses:18	TIGR04210, bunya_NSm, bunyavirus nonstructural protein NSm.  This model describes a protein region that is cleaved from a bunyavirus polyprotein to become the nonstructural protein NSm (encoded by the M segment). It is flanked by glycoprotein GP2 and glycoprotein GP1.
CDD:234501	198	PRK	Bacteria:49	TIGR04211, SH3_and_anchor, SH3 domain protein.  Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.
CDD:211936	153	PRK	Bacteria:8	TIGR04213, PGF_pre_PGF, PGF-pre-PGF domain.  This domain occurs in archaeal species. Most domains in this family end with a motif PGF, after which the member sequences change in character to low-complexity sequence (usually Thr-rich) for about 40 residues. The low complexity region usually is followed by a PGF-CTERM domain (TIGR04126), which we suggest is the recognition sequence for archaeosortase A (TIGR04125), a putative protein-sorting transpeptidase. The ...
CDD:211937	27	PRK	Bacteria:13	TIGR04214, CSLREA_Nterm, CSLREA domain.  This model describes an N-terminal region, with a motif CSLREA, shared by tandem genes in Acinetobacter that both have the GlyGly-CTERM putative protein-sorting domain. Many proteins with this domain are putative outer membrane proteins (OMPs) with predicted beta strand-forming repeats.
CDD:234503	249	EUKprk	Bacteria:45,Environmental:1,Plants:1	TIGR04215, choice_anch_A, choice-of-anchor A domain.  This domain may occur as essentially the full length of a protein, except for an N-terminal sequence and a C-terminal protein-sorting signal such as PEP-CTERM or LPXTG. Most often, the putative surface protein is longer and contains repetitive sequence regions. This is one of very few domains for which both anchoring domains occur, and designated choice-of-anchor A domain. The best ...
CDD:234505	234	PRK	Bacteria:31	TIGR04219, OMP_w_GlyGly, outer membrane protein.  Members of this protein family are outer membrane proteins (OMP), as can be seen by their homology to YfaZ protein (see PMID:16522795) and by the OMP targeting region at the C-terminus, including a C-terminal Phe residue. Members of this protein family are found in the great majority of genomes with the GlyGly-CTERM protein sorting signal and the rhombosortase putative sorting enzyme, although the relationship may ...
CDD:234507	229	PRK	Bacteria:42	TIGR04222, near_uncomplex, TIGR04222 domain.  The majority of the proteins with a domain as described by this model have an extreme C-terminal sequence that is consists of extremely low-complexity sequence, rich in Ser or in Gly interspersed with Cys. That C-terminal region resembles ribosomal natural product precursors, although there is no evidence that C-terminal regions of these proteins undergo any modification or have any such function.
CDD:234508	37	PRK	Bacteria:92	TIGR04223, quorum_AgrD, cyclic lactone autoinducer peptide.  Members of this family of short peptides are precursors to thiolactone (unless Cys is replaced by Ser) cyclic autoinducer peptides, used in quorum-sensing systems in Gram-positive bacteria. The best characterized is the AgrD precursor, processed by the AgrB protein. Nearby proteins regularly encountered include a histidine kinase and a response regulator. This model is related to pfam05931 but is newer and ...
CDD:234509	50	PRK	Bacteria:16	TIGR04224, ser_adhes_Nterm, serine-rich repeat adhesion glycoprotein AST domain.  This model describes a definitive conserved N-terminal domain shared by Streptococcal serine-rich adhesion glycoproteins. These highly repetitive proteins may exceed 4000 amino acids in length, consisting largely of long regions in which every second amino acid is Ser. Members of this family, if sequenced completely and assigned the correct start site, begin with a KxYKxGKxW motif ...
CDD:234510	103	PRK	Bacteria:11	TIGR04225, CshA_fibril_rpt, CshA-type fibril repeat.  Many proteins with this repeat are LPXTG-anchored surface proteins of Firmicutes species, but the repeat occurs more broadly. Members include CshA from Streptococcus gordonii.
CDD:234511	124	PRK	Bacteria:139	TIGR04226, RrgB_K2N_iso_D2, fimbrial isopeptide formation D2 domain.  The Streptococcus Pneumoniae pilus backbone protein, RrgB, has three tandem domains with Lys-to-Asn isopeptide bonds, but these three regions are extremely divergent in sequence. This model represents the homology domain family of the D2 domain. It occurs just once in many surface proteins but up to twenty times in some pilin subunit proteins. Three of every four members have the typical ...
CDD:234512	173	PRK	Bacteria:28	TIGR04228, isopep_sspB_C2, adhesin isopeptide-forming domain, sspB-C2 type.  This domain has a conserved Lys (position 3 in seed alignment) and Asn at 177 that form an intramolecular isopeptide bond. The Asp (or Glu) at position 59.
CDD:234518	271	PRK	Bacteria:18	TIGR04239, rhombo_GlpG, rhomboid family protease GlpG.  GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. ...
CDD:213897	97	PRK	Synthetic:1,Viruses:30	TIGR04240, flavi_E_stem, flavivirus envelope glycoprotein E, stem/anchor domain.  This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.
CDD:211964	81	PRK	Viruses:12	TIGR04241, adenoE3CR1rpt, mastadenovirus E3 CR1-alpha-1.  This domain occurs only in the adenovirus E3 region CR1-alpha-1 protein. It may occur once, twice, or three times.
CDD:234521	377	PRK	Bacteria:33	TIGR04247, NosD_copper_fam, nitrous oxide reductase family maturation protein NosD.  Members of this family include NosD, a repetitive periplasmic protein required for the maturation of the copper-containing enzyme nitrous-oxide reductase. NosD appears to be part of a complex with NosF (an ABC transporter family ATP-binding protein) and NosY (a six-helix transmembrane protein in the ABC-2 permease family). However, NosDFY-like complexes appear to occur also in ...
CDD:234523	136	PRK	Bacteria:1	TIGR04254, OpituPEPCTERM_1, putative globular PEP-CTERM protein.  Representatives of this family include a 13-member paralogous family of proteins about 215 amino acids in length from the termite gut bacterium Opitutaceae bacterium TAV2, a member of the Verrucomicrobia. The signal peptide (N-terminal) and PEP-CTERM putative protein sorting signal (C-terminal) are not included in the seed alignment. Conserved residues such as an invariant Arg and a lack of ...
CDD:234524	249	PRK	Bacteria:64,nodiv:1	TIGR04255, sporadTIGR04255, TIGR04255 family protein.  Members of this uncharacterized protein family are found broadly but sporadically among bacteria and archaea, including members of the genera Mycobacterium, Nostoc, Acinetobacter, Planctomyces, Geobacter, Streptomyces, Methanospirillum, etc. The function is unknown.
CDD:211979	116	PRK	Bacteria:93,Environmental:1	TIGR04256, GxxExxY, GxxExxY protein.  Members of this protein family average about 130 residues in length and include an almost perfectly conserved motif GxxExxY. Members occur in a wide range of prokaryotes, including Proteobacteria, Perrucomicrobia, Cyanobacteria, Bacteriodetes, Archaea, etc.
CDD:211980	75	PRK	Bacteria:13	TIGR04257, nanowire_3heme, c(7)-type cytochrome triheme domain.  This domain binds three hemes, and itself occurs as a repeating unit. It occurs, for instance, four times in the dodecaheme c-type cytochrome protein GSU_1996, whose crystal structure shows elongation and a nanowire-like arrangement of twelve hemes that could function in extracellular electron transport processes.
CDD:211981	49	PRK	Bacteria:19	TIGR04258, 4helix_suffix, four helix bundle suffix domain.  This domain occurs as a suffix domain to some members of the much broader protein family TIGR02436, a few of whose other members are encoded within intervening sequences of bacterial 23S ribosomal RNA. Some proteins with this domain, in turn, are followed by a predicted DNA topoisomerase type C4 zinc finger.
CDD:234526	119	PRK	Bacteria:15	TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.  Members of this protein family average 125 in length, roughly half of which is the repetitive and extremely Gly-rich C-terminal region. Virtually all members occur in the Cyanobacteria, in a neighborhood that includes a radical SAM/SPASM domain, often a marker of peptide modification systems.
CDD:211984	363	PRK	Bacteria:12	TIGR04261, rSAM_GlyRichRpt, radical SAM/SPASM domain protein, GRRM system.  Members of this protein family are radical SAM/SPASM domain proteins (see pfam04055 and TIGR04085) related to anaeroboic sulfatase maturating enzymes and the peptide modification enzyme PqqE. Members are found primarily in Cyanobacteria adjacent to a short protein, ~150 residues, in which the last ~60 residues tends to be repetitive and highly glycine-rich (see TIGR04260). The arrangement ...
CDD:234527	366	PRK	Bacteria:14	TIGR04263, SasC_Mrp_aggreg, SasC/Mrp/FmtB intercellular aggregation domain.  This domain, about 375 amino acids long on average, occurs only in Staphylococcus and Streptococcus. It occurs as a non-repetitive N-terminal domain of LPXTG-anchored surface proteins, including SasC, Mrp, and FmtB. This region in SasC was shown to be involved in cell aggregation and biofilm formation, which may explain the methicillin resistance seen for Mrp and FmtB.
CDD:234529	399	PRK	Bacteria:24	TIGR04267, mod_HExxH, HEXXH motif domain.  Some proteins with this domain toward the C-terminus have an N-terminal region with a radical SAM domain (pfam04055) and a SPASM domain (TIGR04085), a combination frequently associated with peptide modification. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a motif HEXXH that suggests metalloprotease activity. A role in peptide or protein maturation is suggested.
CDD:211994	101	PRK	Bacteria:13	TIGR04271, ThiI_C_thiazole, thiazole biosynthesis domain.  The ThiI protein of Escherichia coli is a bifunctional protein in which most of the length of the protein is responsible for sulfurtransferase activity in 4-thiouridine modification to tRNA (EC 2.8.1.4 - see model TIGR00342). This rhodanese-like C-terminal domain, by itself, is able to synthesize the thiazole moiety during thiamin biosynthesis. Note that the invariant Cys residue in this domain is unusual ...
CDD:211995	37	PRK	Bacteria:36,Environmental:1	TIGR04272, cxxc_cxxc_Mbark, CxxC-x17-CxxC domain.  This domain, with a pair of CXXC motifs separated by 17 amino acids, is a candidate zinc finger domain based on these motifs. Some proteins have two copies of the domain, while others are fused to another probable zinc-binding domain, described by pfam13451.
CDD:211998	40	PRK	Bacteria:11	TIGR04275, beta_prop_Msarc, beta propeller repeat, Methanosarcina surface protein type.  This model describes a repeat region found mostly in cell surface proteins of various methanogens. Methanosarcina barkeri, for example, has twenty such proteins, often with either seven or fourteen repeats. These repeats resemble the beta propeller repeats of the TolB periplasmic protein of Gram-negative bacteria, part of a complex associated with various functions including ...
CDD:212004	330	PRK	Bacteria:10	TIGR04281, peripla_PGF_1, putative ABC transporter PGF-CTERM-modified substrate-binding protein.  Members of this archaeal protein family resemble periplasmic substrate-binding proteins of ABC transporters and appear in gene neighborhoods with permease and ATP-binding cassette proteins. Notably, essentially all members also have the PGF-CTERM putative protein-sorting domain at the C-terminus, while more distant homologs (excluded by the trusted cutoff) instead have ...
CDD:234531	189	PRK	Bacteria:94,Environmental:1	TIGR04282, glyco_like_cofC, transferase 1, rSAM/selenodomain-associated.  Members of this protein family show strongly correlated phylogenetic distribution, and in most cases co-clustering, with an unusual radical SAM enzyme (TIGR04167) whose C-terminal pfam12345 domain often contains a selenocysteine residue. Other members of the conserved gene neighborhood include another putative glycosyltransferase, an alkylhydroperoxidase family protein ...
CDD:234532	220	PRK	Bacteria:61	TIGR04283, glyco_like_mftF, transferase 2, rSAM/selenodomain-associated.  This enzyme may transfer a nucleotide, or it sugar moiety, as part of a biosynthetic pathway. Other proposed members of the pathway include another transferase (TIGR04282), a phosphoesterase, and a radical SAM enzyme (TIGR04167) whose C-terminal domain (pfam12345) frequently contains a selenocysteine [Unknown function, Enzymes of unknown specificity].
CDD:234533	255	PRK	Bacteria:41	TIGR04285, nucleoid_noc, nucleoid occlusion protein.  This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete.
CDD:234534	920	PRK	Bacteria:7	TIGR04286, MSEP-CTERM, MSEP-CTERM protein.  Members of this protein family average over 900 residues in length and appear to have multiple membrane-spanning helices in the N-terminal half. The extreme C-terminal region consists of a motif with consensus sequence MSEP, then a transmembrane alpha helix, then a short region with several basic residues. This region, hereby dubbed MSEP-CTERM, resembles other putative sorting signals associated with the ...
CDD:213900	163	PRK	Bacteria:7,Environmental:1	TIGR04287, exosort_XrtK, exosortase K.  Members of this protein family are exosortase K, a bacterial branch of the archaeosortase/exosortase family of protein-processing enzymes (see TIGR04178). All members of the seed alignment are encoded next to a member of family TIGR04286, which has the putative processing signal MSEP-CTERM (see family TIGR04286) at the extreme C-terminus.
CDD:213901	20	PRK	Bacteria:11	TIGR04288, CGP_CTERM, CGP-CTERM domain.  This domain has an essentially invariant motif, Cys-Gly-Pro, followed by a highly hydrophobic transmembrane domain, always at the protein C-terminus. It occurs, so far, strictly in the family Thermococcaceae (includes Thermococcus and Pyrococcus) within the Euryarchaeota. It occurs in ten proteins per genome on average, and proteins with the domain may lack similarity elsewhere. The presumed sorting/processing protein, for ...
CDD:213902	52	EUKprk	Bacteria:9,Invertebrates:1	TIGR04289, heavy_Cys, eight-cysteine-cluster domain.  In this domain of about 50 residues, eight of twelve invariant residues are Cys. Proteins with this domain tend to have N-terminal signal sequences, suggesting an extracytoplasmic location for this domain.
CDD:213907	16	PRK	Bacteria:15	TIGR04294, pre_pil_HX9DG, prepilin-type processing-associated H-X9-DG domain.  This model describes a region of ~16 residues found typically about 30 residues away from the C-terminus of large numbers of proteins in the Planctomycetes, Lentisphaerae, and Verrucomicrobia, on proteins with a prepilin-type N-terminal cleavage/methylation domain (see TIGR02532). The motif H-X(9)-D-G is nearly invariant. Single genomes may encode over 200 such proteins.
CDD:213909	30	PRK	Bacteria:4	TIGR04296, PEFG-CTERM, PEFG-CTERM domain.  This putative protein sorting/processing domain occurs about ten times per genome in members of the Thaumarchaeota. Its putative handling protein, a member of the archaeosortase/exosortase protein family, is exceptional in having a Ser rather than Cys at the putative active site. The highly conserved motif resembles the PEF-CTERM protein sorting domain of family TIGR03024, but membership does not overlap.
CDD:213918	212	PRK	Bacteria:9	TIGR04305, fol_rel_CADD, putative folate metabolism protein, CADD family.  This protein family, related to but outside the family of PqqC proteins involved in PQQ biosynthesis, includes the well-studied Chlamydia protein CADD (Chlamydia protein Associating with Death Domains), which can induce apoptosis in a host cell. Other members of this family occur in Rickettsia and Wolbachia, unrelated in terms of phylogeny (both are alphaproteobacteria) but similar in living ...
CDD:213920	23	PRK	Bacteria:2	TIGR04307, ProTailRpt, proline-rich tail region repeat.  This model describes a proline-rich tandem repeat of about 24 residues found in C-terminal regions of Gram-positive surface proteins with LPXTG sequences for processing and cell surface attachment by sortase.
CDD:234535	49	PRK	Bacteria:29	TIGR04308, repeat_SSSPR51, surface protein repeat SSSPR-51.  This repeat domain is designated SSRS51, Streptococcal and Staphylococcal Surface Protein Repeat of size 51. These repeats are homologous to the listerial repeats of pfam13461, but shorter on average by about 8 amino acids. Up to twelve tandem repeats can occur, on some of the longest proteins of their respective species. Nearly all member proteins carry the C-terminal sortase target sequence, LPXTG, ...
CDD:213924	423	PRK	Bacteria:12	TIGR04311, rSAM_Geo_metal, putative metalloenzyme radical SAM/SPASM domain maturase.  This model describes a family of radical SAM/SPASM enzymes largely from the deltaproteobacteria. The family is most closely related to radical SAM enzyme family regularly in archaea in the vicinity of tungsten-containing oxidoreductases. A single member of the family in archaea may correspond to multiple tungsten enzymes, e.g. five in Pyrococcus furiosus. Therefore, the lack of a ...
CDD:234536	364	PRK	Bacteria:8	TIGR04312, choice_anch_B, choice-of-anchor B domain.  This domain, about 385 amino acids long, can have either of at least two types of C-terminal sorting signal. Members from Shewanella and allies have the rhombosortase target domain GlyGly-CTERM (TIGR03501), while members of the Bacteroidetes have the Por secretion system C-terminal domain (TIGR04183). Most other members lack any C-terminal extension, but in most of those, the normal signal sequence is replaced by ...
CDD:234537	297	PRK	Bacteria:17	TIGR04313, aro_clust_Mycop, aromatic cluster surface protein.  Members of this family are absolutely restricted to the Mollicutes (Mycoplasma and Ureaplasma). All have a signal peptide, usually of the lipoprotein type, suggesting surface expression. Most members have lengths of about 280 residues but some members have a nearly full-length duplication. The mostly nearly invariant residue, a Trp,is part of a strongly conserved 9-residue motif, ...
CDD:234538	440	PRK	Bacteria:19	TIGR04315, octaheme_Shew, octaheme c-type cytochrome, tetrathionate reductase family.  Members of this protein family bind heme covalently and contain eight (at least) CXXCH heme-binding motifs. A characterized member is the respiratory enzyme octaheme tetrathionate reductase from Shewanella.
CDD:213929	250	PRK	Bacteria:10	TIGR04316, dhbA_paeA, 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase.  Members of this family are 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28), the third enzyme in the biosynthesis of 2,3-dihydroxybenzoic acid (DHB) from chorismate. The first two enzymes are isochorismate synthase (EC 5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is often followed by adenylation by the enzyme DHBA-AMP ligase (EC 2.7.7.58) to activate (DHB) for a ...
CDD:234539	349	PRK	Bacteria:10	TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical SAM maturase.  Members of this family are radical SAM enzymes involved in the maturation of tungsten (W)-containing cofactors in the enzymes aldehyde ferredoxin oxidoreductase, formaldehyde ferredoxin oxidoreductase, and others, and tend to be encoded by an adjacent gene.
CDD:213932	175	PRK	Bacteria:1,nodiv:1	TIGR04319, SerAla_Lrha_rpt, surface protein repeat Ser-Ala-175.  This serine and alanine-rich surface protein repeat, about 175 amino acids long, occurs up to nine times in surface proteins of some Lactobacillus strains, particularly in Lactobacillus rhamnosus. Members proteins have the N-terminal variant signal sequence described by TIGR03715 and C-terminal LPXTG signals for surface attachment by sortase.
CDD:234541	356	PRK	Bacteria:52,nodiv:3	TIGR04320, Surf_Exclu_PgrA, SEC10/PgrA surface exclusion domain.  This model describes a conserved domain found in surface proteins of a number of Firmutes. Many members have LPXTG C-terminal anchoring motifs and a substantial number have the KxYKxGKxW putative sorting signal at the N-terminus. The tetracycline resistance plasmid pCF10 in Enterococcus faecalis promotes conjugal plasmid transfer in response to sex pheromones, but PgrA/Sec10 encoded by that ...
CDD:234542	507	PRK	Bacteria:15	TIGR04321, spiroSPASM, spiro-SPASM protein.  This three-domain protein is restricted to the spirochetes and widely distributed (excepting Borrelia). It has a conserved C-terminal SPASM domain, a 4Fe-4S binding domain shared by a number of peptide-modifying and heme-modifying radical SAM proteins. It has a central radical SAM domain, although half the members have lost the signature 4Fe-4S-binding Cys residues, fail to register with the radical SAM domain definition ...
CDD:213935	215	PRK	Bacteria:20	TIGR04322, rSAM_QueE_Ecoli, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE.  Members of this radical SAM domain protein family appear to be the E. coli form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in species that lack known forms of QueE but usually are ...
CDD:213936	122	PRK	Bacteria:11	TIGR04323, SpoChoClust_1, sporadic carbohydrate cluster protein, LIC12192 family.  Members of this uncharacterized protein family mark a rare but widely distributed carbohydrate biosynthesis cluster found sporadically in genera Bradyrhizobium, Leptospira, Magnetospirillum, Oscillatoria, Prochlorococcus, etc.
CDD:234543	248	PRK	Bacteria:9	TIGR04324, SpoChoClust_2, sporadic carbohydrate cluster 2OG-Fe(II) oxygenase.  This family, related to streptomycin biosynthesis protein StrG and to phytanoyl-CoA dioxygenase, belongs to the 2-oxoglutarate and Fe(II)-dependent oxygenase superfamily, which includes not just dioxygenases, but also some chlorinating enzymes involved in natural product biosynthesis. Most members of this family are adjacent to a member of TIGR04323, and occur in a larger carbohydrate ...
CDD:234544	235	PRK	Bacteria:23	TIGR04325, MTase_LIC12133, putative methyltransferase, LIC12133 family.  Members of this family tend to occur next to glycosyltransferases and other characteristic enzymes of O-antigen biosynthetic regions. The founding member is LIC12133 from Leptospira interrogans serovar Copenhageni. PSI-BLAST reveals distant homology to known SAM-dependent methyltransferases, as in pfam13489.
CDD:234548	585	PRK	Bacteria:13,Environmental:1	TIGR04331, o_ant_LIC12162, putative transferase, LIC12162 family.  This protein family shows C-terminal sequence similarity to various surface carbohydrate biosynthesis enzymes: spore coat polysaccharide biosynthesis protein SpsB, UDP-N-acetyl-D-glucosamine 2-epimerase, lipid A disaccharide synthetase LpxB, etc. It may occur in O-antigen biosythesis regions.
CDD:234549	307	PRK	Bacteria:21	TIGR04332, gamma_Glu_sys, poly-gamma-glutamate system protein.  Poly(gamma-glutamic acid), or PGA, is an extracellular structural polymer found in Bacillus subtilis and a number of other species. PGA is sometimes capsule-forming, sometimes secretory, and may be produced by Gram-positive (single plasma membrane) and Gram-negative (inner and outer membranes), so export and/or attachment machinery may differ from system to system. Members of this family occur in a ...
CDD:234550	175	PRK	Bacteria:38	TIGR04335, AmmeMemoSam_A, AmmeMemoRadiSam system protein A.  Members of this protein family belong to the same domain family as AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. Members of the present family occur as part of a three gene system with a homolog of the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility), and an uncharacterized radical SAM enzyme.
CDD:234551	269	PRK	Bacteria:58	TIGR04336, AmmeMemoSam_B, AmmeMemoRadiSam system protein B.  Members of this protein family belong to the same domain family as the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility). Members of the present family occur as part of a three gene system with an uncharacterized radical SAM enzyme and a homolog of the mammalian protein AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. ...
CDD:213950	349	PRK	Bacteria:21	TIGR04337, AmmeMemoSam_rS, AmmeMemoRadiSam system radical SAM enzyme.  Members of this protein family are uncharacterized radical SAM enzymes that occur in a prokaryotic three-gene system along with homologs of mammalian proteins Memo (Mediator of ErbB2-driven cell MOtility) and AMMERCR1 (Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis). Among radical SAM enzymes that have been experimentally characterized, the most closely related in ...
CDD:234552	159	PRK	Bacteria:15	TIGR04338, HEXXH_Rv0185, putative metallohydrolase, TIGR04338 family.  This protein family is restricted to the Actinomycetales, including Mycobacterium, Rhodococcus, Nocardia, Gordonii, and others. The invariant motif HEXXH, at the core of the best conserved region in the protein, suggests metallohydrolase activity, as does local sequence similarity in this region to other metallohydrolases.
CDD:234553	124	PRK	Bacteria:21	TIGR04342, EXLDI, EXLDI protein.  The most conserved region in this protein family is the C-terminal pentapeptide, with motif ExLDI. Members from the Firmicutes average about 120 amino acids in length, while members from the Actinobacteria have an additional 45-residue amino-terminal segment not included in the model. In PMID:21756306 it is suggested that the member from Streptococcus mutans UA159, and its homologs, participate in bacteriocin production, export, or immunity.
CDD:234555	442	EUKprk	Bacteria:17,Invertebrates:3	TIGR04344, ovoA_Nterm, 5-histidylcysteine sulfoxide synthase.  Ovothiol A is N1-methyl-4-mercaptohistidine. In the absence of S-adenosylmethione, a methyl donor, the intermediate produced is 4-mercaptohistidine. In both Erwinia tasmaniensis and Trypanosoma cruzi, a protein occurs with 5-histidylcysteine sulfoxide synthase activity, but these two enzymes and most homologs share an additional C-terminal methyltransferase domain. Thus OvoA may be a ...
CDD:234556	242	EUKprk	Bacteria:12,Environmental:1,Invertebrates:5	TIGR04345, ovoA_Cterm, putative 4-mercaptohistidine N1-methyltranferase.  Ovothiol A is N1-methyl-4-mercaptohistidine. In the absence of S-adenosylmethione, a methyl donor, the intermediate produced is 4-mercaptohistidine. In both Erwinia tasmaniensis and Trypanosoma cruzi, a protein occurs with 5-histidylcysteine sulfoxide synthase activity, but these two enzymes and most homologs share an additional C-terminal methyltransferase ...
CDD:234557	652	PRK	Bacteria:19	TIGR04346, DotA_TraY, conjugal transfer/type IV secretion protein DotA/TraY.  Members of this protein family include transfer protein TraY of IncI1 plasmid R64 and DotA (defect in organelle trafficking A) of Legionella pneumophila.
CDD:213961	310	PRK	Bacteria:13	TIGR04348, TIGR04348, putative glycosyltransferase, TIGR04348 family.  This putative glycosyltransferase is found in marine bacteria such as Marinobacter and soil bacteria such as Anaeromyxobacter, but does not seem to occur in known pathogenic bacteria.
CDD:213962	210	PRK	Bacteria:34	TIGR04349, rSAM_QueE_gams, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type.  Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack ...
CDD:213963	384	PRK	Bacteria:11	TIGR04350, C_S_lyase_PatB, putative C-S lyase.  Members of this subfamily are probable C-S lyases from a family of pyridoxal phosphate-dependent enzymes that tend to be (mis)annotated as probable aminotransferases. One member is PatB of Bacillus subtilis, a proven C-S-lyase. Another is the virulence factor cystalysin from Treponema denticola, whose hemolysin activity may stem from H2S production. Members of the seed alignment occur next to examples of the enzyme ...
CDD:213965	280	PRK	Bacteria:12	TIGR04352, HprK_rel_A, HprK-related kinase A.  A number of protein families resemble HPr kinase (see TIGR00679) but do not belong to that system. They include this family, which appears instead to be the marker for a different type of gene neighborhood, in which one of the conserved neighboring proteins resembles (but is distinct from) PqqD.
CDD:234558	73	PRK	Bacteria:23	TIGR04353, PqqD_rel_X, PqqD family protein, HPr-rel-A system.  Members of this protein show distant homology to PqqD, and belong to a three-gene cassette that included the HPr kinase related protein family of TIGR04352. The role of the cassette, and of this protein, are unknown.
CDD:213967	67	PRK	Bacteria:56	TIGR04354, amphi-Trp, amphi-Trp domain.  This domain usually comprises most of the span of bacterial or archaeal proteins with a length of about 90 amino acids. Some members, however, are extended by one or two copies of domain pfam07411 in the C-terminal region. No residue in this domain is invariant. A striking feature of this domain is a C-terminal region that alternates strongly charged with strongly hydrophobic residues and usually ends with a Trp residue, e.g. ...
CDD:213970	368	PRK	Bacteria:16	TIGR04357, CofD_rel_GAK, CofD-related protein, GAK system.  Members of this family are distantly related to CofD, the enzyme LPPG:FO 2-phospho-L-lactate transferase, involved in coenzyme F420 biosynthesis. This family appears to belong to a biosynthesis cassette of unknown function.
CDD:234559	90	PRK	Bacteria:8	TIGR04358, XXXCH_domain, XXXCH domain.  Members of this family show C-terminal sequence similarity, perhaps indicating distant homology, to cytochrome c-prime (see pfam01322). However, the motif CxxCH is replaced by xxxCH. Genes for this protein occur in a sporadically distributed genome context, largely in deltaProteobacteria, in which an ATP-grasp family glutamate ligase homolog and a CofD (LPPG:FO 2-phospho-L-lactate transferase) homolog suggest a novel biosynthesis.
CDD:213973	74	PRK	Bacteria:21,Environmental:1	TIGR04360, other_trbK, conjugative transfer region protein TrbK.  Members of this family regularly are encoded between the TrbJ and TrbL proteins essential for P-type conjugal transfer, and therefore are designated TrbK. Positional analogy to family TIGR04359 (the entry exclusion lipoprotein TrbK of IncP plasmid RP4), which is a lipoprotein and not homologous, suggests this protein may also be involved in entry exclusion. Members of this family are ...
CDD:234561	63	PRK	Bacteria:14	TIGR04361, TrbK_Ti, entry exclusion protein TrbK, Ti-type.  Members of this family are encoded between the genes for TrbJ and TrbL of P-type plasmid conjugal transfer systems, and therefore are TrbK, a member of a guild of unrelated TrbK protein families. The similarly located TrbK of plasmid RP4 (family TIGR04359) functions in entry exclusion, and the current family may as well, despite lacking any detectable homology. Members of this family include TrbK of the Ti ...
CDD:234562	157	PRK	Bacteria:14	TIGR04362, choice_anch_C, choice-of-anchor C domain.  This family describes an extracellular bacterial domain that occurs on a number of proteins with PEP-CTERM (exosortase recognition site) sequences at the C-terminus, as well some with an apparent alternate anchor sequence. Note that related pfam04862 (DUF642), as of release 26, is double the length of this model because it has two tandem regions homologous to this domain. pfam04862, in turn, belongs to a Pfam ...
CDD:213976	37	PRK	Bacteria:17	TIGR04363, LD_lanti_pre, FxLD family lantipeptide.  Members of this protein family occur with a cassette of lanthionine-type peptide modification enzymes. Members are small (about 60 amino acids long), rich in Cys, and variable in copy number per genome (from one to three). These features suggest that members of this family are modified to become lantipeptides, although not necessarily a lantibiotic. There is no GlyGly cleavage motif to separate a leader peptide ...
CDD:234563	394	PRK	Bacteria:10	TIGR04364, methyltran_FxLD, methyltransferase, FxLD system.  Members of this family resemble occur regularly in the vicinity of lantibiotic biosynthesis enzymes and their probable target, the FxLD family of putative ribosomal natural product precursor (TIGR04363). Members resemble protein-L-isoaspartate O-methyltransferase (TIGR00080) and a predicted methyltranserase, TIGR04188, of another putative peptide modification system.
CDD:213979	132	PRK	Bacteria:46	TIGR04366, cupin_WbuC, cupin fold metalloprotein, WbuC family.  Members of this family show sequence similarity to cupin fold proteins (see pfam07883), including conserved His residues likely to serve as metal-binding ligands. Many members occur in bacterial O-antigen biosynthesis regions. Some members have acquired the gene symbol wbuC (e.g. Jarvis, et al, 2011), but publications using this term do not ascribe a function.
CDD:237975	151	PRK	Bacteria:10	cd00001, PTS_IIB_man, PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their ...
CDD:237976	152	PRK	Bacteria:97	cd00002, YbaK_deacylase, This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain.  The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase.   YbaK also ...
CDD:237977	234	EUKprk	Bacteria:29,Environmental:1,Invertebrates:1	cd00003, PNPsynthase, Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and ...
CDD:99708	128	PRK	Bacteria:16	cd00004, Sortase, Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on ...
CDD:187674	185	PRK	Bacteria:28	cd00005, CBM9_like_1, DOMON-like type 9 carbohydrate binding module of xylanases.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues ...
CDD:237978	122	PRK	Bacteria:18,nodiv:1	cd00006, PTS_IIA_man, PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their ...
CDD:99707	151	EUKprk	Bacteria:35,Invertebrates:4,Plants:9,Primates:1,Rodents:2,Viruses:2	cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of ...
CDD:237980	63	EUK	Plants:11	cd00010, AAI_LTSS, AAI_LTSS: Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein family; a protein family unique to higher plants that includes cereal-type alpha-amylase inhibitors, lipid transfer proteins, seed storage proteins, and similar proteins. Proteins in this family are known to play important roles, in defending plants from insects and pathogens, lipid transport between intracellular membranes, and nutrient storage. Many ...
CDD:212657	185	EUKprk	Bacteria:48,Invertebrates:5,Mammals:1,Plants:9,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00012, NBD_sugar-kinase_HSP70_actin, Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily.  This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as ...
CDD:200435	97	EUK	Mammals:1,Plants:3,Primates:1,Rodents:1	cd00013, ADF_gelsolin, Actin depolymerization factor/cofilin- and gelsolin-like domains.  Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
CDD:237981	107	EUK	Invertebrates:8,Plants:4,Primates:1,Rodents:2	cd00014, CH, Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
CDD:237982	185	EUK	Mammals:5,Primates:2,Rodents:3,Vertebrates:7	cd00015, ALBUMIN, Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; alpha-albumin which binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs; and afamin of which little is known; these belong ...
CDD:237983	384	EUKprk	Bacteria:6,Invertebrates:4,Mammals:1,Plants:2,Primates:1	cd00016, alkPPc, Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity.
CDD:237984	70	EUK	Invertebrates:2,Mammals:3,Primates:1,Rodents:3,Vertebrates:13	cd00017, ANATO, Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to repeats in fibulins.
CDD:237985	61	EUK	Plants:5	cd00018, AP2, DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a ...
CDD:237986	279	EUKprk	Bacteria:8,Invertebrates:3,Plants:1,Viruses:3	cd00019, AP2Ec, AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar. .
CDD:237987	120	EUK	Invertebrates:2,Mammals:1,Plants:4,Primates:1,Rodents:2,nodiv:1	cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been ...
CDD:237988	39	EUK	Invertebrates:3,Plants:6,Primates:1,Rodents:2,Vertebrates:1	cd00021, BBOX, B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
CDD:237989	69	EUKprk	Invertebrates:3,Plants:3,Primates:1,Rodents:1,Vertebrates:2,Viruses:14,nodiv:1	cd00022, BIR, Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one ...
CDD:237990	55	EUK	Plants:13	cd00023, BBI, Bowman-Birk type proteinase inhibitor (BBI); family of plant serine protease inhibitors that block trypsin or chymotrypsin.They are either single-headed (one reactive site, one inactive site, present mainly in monocotyledonous seeds) or double-headed (two reactive sites, present mainly in dicotyledonous seeds).
CDD:237991	55	EUKprk	Invertebrates:7,Plants:16,Primates:1,Rodents:2,Vertebrates:3,Viruses:1	cd00024, CHROMO, Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, ...
CDD:237992	223	EUK	Invertebrates:1,Mammals:1,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd00025, BPI1, BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with ...
CDD:237993	200	EUK	Mammals:2,Primates:1	cd00026, BPI2, BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets ...
CDD:237994	72	EUKprk	Bacteria:7,Invertebrates:5,Plants:9,Primates:1,Rodents:2,Vertebrates:5	cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
CDD:237995	116	EUKprk	Bacteria:1,Invertebrates:1,Plants:20	cd00028, B_lectin, Bulb-type mannose-specific lectin. The domain contains a three-fold internal repeat (beta-prism architecture). The consensus sequence motif QXDXNXVXY is involved in alpha-D-mannose recognition. Lectins are carbohydrate-binding proteins which specifically recognize diverse carbohydrates and mediate a wide variety of biological processes, such as cell-cell and host-pathogen interactions, serum glycoprotein turnover, and ...
CDD:237996	50	EUK	Invertebrates:2,Mammals:1,Plants:4,Primates:1,Rodents:3	cd00029, C1, Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor ...
CDD:175973	102	EUKprk	Bacteria:1,Invertebrates:50,Mammals:4,Plants:49,Primates:2,Rodents:3,Vertebrates:4,nodiv:2	cd00030, C2, C2 domain.  The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind ...
CDD:237997	243	EUK	Invertebrates:4,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd00032, CASc, Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of ...
CDD:153056	57	EUKprk	Invertebrates:5,Mammals:5,Primates:1,Rodents:5,Vertebrates:4,Viruses:9,nodiv:1	cd00033, CCP, Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system.  SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately ...
CDD:237998	54	EUK	Invertebrates:3,Plants:4,Rodents:1	cd00034, ChSh, Chromo Shadow Domain,  found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2).
CDD:211311	39	EUK	Invertebrates:2,Plants:12	cd00035, ChtBD1, Hevein or type 1 chitin binding domain.  Hevein or type 1 chitin binding domain (ChtBD1), a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural rubber latex, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it ...
CDD:153057	116	EUKprk	Bacteria:14,Invertebrates:52,Mammals:3,Plants:2,Primates:2,Rodents:4,Vertebrates:42,nodiv:1	cd00037, CLECT, C-type lectin (CTL)/C-type lectin-like (CTLD) domain.  CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are ...
CDD:237999	115	EUKprk	Bacteria:48,Invertebrates:12,Mammals:1,Plants:18,Primates:2,Rodents:2,nodiv:2	cd00038, CAP_ED, effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic ...
CDD:238001	113	EUKprk	Invertebrates:11,Mammals:4,Primates:1,Rodents:2,Vertebrates:9,Viruses:1	cd00041, CUB, CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
CDD:238002	105	EUK	Invertebrates:6,Mammals:1,Plants:12,Primates:1,Rodents:3,Vertebrates:5	cd00042, CY, Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains.
CDD:238003	88	EUKprk	Bacteria:9,Environmental:1,Invertebrates:23,Mammals:1,Plants:35,Primates:1,Rodents:2,Vertebrates:7,Viruses:5	cd00043, CYCLIN, Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
CDD:238004	315	EUKprk	Bacteria:2,Invertebrates:5,Plants:4,Primates:1,Rodents:2	cd00044, CysPc, Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
CDD:260016	77	EUKprk	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:1,Viruses:1,nodiv:1	cd00045, DED, Death Effector Domain: a protein-protein interaction domain.  Death Effector Domains comprise a subfamily of the Death Domain (DD) superfamily. DED-containing proteins include Fas-Associated via Death Domain (FADD), Astrocyte phosphoprotein PEA-15, the initiator caspases (caspase-8 and -10), and FLICE-inhibitory protein (FLIP), among others. These proteins are prominent components of the ...
CDD:238005	144	EUKprk	Bacteria:12,Invertebrates:4,Mammals:1,Plants:7,Primates:1,Rodents:3,Vertebrates:1,Viruses:25	cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
CDD:238006	231	EUKprk	Bacteria:2,Invertebrates:6,Plants:3,Primates:1,Rodents:2,Vertebrates:5	cd00047, PTPc, Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either ...
CDD:238007	68	EUKprk	Bacteria:11,Invertebrates:4,Mammals:1,Plants:3,Primates:2,Rodents:2,Vertebrates:4,Viruses:14,nodiv:1	cd00048, DSRM, Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
CDD:238008	63	EUKprk	Bacteria:2,Invertebrates:14,Mammals:2,Plants:7,Primates:1,Rodents:4,Vertebrates:5	cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
CDD:238009	67	EUK	Invertebrates:4,Plants:4,Primates:1,Rodents:1,Vertebrates:1	cd00052, EH, Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class ...
CDD:238010	36	EUKprk	Invertebrates:15,Mammals:4,Plants:3,Primates:1,Rodents:2,Vertebrates:5,Viruses:2,nodiv:1	cd00053, EGF, Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these ...
CDD:238011	38	EUK	Invertebrates:13,Plants:2,Primates:2,Rodents:3,Vertebrates:5	cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form ...
CDD:238012	50	EUK	Invertebrates:8,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	cd00055, EGF_Lam, Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this ...
CDD:238013	158	EUKprk	Bacteria:23,Invertebrates:2,Plants:4,Primates:1,nodiv:1	cd00056, ENDO3c, endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases.
CDD:238014	143	EUKprk	Bacteria:3,Invertebrates:3,Mammals:1,Plants:1,Primates:1,Rodents:2	cd00057, FA58C, Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
CDD:238015	123	EUKprk	Invertebrates:3,Mammals:1,Primates:1,Rodents:2,Vertebrates:3,Viruses:7	cd00058, FGF, Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate ...
CDD:238016	78	EUK	Invertebrates:3,Plants:2,Primates:1,Rodents:2,Vertebrates:1	cd00059, FH, Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops ...
CDD:238017	102	EUKprk	Bacteria:13,Invertebrates:5,Mammals:2,Plants:13,Primates:1,Rodents:1,Vertebrates:2	cd00060, FHA, Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or ...
CDD:238018	43	EUK	Mammals:2,Primates:1,Rodents:2,Vertebrates:2	cd00061, FN1, Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices.  ...
CDD:238019	48	EUK	Mammals:5,Primates:1,Rodents:1,Vertebrates:1	cd00062, FN2, Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond ...
CDD:238020	93	EUKprk	Bacteria:25,Invertebrates:14,Mammals:3,Phages:3,Plants:1,Primates:1,Rodents:3,Vertebrates:8	cd00063, FN3, Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine ...
CDD:238021	49	EUK	Invertebrates:12,Mammals:1,Primates:1,Rodents:2,Vertebrates:6,nodiv:1	cd00064, FU, Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
CDD:238022	57	EUK	Invertebrates:6,Plants:7,Primates:1,Rodents:2,Vertebrates:1	cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
CDD:206639	315	EUK	Invertebrates:20,Mammals:1,Plants:23,Primates:1,Rodents:2,Vertebrates:4	cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide binding).  The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G ...
CDD:238023	36	EUK	Plants:26	cd00067, GAL4, GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain; found in transcription regulators like GAL4.  Domain consists of two helices organized around a Zn(2)Cys(6 )motif; Binds to sequences containing 2 DNA half sites comprised of 3-5 C/G combinations.
CDD:238024	57	EUK	Invertebrates:3,Mammals:1,Plants:1,Primates:1,Rodents:2	cd00068, GGL, G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors.
CDD:200450	96	EUK	Invertebrates:16,Mammals:8,Primates:7,Rodents:2,Vertebrates:61,nodiv:2	cd00069, GHB_like, Glycoprotein hormone beta chain homologues.  This family of cystine-knot hormones includes the beta chains of gonadotropins, thyrotropins, follitropins, choriogonadotropins and more. The members are reproductive hormones that consist of two glycosylated chains (alpha and beta), which form a tightly bound dimer.
CDD:238025	127	EUKprk	Invertebrates:8,Mammals:3,Plants:2,Primates:1,Rodents:2,Vertebrates:7,Viruses:2	cd00070, GLECT, Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
CDD:238026	137	EUKprk	Bacteria:13,Invertebrates:4,Plants:8,Primates:1,Vertebrates:3,Viruses:1	cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the ...
CDD:238027	57	EUK	Invertebrates:2,Plants:4,Primates:1,Rodents:1,Vertebrates:1	cd00072, GYF, GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
CDD:238028	88	EUK	Invertebrates:21,Plants:15,Primates:1,Rodents:2,Vertebrates:3	cd00073, H15, linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher ...
CDD:238029	115	EUK	Invertebrates:7,Plants:6,Primates:1,Rodents:1,Vertebrates:2	cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
CDD:238030	103	EUKprk	Bacteria:130,Invertebrates:6,Mammals:1,Phages:1,Plants:33,Primates:1,Rodents:2	cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins.
CDD:238032	145	EUKprk	Bacteria:48,Invertebrates:6,Mammals:1,Plants:5,Primates:1,Rodents:1	cd00077, HDc, Metal dependent phosphohydrolases with conserved 'HD' motif.
CDD:238033	352	EUK	Invertebrates:3,Plants:3,Primates:1,Rodents:1,Vertebrates:1	cd00078, HECTc, HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
CDD:238034	131	EUKprk	Bacteria:1,Invertebrates:1,Phages:2,Plants:1,Primates:1,Rodents:1,Viruses:1	cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the ...
CDD:188616	71	EUKprk	Bacteria:242,Environmental:5,Invertebrates:36,Phages:5,Plants:42,Primates:1,Rodents:1,Vertebrates:3	cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination.  The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA ...
CDD:238035	136	EUKprk	Bacteria:14,Invertebrates:3,Phages:1,Plants:3,Primates:1,Rodents:1,Vertebrates:6	cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing ...
CDD:119399	65	EUKprk	Bacteria:65,Invertebrates:1,Plants:5,Viruses:1	cd00082, HisKA, Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator ...
CDD:238036	60	EUK	Invertebrates:7,Mammals:1,Plants:9,Primates:2,Rodents:3,Vertebrates:6,nodiv:1	cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates ...
CDD:238037	66	EUKprk	Invertebrates:20,Plants:23,Primates:1,Rodents:3,Vertebrates:4,Viruses:1	cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, ...
CDD:238038	57	EUKprk	Bacteria:29,Invertebrates:1,Phages:24,Plants:11,Primates:1,Viruses:2,nodiv:1	cd00085, HNHc, HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
CDD:238039	59	EUK	Invertebrates:31,Mammals:2,Plants:23,Primates:1,Rodents:3,Vertebrates:4,nodiv:1	cd00086, homeodomain, Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
CDD:238040	215	EUK	Invertebrates:7,Mammals:1,Primates:2,Rodents:2,Vertebrates:3	cd00087, FReD, Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular ...
CDD:238041	94	EUKprk	Bacteria:14,Plants:5,Viruses:1	cd00088, HPT, Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component ...
CDD:212008	68	EUK	Invertebrates:1,Plants:2,Primates:1,Vertebrates:1	cd00089, HR1, Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases.  The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and ...
CDD:238042	78	EUKprk	Bacteria:42,Phages:1,Vertebrates:1,nodiv:1	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
CDD:238043	241	EUKprk	Bacteria:3,Invertebrates:3,Mammals:1,Plants:3,Primates:1,Rodents:2,Viruses:1	cd00091, NUC, DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
CDD:238044	67	PRK	Bacteria:10	cd00092, HTH_CRP, helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
CDD:238045	58	EUKprk	Bacteria:106,Invertebrates:2,Phages:48,Plants:5,Primates:1,nodiv:2	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
CDD:238046	194	EUK	Invertebrates:4,Mammals:3,Plants:2,Primates:1,Rodents:2,Vertebrates:3	cd00094, HX, Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
CDD:238047	152	EUK	Mammals:7,Primates:1,Rodents:1,Vertebrates:2	cd00095, IFab, Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various ...
CDD:143165	74	EUK	Invertebrates:27,Mammals:22,Primates:4,Rodents:4,Vertebrates:59,nodiv:2	cd00096, Ig, Immunoglobulin domain.  Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and ...
CDD:143166	95	miss	miss	cd00098, IgC, Immunoglobulin Constant domain.  IgC: Immunoglobulin constant domain (IgC). Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the ...
CDD:143167	105	miss	miss	cd00099, IgV, Immunoglobulin variable domain (IgV).  IgV: Immunoglobulin variable domain (IgV). Members of the IgV family are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in ...
CDD:238048	144	EUK	Mammals:5,Primates:1,Rodents:2	cd00100, IL1, Interleukin-1 homologes; Cytokines with various biological functions. Interleukin 1 alpha and beta are also known as hematopoietin and catabolin. This family also contains interleukin-1 receptor antagonists (inhibitors).
CDD:238049	41	EUK	Invertebrates:18,Mammals:9,Primates:3,Rodents:16,Vertebrates:18	cd00101, IlGF_like, Insulin/insulin-like growth factor/relaxin family; insulin family of proteins. Members include a number of active peptides which are evolutionary related including insulin, relaxin, prorelaxin, insulin-like growth factors I and II, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), insect prothoracicotropic hormone ...
CDD:238050	89	EUKprk	Bacteria:13,Invertebrates:11,Plants:3,Primates:1,Rodents:2,Vertebrates:4,Viruses:1	cd00102, IPT, Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in ...
CDD:238051	107	EUKprk	Primates:1,Rodents:1,Vertebrates:4,Viruses:5	cd00103, IRF, Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host ...
CDD:238052	41	EUK	Invertebrates:26,Mammals:5,Plants:3,Primates:2,Rodents:3,Vertebrates:15	cd00104, KAZAL_FS, Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors ...
CDD:238053	64	EUKprk	Bacteria:25,Environmental:1,Invertebrates:16,Mammals:1,Plants:22,Primates:2,Rodents:2,Vertebrates:4	cd00105, KH-I, K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha ...
CDD:238054	328	EUK	Invertebrates:10,Plants:5,Primates:1,Rodents:1,Vertebrates:1	cd00106, KISc, Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and ...
CDD:238055	33	EUK	Invertebrates:18,Plants:19	cd00107, Knot1, The "knottin" fold is stable cysteine-rich scaffold, in which one disulfide bridge crosses the macrocycle made by two other disulfide bridges and the connecting backbone segments. Members include plant lectins/antimicrobial peptides, plant proteinase/amylase inhibitors, plant gamma-thionins, and arthropod defensins.
CDD:238056	83	EUK	Invertebrates:3,Mammals:2,Primates:1,Vertebrates:5	cd00108, KR, Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides.
CDD:238057	54	EUK	Invertebrates:9,Mammals:3,Primates:1,Rodents:2,Vertebrates:10	cd00109, KU, BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
CDD:238058	151	EUKprk	Bacteria:1,Invertebrates:4,Mammals:1,Primates:1,Rodents:2	cd00110, LamG, Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
CDD:238059	44	EUK	Invertebrates:3,Mammals:5,Primates:2,Rodents:1,Vertebrates:8	cd00111, Trefoil, P or trefoil or TFF domain; Trefoil factor family domain peptides are mucin-associated molecules, largely found in epithelia of gastrointestinal tissues. Function is not known but it was originally identified from mucosal tissues, where it may have a regulatory or structural role and has also been implicated as a growth fractor in other tissues.The domain is found in 1 to 6 copies where it occurs.
CDD:238060	35	EUK	Invertebrates:16,Mammals:4,Primates:1,Rodents:2,Vertebrates:7,nodiv:2	cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, ...
CDD:238061	116	EUKprk	Bacteria:2,Invertebrates:4,Mammals:2,Plants:3,Primates:1,Rodents:1,Vertebrates:1	cd00113, PLAT, PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered ...
CDD:238062	307	PRK	Bacteria:9	cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield ...
CDD:238063	141	EUKprk	Bacteria:26,Invertebrates:3,Mammals:1,Plants:4,nodiv:1	cd00115, LMWPc, Low molecular weight phosphatase family;.
CDD:238064	319	EUK	Invertebrates:1,Mammals:1,Plants:1,Primates:1,Rodents:2,Vertebrates:1	cd00116, LRR_RI, Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands ...
CDD:238065	79	EUKprk	Mammals:4,Primates:9,Rodents:3,Vertebrates:1,Viruses:2	cd00117, LU, Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins.
CDD:212030	45	EUKprk	Bacteria:623,Environmental:6,Invertebrates:11,Plants:31,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan.  LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological ...
CDD:238066	123	EUK	Invertebrates:11,Mammals:11,Primates:1,Rodents:3,Vertebrates:6	cd00119, LYZ1, C-type lysozyme (1, 4-beta-N-acetylmuramidase, LYZ) and alpha-lactalbumin (lactose synthase B protein, LA). They have a close evolutionary relationship and similar tertiary structure, however, functionally they are quite different. Lysozymes have primarily bacteriolytic function; hydrolysis of peptidoglycan of prokaryotic cell walls and transglycosylation. LA is a calcium-binding metalloprotein that ...
CDD:238067	59	EUK	Plants:22,Primates:1	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early ...
CDD:238068	126	EUK	Invertebrates:21,Mammals:1,Plants:15,Primates:1,Rodents:1,Vertebrates:4	cd00121, MATH, MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as ...
CDD:238069	62	EUK	Invertebrates:4,Plants:3,Primates:1,Rodents:1,Vertebrates:4	cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as ...
CDD:238071	679	EUK	Invertebrates:16,Plants:5,Primates:1,Rodents:1,Vertebrates:1	cd00124, MYSc, Myosin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A ...
CDD:153091	115	EUK	Invertebrates:11,Mammals:1,Primates:1,Rodents:1,Vertebrates:19	cd00125, PLA2c, PLA2c: Phospholipase A2, a family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic ...
CDD:238072	36	EUK	Invertebrates:5,Mammals:2,Primates:1,Vertebrates:7	cd00126, PAH, Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, ...
CDD:238073	139	EUKprk	Invertebrates:4,Plants:4,Primates:1,Rodents:1,Viruses:8	cd00127, DSPc, Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
CDD:238075	103	EUKprk	Bacteria:19,Invertebrates:5,Plants:2,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
CDD:238077	42	EUK	Invertebrates:3,Plants:4,Primates:1,Rodents:1,Vertebrates:1	cd00132, CRIB, PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, ...
CDD:99904	84	PRK	Bacteria:153	cd00133, PTS_IIB, PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven ...
CDD:238078	218	EUKprk	Bacteria:25,Rodents:1,nodiv:1	cd00134, PBPb, Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for ...
CDD:238079	86	EUKprk	Invertebrates:2,Primates:1,Rodents:2,Vertebrates:2,Viruses:3	cd00135, PDGF, Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the ...
CDD:238080	70	EUKprk	Bacteria:25,Invertebrates:5,Plants:2,Primates:1,Rodents:2,Vertebrates:2	cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated ...
CDD:197200	119	EUKprk	Bacteria:44,Invertebrates:2,Plants:10,Primates:1	cd00138, PLDc_SF, Catalytic domain of phospholipase D superfamily proteins.  Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA ...
CDD:238081	313	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:1	cd00139, PIPKc, Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated ...
CDD:238082	365	EUKprk	Bacteria:60,Invertebrates:1,nodiv:1	cd00140, beta_clamp, Beta clamp domain.  The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria.  The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69).  This structural correspondence further ...
CDD:143386	307	EUKprk	Bacteria:16,Invertebrates:4,Plants:9,Primates:1,Rodents:2,Synthetic:1,Vertebrates:4	cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X DNA Polymerases.  X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol ...
CDD:270621	216	EUK	Invertebrates:3,Mammals:1,Primates:1	cd00142, PI3Kc_like, Catalytic domain of Phosphoinositide 3-kinase and similar proteins.  Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRAPP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K ...
CDD:238083	254	EUKprk	Bacteria:13,Invertebrates:9,Plants:11,Primates:2,Rodents:2,Vertebrates:1,Viruses:2	cd00143, PP2Cc, Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.
CDD:163613	225	EUKprk	Bacteria:47,Invertebrates:18,Mammals:1,Plants:13,Primates:1	cd00144, MPP_PPP_family, phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain.  The PPP (phosphoprotein phosphatase) family is one of two known protein phosphatase families specific for serine and threonine.  This family includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three ...
CDD:99912	323	EUKprk	Bacteria:5,Invertebrates:2,Phages:1,Primates:1	cd00145, POLBc, DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be ...
CDD:238084	81	EUKprk	Bacteria:14,Mammals:1,Primates:1,Rodents:1,Vertebrates:2,Viruses:2	cd00146, PKD, polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.
CDD:132835	438	EUK	Invertebrates:2,Mammals:1,Plants:12,Primates:1,Rodents:1,Vertebrates:3	cd00147, cPLA2_like, Cytosolic phospholipase A2, catalytic domain; hydrolyses arachidonyl phospholipids.  Catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a ...
CDD:238085	127	EUKprk	Bacteria:1,Invertebrates:11,Mammals:1,Plants:5,Primates:1,Rodents:1,nodiv:1	cd00148, PROF, Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by ...
CDD:238086	201	EUK	Invertebrates:1,Mammals:2,Primates:1,Rodents:5,Vertebrates:4	cd00152, PTX, Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and ...
CDD:206640	159	EUK	Invertebrates:23,Mammals:1,Plants:12,Primates:1,Rodents:2,Vertebrates:5	cd00154, Rab, Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases).  Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different ...
CDD:238087	237	EUK	Invertebrates:4,Mammals:1,Plants:5,Primates:1,Rodents:2	cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of ...
CDD:238088	113	EUKprk	Bacteria:88,Plants:4,Primates:1,nodiv:1	cd00156, REC, Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers.
CDD:206641	171	EUK	Invertebrates:11,Plants:10,Primates:1,Vertebrates:1	cd00157, Rho, Ras homology family (Rho) of small guanosine triphosphatases (GTPases).  Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in ...
CDD:238089	89	EUKprk	Bacteria:107,Invertebrates:2,Mammals:1,Plants:11,Primates:1,Vertebrates:2,nodiv:2	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in ...
CDD:238090	169	EUK	Invertebrates:15,Plants:20,Primates:1,Rodents:2,Vertebrates:4	cd00159, RhoGAP, RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, ...
CDD:238091	181	EUK	Invertebrates:4,Plants:3,Primates:1,Rodents:2	cd00160, RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
CDD:238092	124	EUKprk	Bacteria:19,Environmental:1,Invertebrates:7,Mammals:1,Plants:12,Primates:2,Rodents:2	cd00161, RICIN, Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture.
CDD:238093	45	EUKprk	Bacteria:1,Invertebrates:13,Mammals:1,Plants:19,Primates:2,Rodents:2,Vertebrates:6,Viruses:24	cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral ...
CDD:119386	119	EUK	Mammals:6,Primates:2,Rodents:2	cd00163, RNase_A, RNase A family, or Pancreatic RNases family; includes vertebrate RNase homologs to the bovine pancreatic ribonuclease A (RNase A). Many of these enzymes have special biological activities; for example, some stimulate the development of vascular endothelial cells, dendritic cells, and neurons, are cytotoxic/anti-tumoral and/or anti-pathogenic. RNase A is involved in endonucleolytic cleavage of 3'-phosphomononucleotides and ...
CDD:238094	65	EUKprk	Bacteria:35,Invertebrates:2,Plants:7,Primates:1	cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
CDD:238095	70	EUKprk	Bacteria:42,Environmental:1,Invertebrates:9,Plants:26,Primates:1,nodiv:1	cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
CDD:238096	45	EUK	Invertebrates:5,Plants:15,Primates:1,Rodents:2,Vertebrates:2	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
CDD:238097	122	EUKprk	Bacteria:1,Invertebrates:1,Plants:1,Primates:1,Rodents:1,Vertebrates:2	cd00168, SCP, SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal ...
CDD:238098	59	EUKprk	Mammals:1,Primates:1,Rodents:1,Vertebrates:3,Viruses:1	cd00169, Chemokine, Chemokine: small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 subfamilies based on the arrangement of the two N-terminal cysteines; some members can bind multiple receptors and many chemokine receptors ...
CDD:238099	157	EUK	Invertebrates:6,Plants:11,Primates:1,Rodents:2	cd00170, SEC14, Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
CDD:238100	185	EUKprk	Bacteria:1,Invertebrates:3,Mammals:1,Plants:4,Primates:1	cd00171, Sec7, Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
CDD:238101	364	EUKprk	Bacteria:7,Invertebrates:24,Mammals:2,Plants:1,Primates:1,Rodents:1,Vertebrates:6	cd00172, SERPIN, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or ...
CDD:198173	79	EUK	Invertebrates:26,Mammals:1,Plants:6,Primates:1,Rodents:2,Vertebrates:7,nodiv:1	cd00173, SH2, Src homology 2 (SH2) domain.  In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds ...
CDD:212690	51	EUKprk	Bacteria:1,Invertebrates:47,Mammals:1,Plants:42,Primates:1,Rodents:2,Vertebrates:5,nodiv:1	cd00174, SH3, Src Homology 3 domain superfamily.  Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown ...
CDD:238102	129	EUKprk	Bacteria:7,Invertebrates:1,Plants:2,Primates:1	cd00175, SNc, Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
CDD:238103	213	EUK	Invertebrates:4,Primates:1,Rodents:1,Vertebrates:1	cd00176, SPEC, Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are ...
CDD:176851	193	EUKprk	Bacteria:1,Invertebrates:14,Plants:9,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00177, START, Lipid-binding START domain of mammalian STARD1-STARD15 and related proteins.  This family includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and related domains, such as the START domain of the Arabidopsis homeobox protein GLABRA 2. The mammalian STARDs are grouped into 8 subfamilies. This family belongs ...
CDD:238104	172	EUK	Plants:34	cd00178, STI, Soybean trypsin inhibitor (Kunitz) family of protease inhibitors. Inhibit proteases by binding with high affinity to their active sites. Trefoil fold, common to interleukins and fibroblast growth factors.
CDD:238105	151	EUK	Invertebrates:8,Mammals:1,Plants:8,Primates:2,Rodents:2,Vertebrates:2	cd00179, SynN, Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, ...
CDD:270622	215	EUKprk	Bacteria:6,Invertebrates:12,Mammals:1,Plants:11,Primates:1,Rodents:2,Vertebrates:1	cd00180, PKc, Catalytic domain of Protein Kinases.  PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. PKs make up a large family of serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins. Majority ...
CDD:206638	129	PRK	Bacteria:43	cd00181, Tar_Tsr_LBD, ligand binding domain of Tar- and Tsr-related chemoreceptors.  E.coli Tar (taxis to aspartate and repellents) and Tsr (taxis to serine and repellents) are homologous chemoreceptors that have a high specificity for aspartate and serine, respectively. Both are homodimeric receptors and contain an N-terminal periplasmic ligand binding domain, a transmembrane region, a HAMP domain and a C-terminal cytosolic signaling domain.
CDD:238106	188	EUK	Invertebrates:6,Primates:1,Rodents:1,Vertebrates:3	cd00182, TBOX, T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and ...
CDD:238107	76	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:2,Vertebrates:1	cd00183, TFIIS_I, N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme.
CDD:238108	137	EUK	Invertebrates:1,Mammals:3,Primates:1,Rodents:2,Vertebrates:4	cd00184, TNF, Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate ...
CDD:238109	98	EUKprk	Mammals:1,Primates:1,Rodents:2,Vertebrates:7,Viruses:5	cd00185, TNFR, Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within ...
CDD:238110	381	EUKprk	Bacteria:16,Environmental:1,Invertebrates:3,Plants:1,Primates:1	cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer ...
CDD:238111	445	EUKprk	Bacteria:16,Invertebrates:6,Plants:4,Primates:1,Rodents:1,Viruses:1,nodiv:2	cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
CDD:173773	83	EUKprk	Bacteria:246,Invertebrates:21,Mammals:1,Plants:15,Primates:1,Vertebrates:4,nodiv:1	cd00188, TOPRIM, Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which ...
CDD:238112	100	EUKprk	Bacteria:13,Invertebrates:5,Plants:11,Primates:1,Rodents:3,Vertebrates:1	cd00189, TPR, Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common ...
CDD:238113	232	EUKprk	Bacteria:2,Invertebrates:28,Mammals:5,Plants:4,Primates:1,Rodents:4,Vertebrates:13	cd00190, Tryp_SPc, Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
CDD:238114	66	EUK	Invertebrates:4,Mammals:1,Primates:1,Rodents:2,Vertebrates:5	cd00191, TY, Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases.
CDD:270623	262	EUK	Invertebrates:16,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00192, PTKc, Catalytic domain of Protein Tyrosine Kinases.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, ...
CDD:238115	60	EUK	Invertebrates:5,Plants:4,Primates:1,Rodents:1	cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target ...
CDD:270455	28	EUKprk	Bacteria:1,Mammals:1,Plants:1,Primates:1,Rodents:2,Vertebrates:1	cd00194, UBA_like_SF, UBA domain-like superfamily.  The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins ...
CDD:238117	141	EUKprk	Invertebrates:6,Plants:6,Primates:2,Rodents:1,Viruses:1	cd00195, UBCc, Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without ...
CDD:176352	69	EUKprk	Bacteria:68,Invertebrates:31,Mammals:3,Plants:37,Primates:1,Rodents:3,Vertebrates:11,Viruses:3,nodiv:3	cd00196, UBQ, Ubiquitin-like proteins.  Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between ...
CDD:238118	115	EUK	Plants:2,Primates:1,Rodents:1	cd00197, VHS_ENTH_ANTH, VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an ...
CDD:238119	161	EUKprk	Bacteria:53,Environmental:1,Invertebrates:12,Mammals:2,Plants:3,Primates:2,Rodents:2,Vertebrates:1	cd00198, vWFA, Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its ...
CDD:238120	60	EUK	Mammals:4,Primates:1,Rodents:3	cd00199, WAP, whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of ...
CDD:238121	289	EUKprk	Bacteria:2,Invertebrates:6,Mammals:1,Plants:12,Primates:1,Rodents:2,Vertebrates:1	cd00200, WD40, WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a ...
CDD:238122	31	EUKprk	Invertebrates:5,Plants:9,Primates:2,Rodents:2,Synthetic:1,Vertebrates:1,nodiv:1	cd00201, WW, Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which ...
CDD:238123	54	EUK	Invertebrates:3,Plants:9,Primates:1,Vertebrates:2	cd00202, ZnF_GATA, Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.
CDD:238124	167	EUKprk	Bacteria:5,Invertebrates:3,Plants:1,Primates:1,Vertebrates:3	cd00203, ZnMc, Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
CDD:238125	126	EUKprk	Bacteria:5,Invertebrates:7,Mammals:1,Plants:9,Primates:1,Rodents:2,Vertebrates:2,Viruses:12,nodiv:1	cd00204, ANK, ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are ...
CDD:119412	178	PRK	Environmental:1,Viruses:52,nodiv:1	cd00205, rhv_like, Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich.
CDD:119411	64	EUK	Vertebrates:18	cd00206, snake_toxin, Snake toxin domain, present in short and long neurotoxins, cytotoxins and short toxins, and in other miscellaneous venom peptides. The toxin acts by binding to the nicotinic acetylcholine receptors in the postsynaptic membrane of skeletal muscles and preventing the binding of acetylcholine, thereby blocking the excitation of muscles. This domain contains 60-75 amino acids that are fixed by 4-5 disulfide bridges and is nearly all beta sheet; ...
CDD:238126	84	EUKprk	Bacteria:75,Invertebrates:6,Mammals:1,Plants:25,Primates:1,nodiv:1	cd00207, fer2, 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
CDD:100038	78	EUKprk	Bacteria:12,Plants:1,Primates:1	cd00208, LbetaH, Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their ...
CDD:238127	158	EUKprk	Bacteria:57,Invertebrates:11,Phages:2,Plants:9,Primates:1,Vertebrates:2,Viruses:3	cd00209, DHFR, Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA ...
CDD:238128	124	PRK	Bacteria:2	cd00210, PTS_IIA_glc, PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
CDD:238129	136	PRK	Bacteria:16	cd00211, PTS_IIA_fru, PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
CDD:238130	78	PRK	Bacteria:15	cd00212, PTS_IIB_glc, PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
CDD:238131	88	EUK	Mammals:7,Primates:3,Rodents:2,Vertebrates:10	cd00213, S-100, S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as ...
CDD:238132	150	EUK	Invertebrates:2,Primates:1,Rodents:2,Vertebrates:3	cd00214, Calpain_III, Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with ...
CDD:238133	97	PRK	Bacteria:8	cd00215, PTS_IIA_lac, PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their ...
CDD:132995	223	EUK	Invertebrates:7,Plants:5,Primates:1,Vertebrates:3	cd00218, GlcAT-I, Beta1,3-glucuronyltransferase I (GlcAT-I) is involved in the initial steps of proteoglycan synthesis.  Beta1,3-glucuronyltransferase I (GlcAT-I) domain; GlcAT-I is a Key enzyme involved in the initial steps of proteoglycan synthesis. GlcAT-I catalyzes the transfer of a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region of trisaccharide ...
CDD:238135	177	EUKprk	Bacteria:2,Invertebrates:3,Mammals:1,Primates:1,Vertebrates:2	cd00220, VMO-I, Vitelline membrane outer layer protein I (VMO-I) domain, VMO-I is one of the proteins found in the outer layer of the vitelline membrane of poultry eggs; VMO-I, lysozyme, and VMO-II are tightly bound to ovomucin; this complex forms the backbone of the outer layer;  VMO-I has three distinct internal repeats;  all three repeats are used to define the domain here; VMO-I has recently been shown to ...
CDD:238136	115	PRK	Bacteria:17	cd00221, Vsr, Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
CDD:212461	92	PRK	Bacteria:32	cd00222, CollagenBindB, Repeat unit of collagen-binding protein domain B.  The collagen-binding protein mediates bacterial adherence to collagen; the primary sequence has a non-repetitive, collagen-binding A region, followed by instances of this B region repetitive unit. The B region has one to four 23 kDa repeat units (B1-B4), which have been suggested to serve as 'stalks' that project the A region from the bacterial surface and thus facilitate bacterial adherence ...
CDD:173774	160	miss	miss	cd00223, TOPRIM_TopoIIB_SPO, TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11.  This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11.   Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process ...
CDD:238141	187	EUKprk	Bacteria:109,Environmental:1,Invertebrates:1,Mammals:2,Plants:9,Primates:1,Rodents:1,Vertebrates:4,nodiv:2	cd00229, SGNH_hydrolase, SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
CDD:238143	203	EUKprk	Bacteria:24,Invertebrates:2,Plants:6,Primates:1,Vertebrates:2,nodiv:1	cd00232, HemeO, Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This family includes bacterial HO, as well as the mammalian isoforms HO-1, and HO-2. Heme oxygenases play key roles in heme homeostasis, oxidative ...
CDD:238144	201	PRK	Bacteria:8,Phages:3	cd00233, VIP2, VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of biological pathways distinct from classical A-B toxins. A novel family of insecticidal ADP-ribosyltransferses were isolated from Bacillus cereus during vegetative growth, where VIP1 likely ...
CDD:119413	108	PRK	Viruses:11	cd00235, TLP-20, Telokin-like protein-20 (TLP-20) domain; a baculovirus protein that shares some antigenic similarities to the smooth muscle protein telokin, a kinase-related protein.
CDD:238146	93	EUK	Invertebrates:10,Plants:18,Primates:1,Rodents:1,Vertebrates:1	cd00238, ERp29c, ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct ...
CDD:187675	158	EUKprk	Bacteria:63,Invertebrates:2,Plants:10,Primates:1	cd00241, DOMON_like, Domon-like ligand-binding domains.  DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that ...
CDD:119415	122	EUK	Invertebrates:22	cd00243, Lysin-Sp18, Sp18 and Lysin from Archaegastropoda (marine mollusks of the families Halotidae and Trochidae) sperm. Both proteins play an important role in fertilization: sp18 mediates fusion between sperm and egg cell membrane, lysin dissolves the vitelline envelope surrounding the egg; they are believed to be a product of gene duplication and subsequent divergence.
CDD:238149	428	PRK	Bacteria:10	cd00245, Glm_e, Coenzyme B12-dependent glutamate mutase epsilon subunit-like family; contains proteins similar to Clostridium cochlearium glutamate mutase (Glm) and Streptomyces tendae Tu901 NikV. Glm catalyzes a carbon-skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate. The first step in the catalysis is a homolytic cleavage of the Co-C bond of the coenzyme B12 cofactor to generate a 5'-deoxyadenosyl radical. This radical then initiates the ...
CDD:238151	171	EUK	Invertebrates:6,Primates:2,Rodents:1,Vertebrates:5	cd00247, Endostatin-like, Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; endostatin XVIII is monomeric and contains a heparin-binding epitope and zinc binding sites while endostatin XV is trimeric and contains neither of ...
CDD:238152	109	EUKprk	Bacteria:28,Rodents:1	cd00248, Mth938-like, Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer.  2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and ...
CDD:238153	384	EUKprk	Bacteria:6,Mammals:1,Rodents:1,nodiv:1	cd00249, AGE, AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is structurally and mechanistically distinct from the other four types of epimerases. The AGE domain monomer is composed of an alpha(6)/alpha(6)-barrel, the structure of which ...
CDD:238154	262	EUKprk	Bacteria:9,Invertebrates:2,Plants:2,Primates:1,Rodents:1	cd00250, CAS_like, Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to ...
CDD:119403	176	EUK	Invertebrates:10	cd00251, Mth_Ecto, The ectodomain of Methuselah (Mth); Mth mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage; The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family; Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site.
CDD:238155	116	EUK	Invertebrates:1,Primates:1,Rodents:2	cd00252, SPARC_EC, SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with ...
CDD:238156	186	PRK	Bacteria:31,nodiv:1	cd00253, PL_Passenger_AT, Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta) domain of autotransporters forms a pore in the outer membrane through which the N-terminal passenger domain is transported. Following transport, the passenger domain is generally cleaved ...
CDD:238157	113	EUKprk	Bacteria:84,Environmental:1,Invertebrates:1,Phages:14,Plants:1,Vertebrates:1,nodiv:1	cd00254, LT_GEWL, Lytic Transglycosylase (LT)  and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and  insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL).  LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as ...
CDD:238158	224	EUK	Invertebrates:4,Primates:1,Rodents:2,Vertebrates:4	cd00255, nidG2, Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds ...
CDD:238160	119	EUK	Invertebrates:4,Mammals:1,Primates:1,Rodents:1,Vertebrates:1	cd00257, Fascin, Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF).
CDD:238163	110	EUK	Plants:25	cd00261, AAI_SS, AAI_SS: Alpha-Amylase Inhibitors (AAIs) and Seed Storage (SS) Protein subfamily; composed of cereal-type AAIs and SS proteins. They are mainly present in the seeds of a variety of plants. AAIs play an important role in the natural defenses of plants against insects and pathogens such as fungi, bacteria and viruses. AAIs impede the digestion of plant starch and proteins by inhibiting digestive alpha-amylases and proteinases. Also included in this ...
CDD:238164	208	miss	miss	cd00264, BPI, BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of ...
CDD:238165	77	miss	miss	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi.
CDD:238166	83	miss	miss	cd00266, MADS_SRF_like, SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi.
CDD:213179	157	EUKprk	Bacteria:87,Invertebrates:3,Mammals:1,Plants:6,Primates:1,Rodents:1,Synthetic:1,Vertebrates:3,nodiv:2	cd00267, ABC_ATPase, ATP-binding cassette transporter nucleotide-binding domain.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters ...
CDD:238167	203	miss	miss	cd00268, DEADc, DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker  B motif (motif II). This domain contains the ATP- binding region.
CDD:238168	149	EUK	Invertebrates:7,Mammals:1,Primates:1,Vertebrates:3	cd00270, MATH_TRAF_C, Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the ...
CDD:238170	57	EUKprk	Mammals:1,Primates:1,Rodents:3,Vertebrates:8,Viruses:3	cd00272, Chemokine_CC, Chemokine_CC:  1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, ...
CDD:238171	64	EUKprk	Primates:1,Rodents:2,Vertebrates:9,Viruses:3	cd00273, Chemokine_CXC, Chemokine_CXC:  1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif which may be a general requirement for binding to CXC chemokine receptors; those with the ELR motif are chemotatic for neutrophils and have ...
CDD:175974	128	EUK	Invertebrates:37,Plants:39,Primates:1,Rodents:2,Vertebrates:7,nodiv:2	cd00275, C2_PLC_like, C2 domain present in Phosphoinositide-specific phospholipases C (PLC).  PLCs are involved in the hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP2) to d-myo-inositol-1,4,5-trisphosphate (1,4,5-IP3) and sn-1,2-diacylglycerol (DAG).   1,4,5-IP3 and DAG are second messengers in eukaryotic signal transduction cascades. PLC is composed of a N-terminal PH domain followed by a series ...
CDD:175975	134	EUK	Invertebrates:12,Primates:1,Rodents:1,Vertebrates:4,nodiv:2	cd00276, C2B_Synaptotagmin, C2 domain second repeat present in Synaptotagmin.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. There are several classes of Synaptotagmins. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown ...
CDD:238173	79	PRK	Bacteria:5	cd00279, YlxR, Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation.
CDD:100014	328	EUKprk	Bacteria:2,Mammals:1,Primates:1	cd00286, Tubulin_FtsZ, Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ...
CDD:238177	196	EUKprk	Bacteria:15,Environmental:1,Invertebrates:1,Mammals:1,Plants:2,Primates:1	cd00287, ribokinase_pfkB_like, ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and ...
CDD:238178	480	EUKprk	Bacteria:3,Invertebrates:1,Mammals:1,Plants:4,Primates:1	cd00288, Pyruvate_Kinase, Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, ...
CDD:238179	147	EUKprk	Bacteria:3,Invertebrates:3,Mammals:1,Plants:5,Vertebrates:1	cd00290, cytochrome_b_C, Cytochrome b(C-terminus)/b6/petD:  Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are ...
CDD:238180	69	EUKprk	Bacteria:109,Invertebrates:1	cd00291, SirA_YedF_YeeD, SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain.  SirA (also known as UvrY,  and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA.  A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in ...
CDD:238181	88	EUKprk	Bacteria:4,Invertebrates:11,Plants:3,Primates:1,Vertebrates:2	cd00292, EF1B, Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this ...
CDD:238182	130	EUKprk	Bacteria:157,Environmental:1,Invertebrates:4,Plants:18,Synthetic:1,nodiv:3	cd00293, USP_Like, Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals ...
CDD:238184	222	EUKprk	Bacteria:62,Invertebrates:5,Plants:13,Primates:1,Vertebrates:4	cd00296, SIR2, SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many ...
CDD:107219	80	EUKprk	Bacteria:301,Invertebrates:73,Mammals:3,Plants:65,Primates:1,Rodents:2,Vertebrates:9	cd00298, ACD_sHsps_p23-like, This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins.  sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, ...
CDD:198286	100	EUKprk	Bacteria:46,Invertebrates:8,Plants:14,Primates:2,Vertebrates:3,nodiv:1	cd00299, GST_C_family, C-terminal, alpha helical domain of the Glutathione S-transferase family.  Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, ...
CDD:133418	300	EUKprk	Bacteria:7,Plants:3,Primates:1,nodiv:1	cd00300, LDH_like, L-lactate dehydrogenase-like enzymes.  Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. ...
CDD:133136	92	EUKprk	Bacteria:1,Invertebrates:17,Mammals:1,Plants:62,Primates:2,Rodents:1,Vertebrates:2,Viruses:1	cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate proteases.  The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, ...
CDD:238185	98	EUKprk	Bacteria:3,Invertebrates:7,Plants:6,Vertebrates:1,Viruses:3,nodiv:1	cd00304, RT_like, RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group ...
CDD:238186	144	EUKprk	Bacteria:14,Invertebrates:11,Mammals:1,Plants:7,Primates:1,Vertebrates:2,Viruses:7	cd00305, Cu-Zn_Superoxide_Dismutase, Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and ...
CDD:173787	241	EUKprk	Bacteria:130,Environmental:2,Invertebrates:13,Plants:18,Primates:2,Vertebrates:2	cd00306, Peptidases_S8_S53, Peptidase domain in the S8 and S53 families.  Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a ...
CDD:238187	84	EUKprk	Bacteria:9,Plants:1	cd00307, RuBisCO_small_like, Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family ...
CDD:238188	229	EUKprk	Bacteria:13,Plants:1,nodiv:1	cd00308, enolase_like, Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, ...
CDD:238189	464	EUKprk	Bacteria:60,Environmental:1,Invertebrates:34,Plants:18,Primates:1,Vertebrates:3,nodiv:1	cd00309, chaperonin_type_I_II, chaperonin families, type I and type II. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial ...
CDD:238190	242	EUKprk	Bacteria:138,Invertebrates:14,Plants:20,Primates:1,Rodents:1,Vertebrates:3	cd00311, TIM, Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually homodimeric, but in some organisms tetrameric, is ubiqitous and conserved in function across eukaryotes, bacteria and archaea.
CDD:238191	493	EUKprk	Bacteria:1,Invertebrates:8,Mammals:1,Plants:2,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd00312, Esterase_lipase, Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In ...
CDD:173823	255	EUKprk	Bacteria:3,Invertebrates:2,Plants:20	cd00314, plant_peroxidase_like, Heme-dependent peroxidases similar to plant peroxidases.  Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX), which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of ...
CDD:238192	275	EUKprk	Bacteria:15,Plants:2,Primates:1,Rodents:1,Viruses:1	cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional ...
CDD:238193	399	EUKprk	Bacteria:59,Plants:7	cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia.  This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent  nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide ...
CDD:238194	146	EUKprk	Bacteria:26,Environmental:1,Invertebrates:9,Plants:11,Primates:1,Rodents:1,Vertebrates:1	cd00317, cyclophilin, cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin ...
CDD:238195	397	EUKprk	Bacteria:6,Invertebrates:6,Mammals:1,Plants:8	cd00318, Phosphoglycerate_kinase, Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level phosphorylation events in the glycolytic pathway. Substrate-level phosphorylation is defined as production of  ATP by a process, which is catalyzed ...
CDD:238197	93	EUKprk	Bacteria:45,Environmental:2,Invertebrates:13,Phages:3,Plants:8,Vertebrates:3	cd00320, cpn10, Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and ...
CDD:238198	156	EUKprk	Bacteria:42,Invertebrates:3,Plants:15,Primates:1,Vertebrates:2,nodiv:2	cd00321, SO_family_Moco, Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Assimilatory NRs ...
CDD:99778	223	EUKprk	Bacteria:46,Environmental:1,Invertebrates:6,Plants:9,Primates:1,Rodents:1,Vertebrates:3	cd00322, FNR_like, Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone ...
CDD:271245	130	EUKprk	Bacteria:1,Invertebrates:6,Mammals:1,Plants:15,Vertebrates:1	cd00323, uS7, Ribosomal protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and ...
CDD:238199	230	EUKprk	Bacteria:5,Invertebrates:2,Plants:32	cd00325, chitinase_glyco_hydro_19, Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but some are found in bacteria. Class I and II chitinases are similar in their catalytic domains. Class I chitinases have an N-terminal cysteine-rich, ...
CDD:238200	227	EUKprk	Bacteria:36,Invertebrates:17,Mammals:1,Plants:11,Primates:1,Rodents:2,Vertebrates:8,nodiv:1	cd00326, alpha_CA, Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of ...
CDD:238201	254	EUKprk	Bacteria:4,Plants:1,Rodents:1	cd00327, cond_enzymes, Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products.
CDD:238202	107	EUKprk	Bacteria:112,Environmental:2,Invertebrates:15,Plants:18,Primates:1,Vertebrates:4,nodiv:1	cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the ...
CDD:238203	217	EUKprk	Bacteria:113,Environmental:1,Invertebrates:1,Plants:8	cd00331, IGPS, Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the release of carbon dioxide and water. IGPS is active as a separate monomer in most organisms, but is also found fused to other enzymes as part of a ...
CDD:176460	444	EUKprk	Bacteria:44,Invertebrates:4,Plants:9,Primates:1,Vertebrates:3	cd00332, PAL-HAL, Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL).  PAL and HAL are members of the Lyase class I_like superfamily of enzymes that, catalyze similar beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. PAL, present in plants and fungi, catalyzes the conversion of ...
CDD:238204	228	EUKprk	Bacteria:3,Invertebrates:3,Plants:6,Primates:1,nodiv:1	cd00333, MIP, Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and ...
CDD:238205	105	EUKprk	Bacteria:41,Environmental:4,Invertebrates:15,Plants:26,Primates:1,Rodents:1,Vertebrates:3	cd00336, Ribosomal_L22, Ribosomal protein L22/L17e.  L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit.  It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA.  L22 is the largest protein contributor to the surface of the ...
CDD:238206	137	PRK	Bacteria:114,Phages:4,nodiv:1	cd00338, Ser_Recombinase, Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, ...
CDD:238207	152	EUKprk	Bacteria:65,Invertebrates:16,Mammals:1,Plants:14,Primates:1,Vertebrates:4,nodiv:2	cd00340, GSH_Peroxidase, Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection ...
CDD:238208	329	PRK	Bacteria:41,nodiv:1	cd00342, gram_neg_porins, Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane.  Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose ...
CDD:238209	90	EUKprk	Bacteria:71,Invertebrates:1,Plants:2,nodiv:1	cd00347, Flavin_utilizing_monoxygenases, Flavin-utilizing monoxygenases.
CDD:100101	131	EUKprk	Bacteria:30,Environmental:2,Invertebrates:20,Mammals:2,Plants:14,Primates:1,Vertebrates:3,nodiv:1	cd00349, Ribosomal_L11, Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal ...
CDD:238210	33	EUKprk	Bacteria:39,Invertebrates:1,Plants:1	cd00350, rubredoxin_like, Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is ...
CDD:238211	215	EUKprk	Bacteria:35,Invertebrates:5,Plants:6,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd00351, TS_Pyrimidine_HMase, Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the biosynthesis of DNA precursors and are active as homodimers. However, they exhibit distinct pyrimidine base specificities ...
CDD:238212	220	EUKprk	Bacteria:220,Environmental:6,Invertebrates:17,Plants:39,Primates:1,Rodents:1,Synthetic:1,Vertebrates:4,Viruses:1	cd00352, Gn_AT_II, Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus ...
CDD:238213	80	EUKprk	Bacteria:20,Environmental:1,Invertebrates:20,Plants:19,Primates:1,Vertebrates:4	cd00353, Ribosomal_S15p_S13e, Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 ...
CDD:238214	315	EUKprk	Bacteria:14,Invertebrates:6,Mammals:1,Plants:16,Primates:1,Vertebrates:3,nodiv:1	cd00354, FBPase, Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate  into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-biphosphatases that play a role in pentose phosphate pathway (Calvin cycle).
CDD:100098	53	EUKprk	Bacteria:48,Environmental:3,Invertebrates:15,Mammals:1,Plants:18,Primates:1,Vertebrates:6	cd00355, Ribosomal_L30_like, Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome.  The eukaryotic L30 members have N- and/or ...
CDD:238215	221	EUKprk	Bacteria:26,Invertebrates:7,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd00361, arom_aa_hydroxylase, Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and ...
CDD:238216	338	EUKprk	Bacteria:5,Plants:3,Primates:1	cd00363, PFK, Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and  ...
CDD:212658	435	EUKprk	Bacteria:17,Primates:1	cd00366, FGGY, FGGY family of carbohydrate kinases.  This family is predominantly composed of glycerol kinase (GK) and similar carbohydrate kinases including rhamnulokinase (RhuK), xylulokinase (XK), gluconokinase (GntK), ribulokinase (RBK), and fuculokinase (FK). These enzymes catalyze the transfer of a phosphate group, usually from ATP, to their carbohydrate substrates. The monomer of FGGY proteins contains two large domains, which are separated by ...
CDD:238217	77	PRK	Bacteria:71,nodiv:1	cd00367, PTS-HPr_like, Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate is transferred to HPr by enzyme I (EI). Phospho-HPr then transfers the phosphoryl group to one of several ...
CDD:238218	374	EUKprk	Bacteria:139,Environmental:2,Invertebrates:5,Plants:11,Primates:1,Vertebrates:3,nodiv:2	cd00368, Molybdopterin-Binding, Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate ...
CDD:238219	63	EUKprk	Bacteria:32,Invertebrates:2,Mammals:1,Plants:7,Primates:1,Rodents:3	cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of ...
CDD:238220	195	EUKprk	Bacteria:14,Invertebrates:9,Plants:45,Primates:1,Vertebrates:3,nodiv:1	cd00374, RNase_T2, Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. ...
CDD:238221	567	EUKprk	Bacteria:11,Plants:3	cd00375, Urease_alpha, Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of external and internally generated urea as a nitrogen source. The enzyme consists of 3 subunits, alpha, beta and gamma, which can be fused and present on a single protein chain and which ...
CDD:119340	243	EUKprk	Bacteria:119,Environmental:1,Invertebrates:8,Plants:21	cd00377, ICL_PEPM, Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first ...
CDD:99733	402	EUKprk	Bacteria:11,Invertebrates:3,Plants:2,Primates:1,Rodents:1,Vertebrates:1	cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and ...
CDD:238222	155	EUKprk	Bacteria:89,Environmental:2,Invertebrates:23,Plants:23,Primates:1,Vertebrates:4	cd00379, Ribosomal_L10_P0, Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ...
CDD:240504	49	EUKprk	Bacteria:3,Invertebrates:2,Plants:2,Primates:1	cd00380, KOW, KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese).  KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises ...
CDD:238223	325	EUKprk	Bacteria:37,Invertebrates:9,Plants:5,Primates:2,Vertebrates:4	cd00381, IMPDH, IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key ...
CDD:238224	119	EUKprk	Bacteria:85,Invertebrates:5,Plants:26	cd00382, beta_CA, Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes ...
CDD:238225	95	EUKprk	Bacteria:132,Plants:3,nodiv:3	cd00383, trans_reg_C, Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate ...
CDD:238226	314	EUKprk	Bacteria:27,Plants:1,nodiv:1	cd00384, ALAD_PBGS, Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are ...
CDD:173830	243	EUKprk	Bacteria:88,Environmental:1,Invertebrates:10,Plants:49,Primates:1,Vertebrates:1,nodiv:1	cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1.  Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or ...
CDD:238227	183	EUKprk	Bacteria:60,Invertebrates:42,Mammals:1,Plants:23,Vertebrates:3,nodiv:2	cd00386, Heme_Cu_Oxidase_III_like, Heme-copper oxidase subunit III.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types.  This ...
CDD:100102	127	EUKprk	Bacteria:42,Environmental:1,Invertebrates:19,Mammals:2,Plants:25,Vertebrates:3	cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended ...
CDD:238228	71	EUKprk	Bacteria:12,Plants:8	cd00389, microbial_RNases, microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential  for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th,  Pb, N1, and Ms) and bacterial RNases (barnase, binase, RNase Sa) , the majority of which are guanyl specific and fungal ribotoxins.
CDD:238229	96	EUKprk	Bacteria:24,Plants:6	cd00390, Urease_gamma, Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on ...
CDD:238230	114	EUKprk	Bacteria:35,Invertebrates:18,Mammals:1,Plants:14,Primates:1,Vertebrates:2	cd00392, Ribosomal_L13, Ribosomal protein L13.  Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site.  It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 ...
CDD:132923	161	PRK	Bacteria:6	cd00394, Clp_protease_like, Caseinolytic protease (ClpP) is an ATP-dependent protease.  Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and ...
CDD:100027	222	PRK	Bacteria:7	cd00396, PurM-like, AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain.
CDD:271175	167	EUKprk	Bacteria:116,Environmental:1,Invertebrates:1,Phages:4,Plants:3,Primates:1,Viruses:1	cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal catalytic domain.  The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase ...
CDD:238232	209	EUKprk	Bacteria:2,Invertebrates:1,Primates:1	cd00398, Aldolase_II, Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic ...
CDD:238233	383	EUKprk	Bacteria:79,Environmental:2,Plants:1,Primates:1,Rodents:1	cd00400, Voltage_gated_ClC, CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms ...
CDD:240619	402	EUKprk	Bacteria:52,Environmental:1,Invertebrates:18,Plants:10,Primates:1,Rodents:1,Vertebrates:3	cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains.  S-adenosyl-L-homocysteine hydrolase (SAHH, AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and Hyc is sufficiently fast, so that the net ...
CDD:238235	208	EUKprk	Bacteria:56,Environmental:2,Invertebrates:25,Mammals:2,Plants:37,Primates:1,Vertebrates:5	cd00403, Ribosomal_L1, Ribosomal protein L1.  The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA.  In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA.  Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity.  L1 is ...
CDD:238237	203	EUKprk	Bacteria:170,Environmental:1,Plants:19	cd00405, PRAI, Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan ...
CDD:238238	101	EUKprk	Bacteria:26,Invertebrates:1,Plants:2	cd00407, Urease_beta, Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or ...
CDD:188630	281	EUKprk	Bacteria:101,Invertebrates:1,Plants:13,Primates:1,Vertebrates:1,nodiv:2	cd00408, DHDPS-like, Dihydrodipicolinate synthase family.  Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stabilizes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to ...
CDD:238239	155	EUKprk	Bacteria:45,Environmental:1,Invertebrates:10,Plants:13,Primates:1,Vertebrates:3	cd00412, pyrophosphatase, Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
CDD:185683	210	EUKprk	Bacteria:41,Plants:19	cd00413, Glyco_hydrolase_16, glycosyl hydrolase family 16.  The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, ...
CDD:238240	135	EUKprk	Bacteria:99,Invertebrates:6,Plants:6,Primates:1,Vertebrates:3	cd00419, Ferrochelatase_C, Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric ...
CDD:238241	146	EUKprk	Bacteria:73,Plants:11,nodiv:1	cd00421, intradiol_dioxygenase, Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear non-heme iron enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. The members are intradiol-cleaving enzymes ...
CDD:238242	258	EUKprk	Bacteria:15,Invertebrates:2,Plants:3,Rodents:1	cd00423, Pterin_binding, Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH).  DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both ...
CDD:176453	343	EUKprk	Bacteria:9,Plants:1	cd00424, PolY, Y-family of DNA polymerases.  Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions.  Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are ...
CDD:238243	57	EUKprk	Bacteria:90,Environmental:2,Invertebrates:10,Plants:13,Primates:1,Vertebrates:3	cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP.  L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals.  L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for ...
CDD:238244	211	EUKprk	Bacteria:83,Environmental:1,Invertebrates:8,Plants:9,Primates:1,Vertebrates:3	cd00429, RPE, Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn ...
CDD:143481	367	EUKprk	Bacteria:132,Environmental:1,Invertebrates:2	cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase.  This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in ...
CDD:238245	161	EUKprk	Bacteria:71,Invertebrates:6,Plants:3,Primates:1,nodiv:2	cd00431, cysteine_hydrolases, Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the ...
CDD:238246	103	EUKprk	Bacteria:42,Environmental:3,Invertebrates:18,Mammals:1,Plants:10,Primates:1,Rodents:1,Vertebrates:3,nodiv:2	cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in ...
CDD:238247	468	EUKprk	Bacteria:94,Environmental:1,Invertebrates:15,Mammals:1,Plants:5,Primates:1,Vertebrates:3,nodiv:2	cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do ...
CDD:238248	85	EUKprk	Invertebrates:4,Mammals:1,Plants:2,Rodents:1,Synthetic:1,Vertebrates:2	cd00435, ACBP, Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA ...
CDD:238249	105	PRK	Bacteria:1,Phages:2	cd00442, lysozyme_like, lysozyme_like domain.  This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.
CDD:238250	305	EUKprk	Bacteria:3,Invertebrates:4,Plants:2,Primates:1,Rodents:1	cd00443, ADA_AMPD, Adenosine/AMP deaminase. Adenosine deaminases (ADAs) are present in pro- and eukaryotic organisms and catalyze  the zinc dependent irreversible deamination of adenosine nucleosides to inosine nucleosides and ammonia. The eukaryotic AMP deaminase catalyzes a similar reaction leading to the hydrolytic removal of an amino group at the 6 position of the adenine nucleotide ring, a branch point in the ...
CDD:238251	286	EUKprk	Bacteria:2,Invertebrates:2,Plants:3,Rodents:1	cd00445, Uricase, Urate oxidase (UO, uricase) is a peroxisomal enzyme that catalyzes the oxidation of uric acid to allantoin in most fish, amphibian, and mammalian species. The enzymatic process involves catalyzing the oxidative opening of the purine ring during the purine degradation pathway.  In humans and certain other primates, however, the enzyme has been lost by some unknown mechanism. Each monomer contains two instances ...
CDD:271355	136	EUKprk	Bacteria:119,Invertebrates:9,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd00446, GrpE, nucleotide exchange factor GrpE.  GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. In bacteria, the DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis. GrpE participates actively in response to heat shock by preventing aggregation of stress-denatured proteins; unfolded proteins initially bind to DnaJ, the J-domain ...
CDD:238253	129	EUKprk	Bacteria:10,Plants:1	cd00447, NusB_Sun, RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the ...
CDD:100004	107	EUKprk	Bacteria:358,Environmental:2,Invertebrates:19,Mammals:1,Plants:40,Primates:1,Vertebrates:3	cd00448, YjgF_YER057c_UK114_family, YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and ...
CDD:238254	256	EUKprk	Bacteria:27,Environmental:1,Invertebrates:7,Plants:4,Primates:1,nodiv:1	cd00449, PLPDE_IV, PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate lyases (ADCL). BCAT catalyzes the reversible transamination reaction between the L-branched-chain amino and alpha-keto acids. DAAT ...
CDD:212095	258	EUK	Invertebrates:8,Mammals:1,Plants:2,Vertebrates:1	cd00451, GH38N_AMII_euk, N-terminal catalytic domain of eukaryotic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38).  The family corresponds to a group of eukaryotic class II alpha-mannosidases (AlphaMII), which contain Golgi alpha-mannosidases II (GMII), the major broad specificity lysosomal alpha-mannosidases (LAM, MAN2B1), the noval core-specific lysosomal alpha 1,6-mannosidases (Epman, MAN2B2), and similar ...
CDD:188632	190	EUKprk	Bacteria:40,Rodents:1,nodiv:1	cd00452, KDPG_aldolase, KDPG and KHG aldolase.  KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase,  is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and ...
CDD:271265	111	EUKprk	Bacteria:150,Environmental:2,Invertebrates:7,Plants:10	cd00454, TrHb1_N, truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N).  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex ...
CDD:238257	295	EUKprk	Bacteria:13,Invertebrates:4,Plants:1	cd00455, nuc_hydro, nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata,  the xanthosine-inosine-uridine-adenosine-preferring nucleoside ...
CDD:176642	159	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Plants:12,Primates:1,Rodents:2	cd00457, PEBP, PhosphatidylEthanolamine-Binding Protein (PEBP) domain.  PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. ...
CDD:132901	86	EUKprk	Bacteria:4,Plants:1,Vertebrates:1	cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase.  The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that ...
CDD:238259	171	EUKprk	Bacteria:59,Plants:12,Primates:1,Vertebrates:1	cd00462, PTH, Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded ...
CDD:199209	83	EUKprk	Bacteria:10,Invertebrates:5,Mammals:1,Plants:6,Vertebrates:3	cd00463, Ribosomal_L31e, Eukaryotic/archaeal ribosomal protein L31.  Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit.
CDD:238260	154	EUKprk	Bacteria:48,Plants:14,Primates:1,nodiv:1	cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group ...
CDD:238261	306	PRK	Bacteria:3	cd00465, URO-D_CIMS_like, The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of ...
CDD:238262	140	EUKprk	Bacteria:51,Environmental:2,Plants:3,nodiv:1	cd00466, DHQase_II, Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. ...
CDD:100103	54	EUKprk	Bacteria:9,Invertebrates:23,Plants:7,Primates:1,Vertebrates:3,nodiv:1	cd00472, Ribosomal_L24e_L24, Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site.  L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between ...
CDD:259850	219	EUKprk	Bacteria:477,Environmental:10,Invertebrates:34,Plants:57,Primates:1,Vertebrates:3	cd00475, Cis_IPPS, Cis (Z)-Isoprenyl Diphosphate Synthases.  Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS) catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the ...
CDD:238266	524	EUKprk	Bacteria:20,Invertebrates:5,Plants:5,Primates:1,Vertebrates:3	cd00477, FTHFS, Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze ...
CDD:238267	511	EUKprk	Bacteria:23,Invertebrates:4,Plants:7,Vertebrates:1	cd00480, malate_synt, Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle.
CDD:238268	145	EUKprk	Bacteria:4,Invertebrates:9,Plants:5,Primates:1,Vertebrates:2	cd00481, Ribosomal_L19e, Ribosomal protein L19e.  L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small ...
CDD:238269	128	EUKprk	Bacteria:69,Plants:6,nodiv:2	cd00483, HPPK, 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate.  One enzyme from this ...
CDD:238270	508	EUKprk	Bacteria:9,Invertebrates:4,Plants:6	cd00484, PEPCK_ATP, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for ...
CDD:238271	141	EUKprk	Bacteria:67,Environmental:2,Invertebrates:6,Phages:1,Plants:2,Primates:1,Synthetic:1,Vertebrates:2,nodiv:3	cd00487, Pep_deformylase, Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss ...
CDD:238272	75	EUKprk	Bacteria:69,Invertebrates:10,Plants:9,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	cd00488, PCD_DCoH, PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH  (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme.  DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of ...
CDD:238273	85	PRK	Bacteria:8	cd00489, Barstar_like, Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the cell.  Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs  to the same enzyme family as does barnase.
CDD:238275	131	EUKprk	Bacteria:95,Environmental:1,Invertebrates:4,Plants:3,nodiv:2	cd00493, FabA_FabZ, FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ.  FabA is ...
CDD:270213	274	EUKprk	Bacteria:12,Plants:3,Primates:1	cd00494, PBP2_HMBS, Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold.  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, vitamin B12 and related macrocycles. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This family includes ...
CDD:198379	90	EUKprk	Bacteria:324,Environmental:4,Invertebrates:4,Plants:13	cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain.  L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had ...
CDD:238277	218	EUKprk	Bacteria:10,Invertebrates:3,Plants:2,Primates:1	cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate ...
CDD:211322	215	EUKprk	Bacteria:6,Invertebrates:1	cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. ...
CDD:238278	275	EUKprk	Bacteria:29,Invertebrates:1,Plants:1,nodiv:1	cd00498, Hsp33, Heat shock protein 33 (Hsp33):  Cytosolic protein that acts as a molecular chaperone under oxidative conditions.  In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion.  Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on.  Hsp33 is homodimeric in its functional form.
CDD:238279	194	EUKprk	Bacteria:32,Invertebrates:3,Plants:6,Primates:1,Vertebrates:4	cd00501, Peptidase_C15, Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I:  Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from proteolysis by other proteases until the pGlu is removed by a PGP.  PGPs are cysteine proteases with a Cys-His-Glu/Asp catalytic triad. Type I ...
CDD:188633	225	EUKprk	Bacteria:20,Plants:10	cd00502, DHQase_I, Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase).  Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase). Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase ...
CDD:238280	105	EUKprk	Bacteria:5,Invertebrates:3,Plants:1	cd00503, Frataxin, Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold ...
CDD:238281	149	EUKprk	Bacteria:28,Invertebrates:2,Plants:2	cd00504, GXGXG, GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS),  in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC). It is also found in a primarily archeal group of proteins predicted to encode part of the large subunit of GltS. It is characterized by a repeated GXXGXXXG ...
CDD:132996	246	EUKprk	Bacteria:1,Mammals:1,Plants:1,Primates:1,Vertebrates:2	cd00505, Glyco_transf_8, Members of glycosyltransferase family 8 (GT-8) are involved in lipopolysaccharide biosynthesis and glycogen synthesis.  Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. GT-8 comprises enzymes with a number of known activities: lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase, and  ...
CDD:238282	120	PRK	Bacteria:37,nodiv:1	cd00508, MopB_CT_Fdh-Nap-like, This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex  and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and ...
CDD:238284	107	EUKprk	Bacteria:16,Invertebrates:13,Plants:9,Rodents:1,Vertebrates:2	cd00513, Ribosomal_L32_L32e, Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary ...
CDD:238285	183	EUKprk	Bacteria:38,Invertebrates:5,Plants:4,Primates:1	cd00515, HAM1, NTPase/HAM1.  This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides such as XTP to XMP and ITP to IMP, but not the ...
CDD:238286	281	EUKprk	Bacteria:71,Invertebrates:6,Plants:7,Primates:1,Vertebrates:3,nodiv:1	cd00516, PRTase_typeII, Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) ...
CDD:173895	353	EUKprk	Bacteria:6,Environmental:1,Invertebrates:4,Plants:5,Primates:1,Vertebrates:2	cd00517, ATPS, ATP-sulfurylase.  ATP-sulfurylase (ATPS), also known as sulfate adenylate transferase, catalyzes the transfer of an adenylyl group from ATP to sulfate, forming adenosine 5'-phosphosulfate (APS).  This reaction is generally accompanied by a further reaction, catalyzed by APS kinase, in which APS is phosphorylated to yield 3'-phospho-APS (PAPS).  In some organisms the APS kinase is a ...
CDD:99872	139	PRK	Bacteria:100,nodiv:1	cd00518, H2MP, Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg ...
CDD:238287	229	EUKprk	Bacteria:12,Environmental:1,Invertebrates:6,Plants:27,Primates:1,Vertebrates:2	cd00519, Lipase_3, Lipase (class 3).  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo ...
CDD:238288	179	EUKprk	Bacteria:3,Invertebrates:2,Plants:3	cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation.  Thus ribosomes are "recycled" and ready for another round of protein synthesis.  RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear.  RRF is essential for bacterial ...
CDD:238289	123	PRK	Bacteria:7,Phages:1	cd00523, archeal_HJR, Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the ...
CDD:238290	86	PRK	Bacteria:28	cd00524, SORL, Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin.  Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, Fe[His4Cys(Glu)], which in the ...
CDD:238291	136	EUKprk	Bacteria:116,Invertebrates:15,Plants:7,Primates:1,Vertebrates:2	cd00525, AE_Prim_S_like, AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger ...
CDD:238292	220	EUKprk	Bacteria:1,Invertebrates:2,Plants:4,Primates:1	cd00527, IF6, Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members.  All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved ...
CDD:238293	136	EUKprk	Bacteria:39,Invertebrates:3,Plants:5	cd00528, MoaC, MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
CDD:238294	154	EUKprk	Bacteria:4,Plants:2	cd00529, RuvC_resolvase, Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination.  HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's.  These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR.  RuvC and its orthologs are ...
CDD:238295	293	EUKprk	Bacteria:9,Invertebrates:1,Rodents:1,Vertebrates:1	cd00530, PTE, Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif.  The native enzyme contains two zinc ions at the active ...
CDD:238296	124	EUKprk	Bacteria:58,Invertebrates:7,Plants:10,Primates:1,Rodents:1,Vertebrates:2	cd00531, NTF2_like, Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  ...
CDD:238298	118	EUKprk	Bacteria:7,Plants:2	cd00534, DHNA_DHNTPE, Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack ...
CDD:238299	274	EUKprk	Bacteria:36,Environmental:1,Invertebrates:2,Plants:3,Primates:1	cd00537, MTHFR, Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of ...
CDD:238300	126	EUKprk	Bacteria:22,Plants:16,Primates:1,Rodents:1,Vertebrates:3	cd00538, PA, PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and ...
CDD:187726	187	EUKprk	Bacteria:64,Environmental:2,Invertebrates:8,Plants:1,Primates:1,Vertebrates:3,nodiv:1	cd00540, AAG, Alkyladenine DNA glycosylase catalyzes the first step in base excision repair.  Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged ...
CDD:238302	231	PRK	Bacteria:24,nodiv:1	cd00541, OMPLA, The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among Gram-negative bacteria, both in pathogens and nonpathogens. In pathogenic bacteria such as Campylobacter coli and Helicobacter pylori OMPLA is involved in pathogenesis and virulence. In nonpathogenic ...
CDD:238303	303	PRK	Bacteria:32	cd00542, Ntn_PVA, Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins.  PVA has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which PVA belongs.  This nucleophilic cysteine is exposed by post-translational prossessing of the PVA precursor. PVA forms ...
CDD:238304	169	PRK	Bacteria:22	cd00544, CobU, Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.
CDD:238305	312	PRK	Bacteria:10	cd00545, MCH, Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria.  It catalyzes the reversible formation of N(5), N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+) from N(5)-formyltetrahydromethanopterin (formyl- H4MPT), in the third step of the reaction to reduce CO2 to CH4. The protein functions as a ...
CDD:238306	124	PRK	Bacteria:10	cd00546, QFR_TypeD_subunitC, Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C;  QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a ...
CDD:238307	115	PRK	Bacteria:8	cd00547, QFR_TypeD_subunitD, Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a ...
CDD:200451	260	EUKprk	Bacteria:132,Invertebrates:18,Plants:5,Primates:1,Synthetic:1,Vertebrates:2	cd00551, AmyAc_family, Alpha amylase catalytic domain family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as ...
CDD:238308	93	EUKprk	Bacteria:109,Environmental:1,Invertebrates:1,Plants:4,nodiv:1	cd00552, RaiA, RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY,  is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site.  RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the ...
CDD:238309	248	EUKprk	Bacteria:61,Invertebrates:4,Plants:5,Primates:1,Vertebrates:2	cd00553, NAD_synthase, NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD+ occurs via an NAD-adenylate intermediate and requires ATP and Mg2+. The intemediate is subsequently cleaved into NAD+ and AMP. In many ...
CDD:100025	153	EUKprk	Bacteria:83,Invertebrates:4,Plants:5	cd00554, MECDP_synthase, MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea.  MECDP_synthase forms a homotrimer, ...
CDD:238310	180	EUKprk	Bacteria:37,Environmental:1,Invertebrates:5,Plants:2,Primates:1,Vertebrates:1	cd00555, Maf, Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or nucleic acid-binding protein with structural similarity to the hypoxanthine/xanthine NTP pyrophosphatase Ham1 from Methanococcus ...
CDD:238311	99	EUKprk	Bacteria:37,Invertebrates:5,Plants:20,Primates:1,Vertebrates:2	cd00556, Thioesterase_II, Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, ...
CDD:238313	69	EUKprk	Bacteria:44,Plants:11,nodiv:1	cd00559, Cyanase_C, Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate.  It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two ...
CDD:185673	277	EUKprk	Bacteria:21,Plants:3	cd00560, PanC, Pantoate-beta-alanine ligase.  PanC  Pantoate-beta-alanine ligase, also known as pantothenate synthase, catalyzes the formation of pantothenate from pantoate and alanine.  PanC  belongs to a large superfamily of nucleotidyltransferases that includes , ATP sulfurylase (ATPS), phosphopantetheine adenylyltransferase (PPAT), and the amino-acyl tRNA synthetases. The enzymes of this family are structurally similar and share a dinucleotide-binding domain.
CDD:238314	159	PRK	Bacteria:15	cd00561, CobA_CobO_BtuR, ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer,  which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <=> phosphate + diphosphate + adenosylcobalamin.
CDD:238315	102	PRK	Bacteria:50	cd00562, NifX_NifB, This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme.  This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. ...
CDD:238316	145	EUKprk	Bacteria:8,Invertebrates:2,Plants:3,Primates:1	cd00563, Dtyr_deacylase, D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding.
CDD:238317	196	EUKprk	Bacteria:196,Environmental:3,Invertebrates:1,Plants:11,nodiv:2	cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of ...
CDD:176353	65	PRK	Bacteria:7	cd00565, ThiS, ThiaminS ubiquitin-like sulfur carrier protein.  ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria.  The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
CDD:173838	327	EUKprk	Bacteria:22,Invertebrates:3,Mammals:1,Plants:1,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00567, ACAD, Acyl-CoA dehydrogenase.  Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are ...
CDD:238318	168	EUKprk	Bacteria:66,Plants:3,Primates:1,nodiv:2	cd00568, TPP_enzymes, Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes.
CDD:259851	42	PRK	Bacteria:220,Environmental:1	cd00569, HTH_Hin_like, Helix-turn-helix domain of Hin and related proteins.  This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the ...
CDD:238319	71	EUKprk	Bacteria:116,Invertebrates:59,Mammals:1,Plants:39,Primates:2,Rodents:2,Vertebrates:5,nodiv:5	cd00570, GST_N_family, Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. ...
CDD:238320	136	PRK	Bacteria:25,nodiv:1	cd00571, UreE, UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-terminal region of UreE contains a histidine rich nickel binding site.
CDD:238321	356	EUKprk	Bacteria:8,Invertebrates:9,Mammals:5,Primates:1,Rodents:3,Vertebrates:6	cd00575, NOS_oxygenase, Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) ...
CDD:153083	401	PRK	Bacteria:5,Phages:1	cd00576, RNR_PFL, Ribonucleotide reductase and Pyruvate formate lyase.  Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into ...
CDD:238322	248	EUKprk	Bacteria:14,Invertebrates:14,Plants:17,Primates:1,Vertebrates:3	cd00577, PCNA, Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea.  These polymerase processivity factors play a role in DNA replication and repair.  PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors ...
CDD:238323	452	PRK	Bacteria:33	cd00578, L-fuc_L-ara-isomerases, L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to ...
CDD:238324	113	PRK	Bacteria:48	cd00580, CHMI, 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates.  Despite the structural similarity of CHMI with 4-oxalocrotonate ...
CDD:238325	206	PRK	Bacteria:10	cd00581, QFR_TypeB_TM, Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit;  QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and rhodoquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share ...
CDD:238326	210	PRK	Bacteria:8	cd00583, MutH_Sau3AI, MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex.   MutH is homologous to the type II restriction endonuclease Sau3AI which also recognizes the d(GATC) sequence however, Sau3AI cleaves both strands regardless of their methylation state. The active ...
CDD:238327	129	EUKprk	Bacteria:5,Invertebrates:2,Plants:1,Primates:1	cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or ...
CDD:238328	437	EUKprk	Bacteria:16,Invertebrates:1,Plants:7,Primates:1,Vertebrates:3	cd00585, Peptidase_C1B, Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is a cysteine peptidase that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to ...
CDD:238329	110	EUKprk	Bacteria:188,Environmental:3,Invertebrates:3,Plants:20,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd00586, 4HBT, 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites.  There is no evidence to suggest that 4HBT is related to the type I thioesterases functioning in primary or ...
CDD:238331	136	PRK	Bacteria:20	cd00588, CheW_like, CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in the chemotaxis associated histidine kinase CheA binds to CheW, suggesting that these domains can interact ...
CDD:240668	72	EUKprk	Bacteria:4,Invertebrates:42,Mammals:1,Plants:65,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	cd00590, RRM_SF, RNA recognition motif (RRM) superfamily.  RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a ...
CDD:259852	85	EUKprk	Bacteria:47,Phages:1,Plants:1	cd00591, HU_IHF, DNA sequence specific (IHF) and non-specific (HU) domains.  This family includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene ...
CDD:133378	100	PRK	Bacteria:73,nodiv:1	cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators.  Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress ...
CDD:238333	133	EUKprk	Bacteria:56,Environmental:2,Invertebrates:6,Plants:14,Primates:1,Vertebrates:3,nodiv:1	cd00593, RIBOc, RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. ...
CDD:238334	272	EUKprk	Bacteria:40,Invertebrates:14,Plants:23,Primates:1,Vertebrates:3	cd00594, KU, Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ...
CDD:238335	133	EUKprk	Bacteria:1,Invertebrates:1,Primates:1,Rodents:1,Vertebrates:1	cd00595, NDPk, Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal ...
CDD:199839	211	EUKprk	Bacteria:20,Invertebrates:2,Plants:1,Primates:1,Vertebrates:1	cd00596, Peptidase_M14_like, M14 family of metallocarboxypeptidases and related proteins.  The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of ...
CDD:119349	210	EUKprk	Bacteria:11,Invertebrates:12,Plants:15,Primates:1	cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded ...
CDD:119373	186	EUKprk	Bacteria:36,Invertebrates:2,Phages:2	cd00599, GH25_muramidase, Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.  This family of muramidases contains a glycosyl hydrolase family 25 (GH25) catalytic domain and is found in bacteria, fungi, slime molds, round worms, protozoans and ...
CDD:212462	63	EUKprk	Bacteria:5,Invertebrates:2,Plants:13,Primates:1,Vertebrates:1	cd00600, Sm_like, Sm and related proteins.  The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded ...
CDD:238336	101	miss	miss	cd00602, IPT_TF, IPT domain of eukaryotic transcription factors NF-kappaB/Rel, nuclear factor of activated Tcells (NFAT), and  recombination signal J-kappa binding protein (RBP-Jkappa). The IPT domains in these proteins are involved in DNA binding. Most NF-kappaB/Rel proteins form homo- and heterodimers, while NFAT proteins are largely monomeric (with TonEBP being an exception). While the majority of sequence-specific DNA binding elements are found in the N-terminal ...
CDD:238337	90	miss	miss	cd00603, IPT_PCSR, IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the macrophage-stimulating receptors and of fibrocystin. Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the ...
CDD:238338	81	PRK	Bacteria:2	cd00604, IPT_CGTD, IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown.
CDD:238341	329	EUKprk	Bacteria:13,Invertebrates:2,Plants:3,Primates:1	cd00608, GalT, Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme contains two identical subunits. It also demonstrates that the active site is formed by amino acid residues from both subunits of the dimer.
CDD:99734	350	EUKprk	Bacteria:70,Invertebrates:7,Mammals:1,Plants:8,Primates:1,Vertebrates:4	cd00609, AAT_like, Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), ...
CDD:99735	413	EUKprk	Bacteria:46,Environmental:1,Invertebrates:2,Mammals:1,Plants:4,Primates:1,Vertebrates:2,nodiv:1	cd00610, OAT_like, Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, ...
CDD:99736	355	EUKprk	Bacteria:2,Invertebrates:1,Plants:1,Vertebrates:1	cd00611, PSAT_like, Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT).  PSAT is active as a dimer and catalyzes the conversion of phosphohydroxypyruvate to phosphoserine.
CDD:99737	398	EUKprk	Bacteria:3,Invertebrates:2,Primates:1,Vertebrates:1	cd00613, GDC-P, Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalysed by this protein ...
CDD:99738	369	EUKprk	Bacteria:9,Invertebrates:3,Plants:5,Primates:1	cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. This subgroup also includes cystathionine gamma-lyases (CGL), O-acetylhomoserine sulfhydrylases and O-acetylhomoserine thiol lyases. CGL's ...
CDD:99739	294	EUKprk	Bacteria:11,Invertebrates:1,Plants:1	cd00615, Orn_deC_like, Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and ...
CDD:99740	352	PRK	Bacteria:42	cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT,  Arnb aminotransferase and pilin glycosylation protein. The prototype of ...
CDD:153092	83	EUKprk	Bacteria:1,Invertebrates:9,Mammals:2,Plants:4,Primates:2,Rodents:2,Vertebrates:4	cd00618, PLA2_like, PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are ...
CDD:238342	130	miss	miss	cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription ...
CDD:238343	126	miss	miss	cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze ...
CDD:143482	362	EUKprk	Bacteria:39,Invertebrates:21,Mammals:1,Plants:15,Primates:1,Rodents:1,Vertebrates:3	cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase.  This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are ...
CDD:238344	396	EUKprk	Bacteria:31,Environmental:1,Invertebrates:2,Plants:3,Primates:1	cd00625, ArsB_NhaD_permease, Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump.
CDD:238345	105	EUKprk	Bacteria:3,Invertebrates:1,Plants:1,Rodents:1	cd00632, Prefoldin_beta, Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea.  Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin ...
CDD:238346	67	EUK	Mammals:6,Primates:2,Rodents:5,Vertebrates:1	cd00633, Secretoglobin, Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer ...
CDD:143483	222	EUKprk	Bacteria:113,Environmental:1,Invertebrates:1,Plants:1	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins.  This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a ...
CDD:238347	148	PRK	Bacteria:116,Environmental:2	cd00636, TroA-like, Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+.  Their ligand binding site is formed in the interface between two globular domains linked by a single helix.  Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH ...
CDD:107202	244	EUKprk	Bacteria:103,Environmental:1,Invertebrates:7,Plants:21,Primates:1,Vertebrates:3	cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine ...
CDD:238348	193	EUKprk	Bacteria:74,Plants:7	cd00641, GTP_cyclohydro2, GTP cyclohydrolase II (RibA).  GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the precursor molecule for the synthesis of  the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential to cell metabolism. The enzyme is present ...
CDD:153081	403	EUKprk	Bacteria:15,Invertebrates:13,Plants:8,Primates:1,Vertebrates:3	cd00643, HMG-CoA_reductase_classI, Class I hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR).  Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class I enzyme, homotetramer. Catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals this is the rate limiting committed step in cholesterol biosynthesis. Class I enzymes are found predominantly in eukaryotes and ...
CDD:153082	417	EUKprk	Bacteria:70,Environmental:1,Invertebrates:2,Plants:2,nodiv:1	cd00644, HMG-CoA_reductase_classII, Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR).  Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class II, prokaryotic enzyme is a homodimer. Class II enzymes are found primarily in prokaryotes and Archaeoglobus fulgidus and are soluble as they lack the membrane region. Enzymes catalyze the synthesis of coenzyme A and mevalonate in isoprenoid ...
CDD:238350	309	PRK	Bacteria:8	cd00645, AsnA, Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia.  AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB.
CDD:270214	196	EUKprk	Bacteria:25,Primates:1,Rodents:1	cd00648, Periplasmic_Binding_Protein_Type_2, Type 2 periplasmic binding fold superfamily.  This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating.  The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology.  They are typically comprised ...
CDD:173824	409	EUKprk	Bacteria:9,Plants:2	cd00649, catalase_peroxidase_1, N-terminal catalytic domain of catalase-peroxidases.  This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These ...
CDD:133419	263	EUKprk	Bacteria:3,Mammals:1,Plants:1,Primates:1	cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family.  Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both ...
CDD:238351	122	EUKprk	Bacteria:2,Invertebrates:2,Plants:1,Primates:1,Rodents:2,Vertebrates:1	cd00651, TFold, Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1),  6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and ...
CDD:238352	174	EUKprk	Bacteria:8,Invertebrates:19,Plants:11,Primates:1,Vertebrates:3	cd00652, TBP_TLF, TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter ...
CDD:238353	866	EUKprk	Bacteria:18,Invertebrates:19,Plants:20,Primates:1,Vertebrates:4	cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that ...
CDD:259791	45	EUKprk	Bacteria:15,Environmental:1,Plants:1,Primates:1	cd00656, Zn-ribbon, C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit.  The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon ...
CDD:153097	130	EUKprk	Bacteria:105,Invertebrates:1,Plants:5,Primates:1	cd00657, Ferritin_like, Ferritin-like superfamily of diiron-containing four-helix-bundle proteins.  Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese ...
CDD:271176	210	EUKprk	Bacteria:5,Invertebrates:4,Plants:6,Primates:1,Vertebrates:2,Viruses:2,nodiv:1	cd00659, Topo_IB_C, DNA topoisomerase IB, C-terminal catalytic domain.  Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded ...
CDD:238356	215	EUK	Invertebrates:8,Plants:6,Primates:1,Vertebrates:2	cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into:  topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then ...
CDD:238357	160	miss	miss	cd00667, ring_hydroxylating_dioxygenases_beta, Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonheme iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons ...
CDD:185674	312	PRK	Bacteria:4	cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases.  Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the ...
CDD:238359	235	PRK	Bacteria:4	cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three ...
CDD:185675	212	EUKprk	Bacteria:13,Invertebrates:2,Plants:1,Primates:1,Vertebrates:1	cd00671, ArgRS_core, catalytic core domain of arginyl-tRNA synthetases.  Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups ...
CDD:173899	213	EUKprk	Bacteria:9,Environmental:1,Invertebrates:3,Primates:1,Vertebrates:2	cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA synthetase.  Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the ...
CDD:238360	232	EUKprk	Bacteria:2,Invertebrates:3,Plants:1,Primates:1	cd00673, AlaRS_core, Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its predicted structure and the presence of three characteristic sequence motifs.
CDD:173900	353	PRK	Bacteria:3	cd00674, LysRS_core_class_I, catalytic core domain of  class I lysyl tRNA synthetase.  Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which ...
CDD:238361	46	EUKprk	Invertebrates:8,Primates:1,Rodents:3,Vertebrates:4,Viruses:1	cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by ...
CDD:176852	188	EUKprk	Bacteria:63,Plants:10	cd00680, RHO_alpha_C, C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial ...
CDD:173831	265	miss	miss	cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Synthases, head-to-head.  These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices ...
CDD:173832	542	miss	miss	cd00684, Terpene_cyclase_plant_C1, Plant Terpene Cyclases, Class 1.  This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene ...
CDD:173833	259	miss	miss	cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail.  These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors,  isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze ...
CDD:173835	303	miss	miss	cd00687, Terpene_cyclase_nonplant_C1, Non-plant Terpene Cyclases, Class 1.  This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or ...
CDD:238362	300	EUKprk	Bacteria:58,Invertebrates:27,Mammals:1,Plants:28,Primates:1,Rodents:2,Vertebrates:9,nodiv:1	cd00688, ISOPREN_C2_like, This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these ...
CDD:173825	253	EUK	Invertebrates:2,Plants:22	cd00691, ascorbate_peroxidase, Ascorbate peroxidases and cytochrome C peroxidases.  Ascorbate peroxidases are a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Along with related catalase-peroxidases, ascorbate peroxidases belong to class I of the plant superfamily. Ascorbate peroxidases are found in the ...
CDD:173826	328	EUK	Plants:10	cd00692, ligninase, Ligninase and other manganese-dependent fungal peroxidases.  Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of ...
CDD:173827	298	EUK	Plants:34	cd00693, secretory_peroxidase, Horseradish peroxidase and related secretory plant peroxidases.  Secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants where they have been implicated in ...
CDD:133420	323	EUK	Invertebrates:6,Plants:2	cd00704, MDH, Malate dehydrogenase.  Malate dehydrogenase (MDH) is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. MDHs belong to the NAD-dependent, lactate dehydrogenase (LDH)-like, 2-hydroxycarboxylate dehydrogenase family, which also includes the GH4 family of glycoside hydrolases. They are part of the ...
CDD:238363	275	EUK	Invertebrates:6,Mammals:2,Primates:1,Rodents:1,Vertebrates:4	cd00707, Pancreat_lipase_like, Pancreatic lipase-like enzymes.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo ...
CDD:100039	167	PRK	Bacteria:11	cd00710, LbH_gamma_CA, Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental ...
CDD:238364	220	miss	miss	cd00712, AsnB, Glutamine amidotransferases class-II (GATase) asparagine synthase_B type.  Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a  glutaminase domain and a synthetase domain. The N-terminal glutaminase domain hydrolyzes glutamine to glutamic acid and ammonia.
CDD:238365	413	miss	miss	cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamic acid and ammonia, and has a fold similar to that of other glutamine amidotransferases such as glucosamine-fructose 6-phosphate ...
CDD:238366	215	miss	miss	cd00714, GFAT, Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans).  The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. In humans, GFAT catalyzes the first and rate-limiting step of hexosamine metabolism, the conversion of D-fructose-6P (Fru6P) into ...
CDD:238367	252	miss	miss	cd00715, GPATase_N, Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of  glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP,  ...
CDD:238368	335	EUKprk	Bacteria:33,Invertebrates:5,Plants:7,Primates:1,Vertebrates:3	cd00717, URO-D, Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction is located at the branching point of the tetrapyrrole biosynthetic pathway, leading to the biosynthesis of heme, chlorophyll or ...
CDD:198380	69	EUKprk	Bacteria:42,Phages:1,Plants:2,Vertebrates:1,Viruses:1	cd00719, GIY-YIG_SF, GIY-YIG nuclease domain superfamily.  The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of ...
CDD:238369	511	miss	miss	cd00727, malate_synt_A, Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA, which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon ...
CDD:238371	34	miss	miss	cd00729, rubredoxin_SM, Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and  believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small ...
CDD:238372	50	PRK	Bacteria:1	cd00730, rubredoxin, Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
CDD:238373	132	miss	miss	cd00731, CheA_reg, CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling mechanism is modulated by the methyl accepting chemotaxis proteins (MCPs). MCPs form a highly interconnected, tightly packed array within the membrane that is organized, at least in part, through ...
CDD:238374	140	miss	miss	cd00732, CheW, CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together with CheA and the methyl-accepting chemotaxis proteins (MCPs), which are involved in response modulation.
CDD:238377	151	PRK	Bacteria:9,Phages:2	cd00736, bacteriophage_lambda_lysozyme, The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes.  But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic ...
CDD:238378	133	PRK	Bacteria:8,Phages:14,nodiv:1	cd00737, endolysin_autolysin, Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall hetropolymer peptidoglycan and cell division.  Both endolysin and autolysin ...
CDD:238379	94	EUKprk	Bacteria:1,Rodents:1	cd00738, HGTP_anticodon, HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory ...
CDD:238380	257	miss	miss	cd00739, DHPS, DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS.  Sulfonamide drugs, which are ...
CDD:238382	153	EUK	Plants:2	cd00741, Lipase, Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad ...
CDD:238383	386	EUKprk	Bacteria:46,Invertebrates:6,Plants:10,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd00751, thiolase, Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and eukaryotes (cytosol, microbodies and mitochondria). There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) ...
CDD:176354	80	miss	miss	cd00754, MoaD, Ubiquitin domain of MoaD-like proteins.  MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This ...
CDD:238384	231	EUKprk	Bacteria:14,Invertebrates:1,Plants:2,nodiv:1	cd00755, YgdL_like, Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy ...
CDD:238385	124	EUKprk	Bacteria:108,Environmental:3,Invertebrates:7,Plants:6,Primates:1,Vertebrates:2	cd00756, MoaE, MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible ...
CDD:238386	228	EUKprk	Bacteria:41,Environmental:1,Invertebrates:5,Plants:3,Primates:1,Vertebrates:1	cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating ...
CDD:238387	133	EUKprk	Bacteria:11,Primates:1,Rodents:1	cd00758, MoCF_BD, MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
CDD:132997	156	EUKprk	Bacteria:177,Environmental:3,Invertebrates:2,Mammals:2,Plants:5,Primates:1,Rodents:2,Synthetic:1,Vertebrates:1	cd00761, Glyco_tranf_GTA_type, Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold.  Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor ...
CDD:238391	211	PRK	Bacteria:5	cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound ...
CDD:238392	198	EUKprk	Bacteria:25,Environmental:1,Invertebrates:3,Plants:2	cd00769, PheRS_beta_core, Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA,  PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains ...
CDD:238393	297	EUKprk	Bacteria:9,Invertebrates:3,Plants:3,Primates:1,Vertebrates:2	cd00770, SerRS_core, Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate.  Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core ...
CDD:238394	298	EUKprk	Bacteria:6,Invertebrates:3,Plants:2,Primates:1	cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the ...
CDD:238396	261	EUKprk	Bacteria:21,Invertebrates:2,Plants:5,Vertebrates:1	cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence ...
CDD:238397	254	EUKprk	Bacteria:2,Invertebrates:3,Plants:2,Rodents:1,Vertebrates:1	cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains ...
CDD:238398	329	EUKprk	Bacteria:6,Invertebrates:3,Rodents:1,Vertebrates:1	cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core domain.  Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea.  However, LysRS belongs to class I aaRS's  in ...
CDD:238399	322	EUKprk	Bacteria:4,Invertebrates:3,Plants:4,Rodents:1,Vertebrates:1	cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II core domain.  Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS.  AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the ...
CDD:238400	280	EUKprk	Bacteria:13,Invertebrates:2,Plants:1,Primates:1	cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this ...
CDD:238401	261	EUKprk	Bacteria:8,Invertebrates:5,Plants:2,Vertebrates:1	cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs ...
CDD:238402	255	EUKprk	Bacteria:5,Invertebrates:4,Plants:3,Primates:1,Vertebrates:1	cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence ...
CDD:238403	119	miss	miss	cd00780, NTF2, Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically ...
CDD:238405	122	miss	miss	cd00782, MutL_Trans, MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins ...
CDD:238407	287	miss	miss	cd00788, KU70, Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit ...
CDD:238408	256	miss	miss	cd00789, KU_like, Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a ...
CDD:238410	412	miss	miss	cd00795, NOS_oxygenase_euk, Nitric oxide synthase (NOS) eukaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . ...
CDD:271177	162	EUKprk	Bacteria:37,Phages:3,Plants:1	cd00796, INT_Rci_Hp1_C, Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain.  Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any ...
CDD:271178	198	PRK	Bacteria:5	cd00797, INT_RitB_C_like, C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio.  Recombinases RitA, RitB (also known as SG4), and RitC are encoded by three adjacent and overlapping genes. They are called recombinase trio. This RitB family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they ...
CDD:271179	172	EUKprk	Bacteria:47,Plants:1	cd00798, INT_XerDC_C, XerD and XerC integrases, C-terminal catalytic domains.  XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA ...
CDD:271180	188	EUKprk	Bacteria:28,Phages:1,Vertebrates:1	cd00799, INT_Cre_C, C-terminal catalytic domain of Cre recombinase (also called integrase).  Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific ...
CDD:271181	161	EUKprk	Bacteria:11,Phages:1,Plants:1	cd00800, INT_Lambda_C, C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase.  Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their ...
CDD:271182	180	PRK	Bacteria:63,Phages:2	cd00801, INT_P4_C, Bacteriophage P4 integrase, C-terminal catalytic domain.  P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent ...
CDD:173901	143	PRK	Bacteria:2	cd00802, class_I_aaRS_core, catalytic core domain of class I amino acyl-tRNA synthetase.  Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, ...
CDD:173902	269	EUKprk	Bacteria:10,Invertebrates:2,Plants:3,Primates:1,Vertebrates:1	cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA synthetase.  Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme ...
CDD:173903	280	EUKprk	Bacteria:16,Invertebrates:4,Plants:3,Primates:1	cd00806, TrpRS_core, catalytic core domain of tryptophanyl-tRNA synthetase.  Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound ...
CDD:185676	238	EUKprk	Bacteria:2,Invertebrates:3,Plants:2,Primates:1,Vertebrates:1	cd00807, GlnRS_core, catalytic core domain of glutaminyl-tRNA synthetase.  Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Gln to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound ...
CDD:173905	239	EUKprk	Bacteria:14,Invertebrates:2,Plants:1,Primates:1	cd00808, GluRS_core, catalytic core domain of discriminating glutamyl-tRNA synthetase.  Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA.  Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core ...
CDD:173906	314	EUKprk	Bacteria:5,Invertebrates:2,Plants:1,Primates:1	cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA synthetases.  Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and ...
CDD:173907	319	EUKprk	Bacteria:19,Invertebrates:3,Primates:1,Vertebrates:2	cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA synthetases.  Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this ...
CDD:185677	382	EUKprk	Bacteria:1,Invertebrates:2,Plants:1,Primates:1,Vertebrates:1	cd00817, ValRS_core, catalytic core domain of valyl-tRNA synthetases.  Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class ...
CDD:173909	338	EUK	Invertebrates:2,Plants:2,Primates:1,Vertebrates:1	cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA synthetases.  Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic ...
CDD:238417	579	EUKprk	Bacteria:13,Invertebrates:6,Plants:1,Primates:1,Synthetic:1,Vertebrates:3	cd00819, PEPCK_GTP, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (GTP) for the phosphoryl ...
CDD:269906	92	EUK	Invertebrates:18,Mammals:1,Plants:12,Primates:1,Rodents:2,Vertebrates:7	cd00821, PH, Pleckstrin homology (PH) domain.  PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity ...
CDD:238419	172	miss	miss	cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are  heterodimers composed of two subunits.  The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and ...
CDD:238420	151	miss	miss	cd00823, TopoIIB_Trans, TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants.  S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. ...
CDD:238423	324	EUKprk	Bacteria:50,Invertebrates:3,Plants:6,Primates:1,Vertebrates:3,nodiv:1	cd00827, init_cond_enzymes, "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the utlization of CoA substrate primers, as well as the nature of their active site residues.
CDD:238424	407	EUKprk	Bacteria:12,Plants:5	cd00828, elong_cond_enzymes, "elongating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type I and II and polyketide synthases.They are characterized by the utlization of acyl carrier protein (ACP) thioesters as primer substrates, as well as the nature of their active site residues.
CDD:238425	375	EUKprk	Bacteria:26,Environmental:1,Invertebrates:3,Plants:4,Vertebrates:2,nodiv:1	cd00829, SCP-x_thiolase, Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2  has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal 3-ketacyl-Coa thiolase specific for branched-chain acyl CoAs, which is proteolytically cleaved from the sterol carrier protein.
CDD:238426	320	EUKprk	Bacteria:75,Invertebrates:1,Plants:5	cd00830, KAS_III, Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA.
CDD:238427	361	EUKprk	Bacteria:21,Invertebrates:2,Plants:13,nodiv:1	cd00831, CHS_like, Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy, after the starter molecule is loaded onto the active site cysteine, a carboxylative condensation reation extends the polyketide chain. Plant-specific PKS are ...
CDD:238428	399	PRK	Bacteria:16	cd00832, CLF, Chain-length factor (CLF) is a factor required for polyketide chain initiation of aromatic antibiotic-producing polyketide synthases (PKSs) of filamentous bacteria. CLFs have been shown to have decarboxylase activity towards malonyl-acyl carrier protein (ACP). CLFs are similar to other elongation ketosynthase domains, but their active site cysteine is replaced by a conserved glutamine.
CDD:238429	421	EUKprk	Bacteria:58,Environmental:1,Invertebrates:5,Plants:13,Primates:1,Vertebrates:2,nodiv:2	cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or more large multifunctional proteins and iterative type II PKSs, complexes of several monofunctional subunits.
CDD:238430	406	EUKprk	Bacteria:74,Environmental:1,Invertebrates:6,Plants:10,Rodents:1,Vertebrates:1,nodiv:2	cd00834, KAS_I_II, Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP.
CDD:269907	118	EUK	Invertebrates:19,Plants:17,Primates:1	cd00835, RanBD_family, Ran-binding domain.  The RanBD is present in RanBP1, RanBP2, RanBP3, Nuc2, and Nuc50. Most of these proteins have a single RanBD, with the exception of RanBP2 which has 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and ...
CDD:269908	93	EUK	Invertebrates:2,Plants:1,Primates:1,Rodents:2,Vertebrates:2	cd00836, FERM_C-lobe, FERM domain C-lobe.  The FERM domain has a cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and ...
CDD:163614	131	EUKprk	Bacteria:228,Environmental:2,Invertebrates:6,Plants:7,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd00838, MPP_superfamily, metallophosphatase superfamily, metallophosphatase domain.  Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ...
CDD:163615	294	EUK	Invertebrates:11,Plants:15,Rodents:1,Vertebrates:1,nodiv:1	cd00839, MPP_PAPs, purple acid phosphatases of the metallophosphatase superfamily, metallophosphatase domain.  Purple acid phosphatases (PAPs) belong to a diverse family of binuclear metallohydrolases that have been identified and characterized in plants, animals, and fungi.   PAPs contain a binuclear metal center and their characteristic pink or purple color derives from a charge-transfer transition between a tyrosine ...
CDD:163616	223	EUKprk	Bacteria:108,Invertebrates:9,Plants:8,Primates:1,Vertebrates:3	cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal metallophosphatase domain.  Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes.  ...
CDD:163617	155	PRK	Bacteria:127	cd00841, MPP_YfcE, Escherichia coli YfcE and related proteins, metallophosphatase domain.  YfcE is a manganase-dependent metallophosphatase, found in bacteria and archaea, that cleaves bis-p-nitrophenyl phosphate, thymidine 5'-monophosphate-p-nitrophenyl ester, and p-nitrophenyl phosphorylcholine, but is unable to hydrolyze 2',3 ' or 3',5' cyclic nucleic phosphodiesters, and various phosphomonoesters, including p-nitrophenyl phosphate. This family also includes ...
CDD:163618	296	EUKprk	Bacteria:3,Invertebrates:21,Plants:17,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd00842, MPP_ASMase, acid sphingomyelinase and related proteins, metallophosphatase domain.  Acid sphingomyelinase (ASMase) is a ubiquitously expressed phosphodiesterase which hydrolyzes sphingomyelin in acid pH conditions to form ceramide, a bioactive second messenger, as part of the sphingomyelin signaling pathway.  ASMase is localized at the noncytosolic leaflet of biomembranes (for example ...
CDD:163619	262	EUK	Invertebrates:12,Plants:10,Rodents:1,Vertebrates:3	cd00844, MPP_Dbr1_N, Dbr1 RNA lariat debranching enzyme, N-terminal metallophosphatase domain.  Dbr1 is an RNA lariat debranching enzyme that hydrolyzes 2'-5' phosphodiester bonds at the branch points of excised intron lariats.  This alignment model represents the N-terminal metallophosphatase domain of Dbr1.  This domain belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a ...
CDD:163620	252	EUKprk	Bacteria:66,Environmental:1,Invertebrates:1,Plants:1	cd00845, MPP_UshA_N_like, Escherichia coli UshA-like family, N-terminal metallophosphatase domain.  This family includes the bacterial enzyme UshA, and related enzymes including SoxB, CpdB, YhcR, and CD73.  All members have a similar domain architecture which includes an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain.  The N-terminal metallophosphatase domain belongs to a large superfamily of ...
CDD:238431	103	miss	miss	cd00851, MTH1175, This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme.  This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another ...
CDD:238432	106	miss	miss	cd00852, NifB, NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
CDD:238433	102	miss	miss	cd00853, NifX, NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB,  and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme.  The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.
CDD:238434	374	EUKprk	Bacteria:24,Invertebrates:2,Plants:2,Primates:1	cd00854, NagA, N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to amino-sugar-nucleotides, which is needed for cell wall peptidoglycan and teichoic acid biosynthesis. Deacetylation of N-acetylglucosamine is also important in ...
CDD:238435	121	EUKprk	Bacteria:1,Invertebrates:1,Plants:2	cd00858, GlyRS_anticodon, GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
CDD:238436	91	EUKprk	Bacteria:2,Invertebrates:2,Plants:2,Primates:1,Rodents:1	cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
CDD:238437	91	EUKprk	Bacteria:6,Invertebrates:1,Plants:2	cd00860, ThrRS_anticodon, ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
CDD:238438	94	EUKprk	Bacteria:1,Invertebrates:1	cd00861, ProRS_anticodon_short, ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
CDD:238439	202	EUKprk	Bacteria:3,Plants:1	cd00862, ProRS_anticodon_zinc, ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific ...
CDD:238440	152	EUKprk	Invertebrates:7,Plants:6,Primates:1,Rodents:1,Vertebrates:2,Viruses:1	cd00864, PI3Ka, Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain ...
CDD:176643	150	EUKprk	Bacteria:222,Environmental:1,Invertebrates:1	cd00865, PEBP_bact_arch, PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea.  PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea).  The members in this subgroup are present in bacterial and archaea.  Members here include Escherichia coli YBHB and YBCL which are thought to regulate protein phosphorylation as ...
CDD:176644	154	EUK	Invertebrates:38,Plants:51,Rodents:2,Vertebrates:4	cd00866, PEBP_euk, PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in eukaryotes.  PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea).  The members in this subgroup are present in eukaryotes.  Members here include those in plants such as Arabidopsis thaliana FLOWERING LOCUS (FT) and TERMINAL FLOWER1 (FT1) which function as a ...
CDD:173836	236	miss	miss	cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.  Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors ...
CDD:173837	284	miss	miss	cd00868, Terpene_cyclase_C1, Terpene cyclases, Class 1.  Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The ...
CDD:238442	166	miss	miss	cd00870, PI3Ka_III, Phosphoinositide 3-kinase (PI3K) class III, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3Ks class III phosphorylate phosphoinositol (PtdIns) only. The prototypical PI3K class III, yeast Vps34, is involved in trafficking proteins from Golgi to the vacuole.
CDD:238443	175	miss	miss	cd00871, PI4Ka, Phosphoinositide 4-kinase(PI4K), accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. PI4K phosphorylates hydroxylgroup at position 4 on the inositol ring of phosphoinositide, the first commited step in the phosphatidylinositol cycle.
CDD:238444	171	miss	miss	cd00872, PI3Ka_I, Phosphoinositide 3-kinase (PI3K) class I, accessory domain ; PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3K class I prefer phosphoinositol (4,5)-bisphosphate as a substrate. Mammalian members interact with active Ras. They form heterodimers with adapter molecules linking them to different signaling pathways.
CDD:238445	300	miss	miss	cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of ...
CDD:238446	326	EUKprk	Bacteria:6,Invertebrates:1,Vertebrates:1	cd00874, RNA_Cyclase_Class_II, RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in all members of this subfamily.
CDD:238447	341	EUK	Invertebrates:2,Plants:6,Primates:1,Vertebrates:1	cd00875, RNA_Cyclase_Class_I, RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded in eukaryotic genomes. They lack a conserved catalytic histidine residue required for cyclase activity, so probably do not function as cyclases. They are believed to play a role in ribosomal RNA processing and assembly.
CDD:206642	160	EUK	Invertebrates:7,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd00876, Ras, Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases).  The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release ...
CDD:206643	166	EUK	Invertebrates:10,Mammals:1,Plants:10,Primates:1,Vertebrates:3	cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of small GTPases.  Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras ...
CDD:206644	158	EUK	Invertebrates:9,Mammals:1,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases.  Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in ...
CDD:206645	191	EUK	Invertebrates:9,Plants:6,Primates:1,Rodents:1,Vertebrates:1	cd00879, Sar1, Sar1 is an essential component of COPII vesicle coats.  Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine ...
CDD:206646	161	EUKprk	Bacteria:33,Invertebrates:3	cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase.  The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent ...
CDD:206647	183	EUKprk	Bacteria:13,Invertebrates:3,Plants:5,Vertebrates:2	cd00881, GTP_translation_factor, GTP translation factor family primarily contains translation initiation, elongation and release factors.  The GTP translation factor family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of ...
CDD:206648	161	EUKprk	Bacteria:22,Invertebrates:11,Plants:6,Primates:1,Rodents:1,Vertebrates:3	cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases).  Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This ...
CDD:238448	182	miss	miss	cd00883, beta_CA_cladeA, Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, ...
CDD:238449	190	miss	miss	cd00884, beta_CA_cladeB, Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, ...
CDD:238450	170	EUKprk	Bacteria:107,Environmental:2,Invertebrates:4,Plants:7,Primates:1,Vertebrates:2	cd00885, cinA, Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
CDD:238451	152	EUKprk	Bacteria:86,Environmental:1,Invertebrates:4,Plants:4,Vertebrates:3	cd00886, MogA_MoaB, MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT).  MogA, together with MoeA, is responsible for the metal ...
CDD:238452	394	EUKprk	Bacteria:171,Environmental:3,Invertebrates:5,Plants:4,Primates:1,Vertebrates:1	cd00887, MoeA, MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT).  MoeA, together with MoaB, is responsible for the ...
CDD:238453	129	miss	miss	cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the ...
CDD:270624	334	EUK	Invertebrates:16,Plants:4,Primates:1	cd00891, PI3Kc, Catalytic domain of Phosphoinositide 3-kinase.  PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided ...
CDD:270625	237	EUK	Invertebrates:23,Plants:26,Primates:1,Vertebrates:3	cd00892, PIKKc_ATR, Catalytic domain of Ataxia telangiectasia and Rad3-related proteins.  ATR is also referred to as Mei-41 (Drosophila), Esr1/Mec1p (Saccharomyces cerevisiae), Rad3 (Schizosaccharomyces pombe), and FRAP-related protein (human). ATR contains a UME domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. Together with its downstream effector ...
CDD:270626	286	EUK	Invertebrates:4,Plants:5,Vertebrates:1	cd00893, PI4Kc_III, Catalytic domain of Type III Phosphoinositide 4-kinase.  PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. There are two types of PI4Ks, types II and III. Type II PI4Ks lack the ...
CDD:270628	346	EUK	Invertebrates:28,Plants:18,Vertebrates:2	cd00896, PI3Kc_III, Catalytic domain of Class III Phosphoinositide 3-kinase.  PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. Class III PI3Ks, also called Vps34 (vacuolar protein sorting 34), contain an N-terminal lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic ...
CDD:132998	300	EUKprk	Bacteria:2,Invertebrates:6,Plants:7,Rodents:1,Vertebrates:3	cd00897, UGPase_euk, Eukaryotic UGPase catalyses the synthesis of UDP-Glucose.  UGPase (UDP-Glucose Pyrophosphorylase) catalyzes the reversible production of UDP-Glucose and pyrophosphate (PPi) from Glucose-1-phosphate and UTP.  UDP-glucose plays pivotal roles in galactose utilization, in glycogen synthesis, and in the synthesis of the carbohydrate moieties of glycolipids, glycoproteins, and proteoglycans. UGPase ...
CDD:132999	219	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd00899, b4GalT, Beta-4-Galactosyltransferase is involved in the formation of the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids.  Beta-4-Galactosyltransferase transfers galactose from uridine diphosphogalactose to the terminal beta-N-acetylglucosamine residues, hereby forming the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. At least seven homologous ...
CDD:269910	89	EUKprk	Bacteria:1,Invertebrates:1,Plants:2,Primates:1,Rodents:1	cd00900, PH-like, Pleckstrin homology-like domain.  The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with ...
CDD:153099	153	EUKprk	Bacteria:62,Plants:1	cd00907, Bacterioferritin, Bacterioferritin, ferritin-like diiron-binding domain.  Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The ...
CDD:238454	127	EUK	Invertebrates:1,Mammals:1,Plants:3,Primates:1	cd00912, ML, The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an ...
CDD:238455	76	miss	miss	cd00913, PCD_DCoH_subfamily_a, PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH  (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme.  DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH).  DCoH also catalyzes the dehydration of ...
CDD:238456	76	miss	miss	cd00914, PCD_DCoH_subfamily_b, PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH  (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme.  DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH).  DCoH also catalyzes the dehydration of ...
CDD:238458	123	EUK	Invertebrates:6,Vertebrates:2	cd00916, Npc2_like, Niemann-Pick type C2 (Npc2) is a lysosomal protein in which a mutation in the gene causes a rare form of Niemann-Pick type C disease, an autosomal recessive lipid storage disorder characterized by accumulation of low-density lipoprotein-derived cholesterol in lysosomes. Although Npc2 is known to bind cholesterol, the function of this protein is unknown. These proteins belong to the ML domain family. .
CDD:238459	122	EUK	Plants:14	cd00917, PG-PI_TP, The phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP) has been shown to bind phosphatidylglycerol and phosphatidylinositol, but the biological significance of this is still obscure. These proteins belong to the ML domain family.
CDD:238461	463	EUKprk	Bacteria:81,Invertebrates:47,Mammals:1,Plants:23,Primates:1,Vertebrates:4,nodiv:2	cd00919, Heme_Cu_Oxidase_I, Heme-copper oxidase subunit I.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane.  The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from ...
CDD:259860	110	EUKprk	Bacteria:17,Mammals:1,Plants:5,Primates:1,Rodents:1	cd00920, Cupredoxin, Cupredoxin superfamily.  Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins, having an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key ...
CDD:238462	136	EUK	Invertebrates:11,Mammals:1,Plants:9,Primates:1,Vertebrates:4	cd00922, Cyt_c_Oxidase_IV, Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three ...
CDD:238463	103	EUK	Invertebrates:8,Mammals:1,Plants:4,Primates:1,Vertebrates:3	cd00923, Cyt_c_Oxidase_Va, Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to ...
CDD:238464	97	EUK	Invertebrates:9,Mammals:1,Plants:8,Primates:1,Vertebrates:3	cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three ...
CDD:238465	86	EUK	Invertebrates:2,Mammals:1,Plants:5,Primates:1,Vertebrates:3	cd00925, Cyt_c_Oxidase_VIa, Cytochrome c oxidase subunit VIa.   Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from ...
CDD:238466	75	EUK	Invertebrates:8,Mammals:1,Plants:11,Primates:1,Vertebrates:2	cd00926, Cyt_c_Oxidase_VIb, Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three ...
CDD:238467	70	EUK	Invertebrates:5,Mammals:1,Primates:1,Vertebrates:3	cd00927, Cyt_c_Oxidase_VIc, Cytochrome c oxidase subunit VIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in ...
CDD:238468	55	EUK	Invertebrates:6,Mammals:1,Primates:1,Vertebrates:5	cd00928, Cyt_c_Oxidase_VIIa, Cytochrome c oxidase subunit VIIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five ...
CDD:238469	46	EUK	Invertebrates:7,Mammals:1,Plants:4,Primates:1,Vertebrates:3	cd00929, Cyt_c_Oxidase_VIIc, Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three ...
CDD:269911	120	EUK	Invertebrates:23,Primates:1,Rodents:2,Vertebrates:6	cd00934, PTB, Phosphotyrosine-binding (PTB) PH-like fold.  PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to bind peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to ...
CDD:238473	50	miss	miss	cd00936, WEPRS_RNA, WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain  ...
CDD:188634	201	EUKprk	Bacteria:52,Environmental:1,Invertebrates:3,Plants:4,Primates:1,Vertebrates:3,nodiv:2	cd00945, Aldolase_Class_I, Class I aldolases.  Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase ...
CDD:238477	276	EUKprk	Bacteria:34,Invertebrates:2,Plants:4	cd00947, TBP_aldolase_IIB, Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as ...
CDD:188635	330	EUKprk	Bacteria:5,Invertebrates:9,Mammals:1,Plants:8,Vertebrates:3	cd00948, FBP_aldolase_I_a, Fructose-1,6-bisphosphate aldolase.  Fructose-1,6-bisphosphate aldolase. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). This family includes proteins found in vertebrates, plants, and bacterial plant pathogens. Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose ...
CDD:188637	284	PRK	Bacteria:1	cd00950, DHDPS, Dihydrodipicolinate synthase (DHDPS).  Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several ...
CDD:188638	289	miss	miss	cd00951, KDGDH, 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH).  5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of ...
CDD:188641	288	miss	miss	cd00954, NAL, N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL).  N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as ...
CDD:188642	338	EUKprk	Bacteria:5,Plants:1	cd00955, Transaldolase_like, Transaldolase-like proteins from plants and bacteria.  Transaldolase-like proteins from plants and bacteria. Transaldolase is found in the non-oxidative branch of the pentose phosphate pathway, that catalyze the reversible transfer of a dihydroxyacetone group from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. They are members of the class I aldolases, who are ...
CDD:188643	211	PRK	Bacteria:23,Phages:1	cd00956, Transaldolase_FSA, Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea.  Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-phosphate, fructose 1,6-phosphate, or dihydroxyacetone phosphate. The enzymes belong to the ...
CDD:188644	313	EUKprk	Bacteria:7,Invertebrates:2,Plants:4,Vertebrates:1,nodiv:1	cd00957, Transaldolase_TalAB, Transaldolases including both TalA and TalB.  Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The catalytic mechanism is similar to other class I aldolases. The enzyme is found in the ...
CDD:188645	235	miss	miss	cd00958, DhnA, Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs).  Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly divergent based on sequence similarity to other class I and class II  (metal dependent) aldolase subfamilies.
CDD:188646	203	EUK	Invertebrates:1	cd00959, DeoC, 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family.  2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes, and its broad substrate specificity confers considerable utility as a biocatalyst, ...
CDD:238478	34	PRK	Bacteria:7	cd00974, DSRD, Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in ...
CDD:238479	221	PRK	Bacteria:10,Viruses:1	cd00978, chitosanase_glyco_hydro_46, Glycosyl hydrolase family 46 chitosanase domain. This family are composed of the chitosanase enzymes which hydrolyzes chitosan, a biopolymer of beta (1,4)-linked -D-glucosamine (GlcN) residues produced by partial or full deacetylation of chitin. Chitosanases play a role in defense against pathogens such as fungi and are found in microorganisms, fungi, viruses, and plants. Microbial chitosanases who members are the most ...
CDD:238480	203	miss	miss	cd00980, FwdC/FmdC, FwdC/FmdC. This domain of unknown function is found in the subunit C of formylmethanofuran dehydrogenase, an enzyme that catalyzes the first step in methane formation from CO2 in methanogenic archaea, hyperthermophiles and bacteria. There are two isoenzymes, a tungsten-containing isoenzyme (Fwd) and a molybdenum-containing isoenzyme (Fmd). The subunits C of both isoenzymes (FwdC/FmdC) are characterized by a repeated GXXGXXXG motif.
CDD:238481	232	miss	miss	cd00981, arch_gltB, Archaeal-type gltB domain. This domain shares sequence similarity with a region of unknown function found in the large subunit of glutamate synthase, which is encoded by gltB and found in most bacteria and eukaryotes.  It is predicted to be homologous to the C-terminal domain of glutamate synthase based upon sequence similarity coupled with genome organization data, showing that this domain is found in a gene cluster with other domains of Glts, which ...
CDD:238482	251	miss	miss	cd00982, gltB_C, gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS).  GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear ...
CDD:238483	325	EUKprk	Bacteria:11,Invertebrates:1,Plants:2	cd00983, recA, RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange.
CDD:238484	242	EUKprk	Bacteria:13,Phages:7,Plants:3	cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the  chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal ...
CDD:238485	131	EUK	Plants:1	cd00985, Maf_Ham1, Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides, such as hypoxanthine/xanthine NTP, but not standard nucleotides.
CDD:238487	90	EUKprk	Bacteria:65,Invertebrates:3,Plants:5,Primates:1,Rodents:1,Synthetic:1	cd00987, PDZ_serine_protease, PDZ domain of trypsin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this ...
CDD:238488	85	EUKprk	Bacteria:24,Plants:2	cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
CDD:238489	79	EUKprk	Bacteria:47,Plants:2	cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of ...
CDD:238491	79	PRK	Bacteria:2	cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a ...
CDD:238492	82	EUK	Invertebrates:7,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove ...
CDD:270215	225	PRK	Bacteria:14	cd00993, PBP2_ModA_like, Substrate binding domain of molybdate-binding proteins, the type 2 periplasmic binding protein fold.  Molybdate binding domain ModA. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial receptors in the ABC transport of molybdate mostly in eubacteria and ...
CDD:270216	218	EUKprk	Bacteria:21,Plants:1	cd00994, PBP2_GlnH, Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold.  This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a ...
CDD:173853	466	EUKprk	Bacteria:203,Vertebrates:1,nodiv:1	cd00995, PBP2_NikA_DppA_OppA_like, The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ...
CDD:270217	227	PRK	Bacteria:37	cd00996, PBP2_AatB_like, Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily.  This subfamily includes periplasmic binding domain of ATP-binding cassette transporter-like systems that serve as initial receptors in the ABC transport of amino acids and their derivatives in eubacteria.  After binding their ligand with high affinity, they interact with a cognate ...
CDD:270218	218	PRK	Bacteria:14	cd00997, PBP2_GluR0, Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold.  Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain.  ...
CDD:270219	243	EUK	Invertebrates:3,Plants:2,Rodents:1	cd00998, PBP2_iGluR_ligand_binding, The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily.  This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities:  AMPA ...
CDD:270220	223	PRK	Bacteria:9	cd00999, PBP2_ArtJ, The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold protein superfamily.  An arginine-binding protein found in Chlamydiae trachomatis (CT-ArtJ) and pneumoniae (CPn-ArtJ) and its closely related proteins. CT- and CPn-ArtJ are shown to have different immunogenic properties despite a high sequence similarity. The ArtJ proteins display the type 2 periplasmic binding fold organized in two alpha-beta domains with ...
CDD:270221	228	PRK	Bacteria:7	cd01000, PBP2_Cys_DEBP_like, Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold.  This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins.  The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose ...
CDD:270222	228	PRK	Bacteria:12	cd01001, PBP2_HisJ_LAO_like, Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and related proteins; the type 2 periplasmic-binding protein fold.  This family comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 ...
CDD:270223	242	PRK	Bacteria:21	cd01002, PBP2_Ehub_like, Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 periplasmic binding protein fold.  This family represents the periplasmic substrate-binding component of ABC transport systems that involved in uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained ...
CDD:270225	230	PRK	Bacteria:28,nodiv:1	cd01004, PBP2_MidA_like, Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold.  This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and ...
CDD:270226	307	EUKprk	Bacteria:11,Plants:2	cd01005, PBP2_CysP, Substrate binding domain of an active sulfate transporter, a member of the type 2 periplasmic binding fold superfamily.  This family contains sulfate binding domain of CysP proteins that serve as initial receptors in the ABC transport of sulfate and thiosulfate in eubacteria. After binding the ligand, CysP interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ...
CDD:270228	220	PRK	Bacteria:149,Environmental:1	cd01007, PBP2_BvgS_HisK_like, The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins.  This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane ...
CDD:270229	212	PRK	Bacteria:28	cd01008, PBP2_NrtA_SsuA_CpmA_like, Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily.  This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range ...
CDD:270230	223	PRK	Bacteria:54	cd01009, PBP2_YfhD_N, The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily.  This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory ...
CDD:238493	196	miss	miss	cd01011, nicotinamidase, Nicotinamidase/pyrazinamidase (PZase).  Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA).
CDD:238494	157	PRK	Bacteria:1	cd01012, YcaC_related, YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.
CDD:238495	203	miss	miss	cd01013, isochorismatase, Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems. Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria.
CDD:238496	155	miss	miss	cd01014, nicotinamidase_related, Nicotinamidase_ related amidohydrolases.  Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
CDD:238498	276	miss	miss	cd01016, TroA, Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species.  The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these ...
CDD:238499	282	miss	miss	cd01017, AdcA, Metal binding protein AcdA.  These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion.  The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains.  ...
CDD:238500	266	miss	miss	cd01018, ZntC, Metal binding protein ZntC.  These proteins are predicted to function as initial receptors in ABC transport of metal ions.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains.  In addition, many of these proteins possess a ...
CDD:238501	286	PRK	Bacteria:11	cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism.  They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains.  A typical TroA protein is comprised of two globular ...
CDD:238502	264	miss	miss	cd01020, TroA_b, Metal binding protein TroA_b.  These proteins are predicted to function as initial receptors in ABC transport of metal ions.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes ...
CDD:238503	166	EUK	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:7	cd01021, GEWL, Goose Egg White Lysozyme domain. Eukaryotic "goose-type" lysozymes (GEWL). These enzymes catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc).  Members include tunicate, Japanese flounder, ostrich, and mouse.
CDD:212096	313	PRK	Bacteria:9	cd01022, GH57N_like, N-terminal catalytic domain of heat stable retaining glycoside hydrolase family 57.  Glycoside hydrolase family 57(GH57) is a chiefly prokaryotic family with the majority of thermostable enzymes coming from extremophiles (many of these are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC ...
CDD:173775	112	miss	miss	cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR.  RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two ...
CDD:173776	97	miss	miss	cd01026, TOPRIM_OLD, TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family.  The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. ...
CDD:173777	81	miss	miss	cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea.  RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved ...
CDD:173778	142	miss	miss	cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA).  This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. ...
CDD:173779	79	miss	miss	cd01029, TOPRIM_primases, TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one ...
CDD:173780	115	miss	miss	cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved ...
CDD:238504	402	PRK	Bacteria:28	cd01031, EriC, ClC chloride channel EriC.  This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked proton utilization. As shown for Escherichia coli EriC, these channels can counterbalance the electric current produced by the outwardly directed virtual proton pump linked to amino acid ...
CDD:238505	388	PRK	Bacteria:11	cd01033, ClC_like, Putative ClC chloride channel.  Clc proteins are putative halogen ion (Cl-, Br- and I-) transporters found in eubacteria. They belong to the ClC superfamily of halogen ion channels, which share a unique double-barreled architecture and voltage-dependent gating mechanism.  This superfamily lacks any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  The voltage-dependent ...
CDD:238506	390	PRK	Bacteria:18	cd01034, EriC_like, ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a unique double-barreled architecture and voltage-dependent gating mechanism.  This superfamily lacks any structural or sequence similarity to other known ion channels and exhibit unique properties ...
CDD:238507	416	EUK	Invertebrates:3	cd01036, ClC_euk, Chloride channel, ClC.  These domains are found in the eukaryotic halogen ion (Cl-, Br- and I-) channel proteins that perform a variety of functions including cell volume regulation, membrane potential stabilization, charge compensation necessary for the acidification of intracellular organelles, signal transduction and transepithelial transport.  They are also involved in many pathophysiological processes and are responsible for a number of ...
CDD:238508	80	PRK	Bacteria:26,Phages:6,nodiv:2	cd01037, Restriction_endonuclease_like, Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
CDD:238509	108	miss	miss	cd01038, Endonuclease_DUF559, Domain of unknown function, appears to be related to a diverse group of endonucleases.
CDD:271266	132	EUKprk	Bacteria:89,Environmental:1,Invertebrates:98,Plants:33,Primates:1,Rodents:1,Vertebrates:11	cd01040, Mb_like, myoglobin_like; M family globin domain.  This family includes chimeric (FHbs/flavohemoglobins) and single-domain globins: FHbs, Ngbs/neuroglobins, Cygb/cytoglobins, GbE/avian eye specific globin E, GbX/globin X, amphibian GbY/globin Y, Mb/myoglobin, HbA/hemoglobin-alpha, HbB/hemoglobin-beta, SDgbs/single-domain globins related to FHbs, and Adgb/androglobin. The M ...
CDD:153100	134	EUKprk	Bacteria:80,Invertebrates:2,Plants:1	cd01041, Rubrerythrin, Rubrerythrin, ferritin-like diiron-binding domain.  Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a ...
CDD:153101	165	EUKprk	Bacteria:43,Environmental:2,Invertebrates:10,Plants:4,Vertebrates:3,nodiv:1	cd01042, DMQH, Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain.  Demethoxyubiquinone hydroxylases (DMQH) are members of the ferritin-like, diiron-carboxylate family which are present in eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the Coq7 family). DMQH participates in one of the last steps of ubiquinone biosysnthesis and is responsible for DMQ hydroxylation, resulting in ...
CDD:153102	139	EUKprk	Bacteria:151,Environmental:1,Plants:2	cd01043, DPS, DPS protein, ferritin-like diiron-binding domain.  DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into ...
CDD:153103	125	PRK	Bacteria:61	cd01044, Ferritin_CCC1_N, Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain.  Ferritin-like N-terminal domain present in an uncharacterized family of proteins found in bacteria and archaea.  These proteins also have a C-terminal CCC1-like transmembrane domain and are thought to be involved in iron and/or manganese transport.  This domain has the conserved residues of a diiron center found in other ferritin-like proteins.
CDD:153104	139	PRK	Bacteria:92,Environmental:2	cd01045, Ferritin_like_AB, Uncharacterized family of ferritin-like proteins found in archaea and bacteria.  Ferritin-like domain found in archaea and bacteria (Ferritin_like_AB).  This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown.  This family includes unknown or hypothetical proteins which were sequenced from mostly anaerobic or microaerophilic metal-metabolizing ...
CDD:153105	123	PRK	Bacteria:9,Environmental:1	cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding domain.  Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center ...
CDD:153106	323	EUKprk	Bacteria:4,Environmental:1,Plants:7	cd01047, ACSF, Aerobic Cyclase System Fe-containing subunit (ACSF), ferritin-like diiron-binding domain.  Aerobic Cyclase System, Fe-containing subunit (ACSF) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrivivax gelatinosus acsF codes for a conserved, putative binuclear iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethyl ester. AcsF and ...
CDD:153107	135	PRK	Bacteria:35	cd01048, Ferritin_like_AB2, Uncharacterized family of ferritin-like proteins found in archaea and bacteria.  Ferritin-like domain found in archaea and bacteria, subgroup 2 (Ferritin_like_AB2).  This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron center are present within the putative active site.
CDD:153108	288	EUKprk	Bacteria:47,Environmental:1,Invertebrates:23,Phages:4,Plants:8,Primates:1,Vertebrates:4,Viruses:16,nodiv:1	cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain.  Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several ...
CDD:153109	297	EUKprk	Bacteria:17,Plants:9	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain.  Acyl-Acyl Carrier Protein Desaturase (Acyl_ACP_Desat) is a mu-oxo-bridged diiron-carboxylate enzyme, which belongs to a broad superfamily of ferritin-like proteins and catalyzes the NADPH and O2-dependent formation of a cis-double bond in acyl-ACPs.  Acyl-ACP desaturases are found in higher plants and a few bacterial species (Mycobacterium tuberculosis, M. leprae, M. ...
CDD:153110	156	EUKprk	Bacteria:26,Plants:1	cd01051, Mn_catalase, Manganese catalase, ferritin-like diiron-binding domain.  Manganese (Mn) catalase is a member of a broad superfamily of ferritin-like diiron enzymes. While many diiron enzymes catalyze dioxygen-dependent reactions, manganese catalase performs peroxide-dependent oxidation-reduction. Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Manganese ...
CDD:153111	148	PRK	Bacteria:16,Environmental:1	cd01052, DPSL, DPS-like protein, ferritin-like diiron-binding domain.  DPSL (DPS-like).  DPSL is a phylogenetically distinct class within the ferritin-like superfamily, and similar in many ways to the DPS (DNA Protecting protein under Starved conditions) proteins. Like DPS, these proteins are expressed in response to oxidative stress, form dodecameric cage-like particles, preferentially utilize hydrogen peroxide in the controlled oxidation of iron, ...
CDD:153112	168	EUKprk	Bacteria:4,Invertebrates:5,Plants:14	cd01053, AOX, Alternative oxidase, ferritin-like diiron-binding domain.  Alternative oxidase (AOX) is a mitochondrial ubiquinol oxidase found in plants and some fungi and protists. AOX is a member of the ferritin-like diiron-carboxylate superfamily. The plant mitochondrial protein alternative oxidase catalyses dioxygen dependent ubiquinol oxidation to yield ubiquinone and water. AOX is a cyanide-resistant, salicylhydroxamic ...
CDD:153113	156	EUKprk	Bacteria:129,Environmental:1,Invertebrates:2,Plants:1	cd01055, Nonheme_Ferritin, nonheme-containing ferritins.  Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this ...
CDD:153114	161	EUK	Invertebrates:41,Mammals:4,Plants:7,Primates:1,Rodents:2,Vertebrates:5,nodiv:1	cd01056, Euk_Ferritin, eukaryotic ferritins.  Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of ...
CDD:153115	465	PRK	Bacteria:23	cd01057, AAMH_A, Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain.  Aromatic and Alkene Monooxygenase Hydroxylases, subunit A  (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded ...
CDD:153116	304	EUKprk	Bacteria:32,Environmental:1,Invertebrates:1	cd01058, AAMH_B, Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain.  Aromatic and Alkene Monooxygenase Hydroxylases, subunit B (AAMH_B). Subunit B (beta) of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit ...
CDD:153121	143	EUKprk	Bacteria:34,Invertebrates:5,Plants:11	cd01059, CCC1_like, CCC1-related family of proteins.  CCC1_like: This protein family includes the proteins related to CCC1, a yeast vacuole transmembrane protein responsible for the iron and manganese transport from the cytosol into vacuole. It also includes the proteins similar to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. .
CDD:238511	122	EUKprk	Bacteria:125,Environmental:1,Invertebrates:15,Plants:42,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd01060, Membrane-FADS-like, The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved ...
CDD:238512	195	miss	miss	cd01061, RNase_T2_euk, Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as ...
CDD:238513	184	miss	miss	cd01062, RNase_T2_prok, Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as ...
CDD:133443	155	EUKprk	Bacteria:34,Plants:4	cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate dehydrogenase.  Shikimate dehydrogenase (DH) is an amino acid DH family member. Shikimate pathway links metabolism of carbohydrates to de novo biosynthesis of aromatic amino acids, quinones and folate. It is essential in plants, bacteria, and fungi but absent in mammals, thus making enzymes involved in this pathway ideal targets for broad spectrum antibiotics and herbicides. Shikimate DH ...
CDD:238514	207	EUKprk	Bacteria:46,Invertebrates:2,Plants:3,Primates:1,Rodents:1,nodiv:1	cd01066, APP_MetAP, A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation.
CDD:271267	125	EUKprk	Bacteria:26,Plants:2	cd01067, Globin_like, Globin-like proteins.  This globin-like domain superfamily contains a wide variety of all-helical proteins that bind porphyrins, phycobilins, and other non-heme cofactors, and play various roles in all three kingdoms of life, including sensors or transporters of oxygen. It includes the M/myoglobin-like, S/sensor globin, and T/truncated globin (TrHb) families, and the phycobiliproteins (PBPs). The M family includes chimeric ...
CDD:271268	148	PRK	Bacteria:175,Environmental:2,nodiv:2	cd01068, globin_sensor, Globin sensor domain of globin-coupled-sensors (GCSs), protoglobins (Pgbs), and sensor single-domain globins (SSDgbs); S family.  This family includes sensor domains which binds porphyrins, and other non-heme cofactors. GCSs have an N-terminal sensor domain coupled to a functional domain. For heme-bound oxygen sensing/binding globin domains, O2 binds to/dissociates from the heme iron complex inducing a structural ...
CDD:270231	232	EUKprk	Bacteria:11,Plants:1	cd01069, PBP2_PheC, Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily.  This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea.  The PheC proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand ...
CDD:270232	253	PRK	Bacteria:39	cd01071, PBP2_PhnD_like, Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily.  This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake ...
CDD:270233	238	PRK	Bacteria:12,nodiv:1	cd01072, PBP2_SMa0082_like, The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic binding protein fold.  This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Sinorhizobium meliloti and its related proteins. The putative SMa0082-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake ...
CDD:133444	200	PRK	Bacteria:23	cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase.  Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino ...
CDD:133445	227	EUKprk	Bacteria:28,Invertebrates:7,Plants:4,Primates:1,Vertebrates:3	cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate dehydrogenase, subgroup 1.  Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of ...
CDD:133446	194	PRK	Bacteria:8	cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene tetrahydromethanopterin dehydrogenase.  Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous ...
CDD:133448	168	EUKprk	Bacteria:20,Invertebrates:9,Mammals:1,Plants:4,Primates:1,Vertebrates:2	cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.  NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme.   Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and ...
CDD:185695	284	EUKprk	Bacteria:45,Plants:1,Primates:1	cd01081, Aldose_epim, aldose 1-epimerase superfamily.  Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, ...
CDD:238517	693	PRK	Bacteria:24	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family. This family consists of a group of secreted bacterial lyase enzymes capable of acting on glycosaminoglycans, such as hyaluronan and chondroitin, in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. These are broad-specificity glycosaminoglycan lyases which recognize uronyl residues in polysaccharides and cleave their glycosidic bonds via a ...
CDD:238518	224	EUKprk	Bacteria:13,Invertebrates:5,Plants:4,Primates:1,Vertebrates:1	cd01085, APP, X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide.
CDD:238519	238	EUKprk	Bacteria:24,Invertebrates:4,Plants:2,Primates:1,Vertebrates:1	cd01086, MetAP1, Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
CDD:238520	243	EUKprk	Bacteria:18,Environmental:1,Invertebrates:4,Plants:4,Primates:1,Vertebrates:2	cd01087, Prolidase, Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro-Pro.
CDD:238521	291	EUKprk	Bacteria:4,Invertebrates:5,Plants:3,Vertebrates:2	cd01088, MetAP2, Methionine Aminopeptidase 2. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
CDD:238522	228	EUK	Invertebrates:4,Plants:3,Primates:1,Vertebrates:2	cd01089, PA2G4-like, Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control.
CDD:238524	243	EUK	Invertebrates:4,Plants:5,Primates:1,Vertebrates:1	cd01091, CDC68-like, Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor.
CDD:238525	208	PRK	Bacteria:29	cd01092, APP-like, Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline.
CDD:238526	46	EUK	Invertebrates:5,Plants:4,Primates:1,Vertebrates:2	cd01093, CRIB_PAK_like, PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
CDD:238527	244	miss	miss	cd01094, Alkanesulfonate_monoxygenase, Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin mononucleotide (FMNH2), which is provided by the NADPH-dependent FMN oxidoreductase (SsuE).
CDD:238528	358	miss	miss	cd01095, Nitrilotriacetate_monoxgenase, nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2.
CDD:238530	202	miss	miss	cd01097, Tetrahydromethanopterin_reductase, N5,N10-methylenetetrahydromethanopterin reductase (Mer) catalyzes the reduction of N5,N10-methylenetetrahydromethanopterin with reduced coenzyme F420 to N5-methyltetrahydromethanopterin and oxidized coenzyme F420.
CDD:238531	84	EUK	Plants:9	cd01098, PAN_AP_plant, Plant PAN/APPLE-like domain; present in plant S-receptor protein kinases and secreted glycoproteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions. S-receptor protein kinases and S-locus glycoproteins are involved in sporophytic self-incompatibility response in Brassica, one of probably many molecular mechanisms, by which hermaphrodite flowering plants avoid self-fertilization.
CDD:238532	80	EUK	Invertebrates:4,Mammals:1,Primates:1,Vertebrates:3	cd01099, PAN_AP_HGF, Subfamily of PAN/APPLE-like domains; present in N-terminal (N) domains of plasminogen/hepatocyte growth factor proteins, and various proteins found in Bilateria, such as leech anti-platelet proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions.
CDD:238533	73	EUKprk	Bacteria:3,Invertebrates:3,Plants:1,Primates:1,Rodents:1,nodiv:1	cd01100, APPLE_Factor_XI_like, Subfamily of PAN/APPLE-like domains; present in plasma prekallikrein/coagulation factor XI, microneme antigen proteins, and a few prokaryotic proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions.
CDD:238534	92	EUK	Invertebrates:1,Primates:1	cd01102, Link_Domain, The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female ...
CDD:133379	68	PRK	Bacteria:22,nodiv:1	cd01104, HTH_MlrA-CarA, Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA.  Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium.  Its close homolog, CarA from Myxococcus ...
CDD:133380	88	PRK	Bacteria:23	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators.  Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR ...
CDD:133381	103	PRK	Bacteria:51	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA.  Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, ...
CDD:133382	108	PRK	Bacteria:37	cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator.  Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) ...
CDD:133383	127	PRK	Bacteria:25	cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators.  Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These ...
CDD:133384	113	PRK	Bacteria:62	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB.  Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators ...
CDD:133385	139	PRK	Bacteria:28,nodiv:1	cd01110, HTH_SoxR, Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator.  Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, ...
CDD:238535	382	miss	miss	cd01115, SLC13_permease, Permease SLC13 (solute carrier 13).  The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is related to renal and intestinal Na+/sulfate cotransporters and a few putative bacterial permeases. The SLC13-type proteins belong to the ArsB/NhaD superfamily of permeases that translocate sodium ...
CDD:238536	413	miss	miss	cd01116, P_permease, Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the intraorganelle pH, together with the ATP-driven proton pump. It shows significant sequence similarity to the Na+/H+ antiporter NhaD from Vibrio parahaemolyticus. Both proteins belong to ArsB/NhaD ...
CDD:238537	384	miss	miss	cd01117, YbiR_permease, Putative anion permease YbiR.  Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to translocate sodium, sulfate, arsenite and organic anions. A typical ArsB/NhaD permease is composed of 8-13 transmembrane domains.
CDD:238538	416	miss	miss	cd01118, ArsB_permease, Anion permease ArsB.  These permeases have been shown to export arsenate and antimonite in eubacteria and archaea.  A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump (ArsAB).  The ArsAB complex is similar in many ways to ATP-binding cassette transporters, which have two groups of six transmembrane-spanning ...
CDD:238540	165	EUKprk	Bacteria:2,Mammals:1,Phages:1,Plants:1,Primates:1	cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
CDD:238541	372	EUKprk	Bacteria:4,Plants:1	cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
CDD:238542	271	EUKprk	Invertebrates:2,Phages:3,Primates:1	cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
CDD:238543	235	EUKprk	Bacteria:2,Invertebrates:6,Plants:9,Primates:1,Rodents:1,Vertebrates:3	cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this ...
CDD:238544	187	PRK	Bacteria:1	cd01124, KaiC, KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
CDD:238545	239	PRK	Bacteria:10	cd01125, repA, Hexameric Replicative Helicase RepA.  RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
CDD:238546	384	miss	miss	cd01126, TraG_VirD4, The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.
CDD:238547	410	PRK	Bacteria:6	cd01127, TrwB, Bacterial conjugation protein TrwB,  ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.
CDD:238549	264	PRK	Bacteria:2	cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP).  It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
CDD:238550	186	PRK	Bacteria:2	cd01130, VirB11-like_ATPase, Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during ...
CDD:238551	198	EUKprk	Bacteria:3,Invertebrates:1	cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
CDD:238552	274	EUKprk	Bacteria:7,Invertebrates:8,Plants:10,Vertebrates:2	cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta ...
CDD:238553	274	EUKprk	Bacteria:10,Invertebrates:9,Mammals:1,Plants:11,Rodents:1,Vertebrates:2	cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1,  is ...
CDD:238554	369	EUKprk	Bacteria:7,Invertebrates:9,Plants:3,Primates:1,Vertebrates:3	cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction.  The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an ...
CDD:238555	276	EUKprk	Bacteria:7,Invertebrates:9,Plants:4,Primates:1,Vertebrates:3	cd01135, V_A-ATPase_B, V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like ...
CDD:238556	326	EUKprk	Bacteria:6,Invertebrates:1	cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell ...
CDD:238557	287	miss	miss	cd01137, PsaA, Metal binding protein PsaA.  These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In ...
CDD:238558	248	miss	miss	cd01138, FeuA, Periplasmic binding protein FeuA.  These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238559	342	miss	miss	cd01139, TroA_f, Periplasmic binding protein TroA_f.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238560	270	miss	miss	cd01140, FatB, Siderophore binding protein FatB.  These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238561	186	miss	miss	cd01141, TroA_d, Periplasmic binding protein TroA_d.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238562	289	miss	miss	cd01142, TroA_e, Periplasmic binding protein TroA_e.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238563	195	miss	miss	cd01143, YvrC, Periplasmic binding protein YvrC.  These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
CDD:238564	245	miss	miss	cd01144, BtuF, Cobalamin binding protein BtuF.  These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between ...
CDD:238565	203	miss	miss	cd01145, TroA_c, Periplasmic binding protein TroA_c.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
CDD:238566	256	miss	miss	cd01146, FhuD, Fe3+-siderophore binding domain FhuD.  These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA-like protein is comprised of two globular subdomains connected by a long alpha helix and binds its specific ligands in the cleft ...
CDD:238567	262	miss	miss	cd01147, HemV-2, Metal binding protein HemV-2.  These proteins are predicted to function as initial receptors in ABC transport of metal ions.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes ...
CDD:238568	284	miss	miss	cd01148, TroA_a, Metal binding protein TroA_a.  These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
CDD:238569	235	miss	miss	cd01149, HutB, Hemin binding protein HutB.  These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
CDD:173839	610	EUKprk	Bacteria:1,Invertebrates:2,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd01150, AXO, Peroxisomal acyl-CoA oxidase.  Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a ...
CDD:173841	380	PRK	Bacteria:8	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26.  Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial ...
CDD:173842	407	PRK	Bacteria:4	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5.  Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled ...
CDD:173843	418	EUKprk	Bacteria:3,Invertebrates:1	cd01154, AidB, Proteins involved in DNA damage response, similar to the AidB gene product.  AidB is one of several genes involved in the SOS adaptive response to DNA alkylation damage, whose expression is activated by the Ada protein. Its function has not been entirely elucidated; however, it is similar in sequence and function to acyl-CoA dehydrogenases. It has been proposed that aidB directly destroys DNA alkylating agents such as ...
CDD:173847	373	EUKprk	Bacteria:4,Invertebrates:2,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases.  Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by ...
CDD:173848	370	PRK	Bacteria:8	cd01159, NcnH, Naphthocyclinone hydroxylase.  Naphthocyclinone is an aromatic polyketide and an antibiotic, which is active against Gram-positive bacteria.  Polyketides are secondary metabolites, which have important biological functions such as antitumor, immunosupressive or antibiotic activities. NcnH is a hydroxylase involved in the biosynthesis of naphthocyclinone and possibly other polyketides.
CDD:173852	377	EUKprk	Bacteria:5,Plants:1	cd01163, DszC, Dibenzothiophene (DBT) desulfurization enzyme C.  DszC is a flavin reductase dependent enzyme, which catalyzes the first two steps of DBT desulfurization in mesophilic bacteria. DszC converts DBT to DBT-sulfoxide, which is then converted to DBT-sulfone. Bacteria with this enzyme are candidates for the removal of organic sulfur compounds from fossil fuels, which pollute the environment. An equivalent enzyme tdsC, is found in thermophilic ...
CDD:238570	289	PRK	Bacteria:42	cd01164, FruK_PfkB_like, 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose 6-phosphate pathway, which responsible for breakdown of the galactose moiety during lactose metabolism by bacteria such as L. lactis.
CDD:238571	294	PRK	Bacteria:52	cd01166, KdgK, 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources.
CDD:238572	295	EUKprk	Bacteria:32,Plants:5,nodiv:1	cd01167, bac_FRK, Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into glucose-6-phosphate. This is in contrast to FRKs [or ketohexokinases (KHKs)] from mammalia and halophilic archaebacteria, which phosphorylate fructose to fructose-1-phosphate.
CDD:238573	312	EUKprk	Bacteria:23,Environmental:2,Invertebrates:8,Plants:10,Vertebrates:3	cd01168, adenosine_kinase, Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular adenosine levels and the preservation of intracellular adenylate pools. Adenosine kinase is involved in the purine salvage pathway. .
CDD:238574	242	EUKprk	Bacteria:70,Invertebrates:3,Plants:10,nodiv:1	cd01169, HMPP_kinase, 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form ...
CDD:238575	242	EUKprk	Bacteria:28,Invertebrates:1,Plants:11,nodiv:1	cd01170, THZ_kinase, 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine and 1-deoxy-D-xylulose-5-phosphate.
CDD:238576	254	EUKprk	Bacteria:75,Environmental:4,Invertebrates:6,Plants:9,Primates:1,Vertebrates:2,nodiv:1	cd01171, YXKO-related, B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily.
CDD:238577	304	PRK	Bacteria:24	cd01172, RfaE_like, RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer membrane of gram-negative bacteria. RfaE consists of two domains, a sugar kinase domain, represented here, and a domain belonging to the cytidylyltransferase superfamily.
CDD:238578	254	EUKprk	Bacteria:19,Invertebrates:5,Plants:12,Vertebrates:1	cd01173, pyridoxal_pyridoxamine_kinase, Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate  (PLP), by catalyzing the phosphorylation of the precursor vitamin B6  in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and require its precursors in the form of vitamin B6 (pyridoxal, pyridoxine, and pyridoxamine) from their diet. Pyridoxal kinase encoding ...
CDD:238579	292	EUKprk	Bacteria:40,Invertebrates:4,Plants:13,Vertebrates:2,nodiv:1	cd01174, ribokinase, Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides and histidine, and for entry into the pentose phosphate pathway. Ribokinase is dimeric in solution.
CDD:238582	102	miss	miss	cd01177, IPT_NFkappaB, IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to certain chemicals. NFkappaB blocking cell apoptosis in several cell types, gives it an important role in cell proliferation and differentiation.
CDD:238584	85	miss	miss	cd01179, IPT_plexin_repeat2, Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
CDD:238585	94	miss	miss	cd01180, IPT_plexin_repeat1, First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
CDD:238586	99	miss	miss	cd01181, IPT_plexin_repeat3, Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
CDD:271183	186	PRK	Bacteria:16	cd01182, INT_RitC_C_like, C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio.  Recombinases RitA (also known as SG5), RitB, and RitC are encoded by three adjacent and overlapping genes. They are called recombinase trio. This RitC family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they ...
CDD:271184	180	PRK	Bacteria:50	cd01184, INT_C_like_1, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain.  Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a ...
CDD:271185	161	PRK	Bacteria:38	cd01185, INTN1_C_like, Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain.  IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the ...
CDD:271187	142	PRK	Bacteria:7	cd01187, INT_tnpB_C_Tn554, Putative Transposase B from transposon Tn554, C-terminal catalytic domain.  This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA ...
CDD:271188	179	PRK	Bacteria:19	cd01188, INT_RitA_C_like, C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio.  Recombinases RitA, RitB, and RitC (also known as pAE1) are encoded by three adjacent and overlapping genes. They are called recombinase trio. This family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are ...
CDD:271189	147	PRK	Bacteria:110,Phages:2	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons.  This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. ...
CDD:271190	150	PRK	Bacteria:9	cd01190, INT_StrepXerD_C_like, Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain.  This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The ...
CDD:271192	178	PRK	Bacteria:13	cd01192, INT_C_like_3, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain.  Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a ...
CDD:271193	176	PRK	Bacteria:16	cd01193, INT_IntI_C, Integron integrase and similar protiens, C-terminal catalytic domain.  Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the ...
CDD:271194	174	PRK	Bacteria:7	cd01194, INT_C_like_4, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain.  Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a ...
CDD:238605	42	miss	miss	cd01200, WHEPGMRS_RNA, EPRS-like_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in three copies in the mammalian bifunctional EPRS in a region that separates the N-terminal GluRS from the C-terminal ProRS. In the Drosophila EPRS, this domain is repeated six times. It is found at the N-terminus of TrpRS, HisRS and GlyR and at the C-terminus of MetRS. This domain consists of a helix- ...
CDD:269912	112	EUK	Invertebrates:29,Mammals:1,Plants:25,Primates:1,Rodents:1,Vertebrates:3	cd01201, PH_BEACH, Pleckstrin homology domain in BEACH domain containing proteins.  The BEACH domain is present in several eukaroyotic proteins CHS, neurobeachin (Nbea), LRBA (also called BGL, beige-like, or CDC4L), FAN, KIAA1607, and LvsA-LvsF. CHS is a rare, autosomal recessive disorder that can cause severe immunodeficiency and albinism in mammals and beige is the name for the CHS disease in mice. The ...
CDD:269913	92	EUK	Invertebrates:20,Mammals:1,Primates:1,Vertebrates:4	cd01202, PTB_FRS2, Fibroblast growth factor receptor substrate 2 phosphotyrosine-binding domain.  FRS2 (also called Suc1-associated neurotrophic factor (SNT)-induced tyrosine-phosphorylated target) proteins are membrane-anchored adaptor proteins. They are composed of an N-terminal myristoylation site followed by a phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a C-terminal effector domain containing ...
CDD:269914	99	EUK	Invertebrates:2,Mammals:6,Primates:1,Rodents:4,Vertebrates:7	cd01203, PTB_DOK1_DOK2_DOK3, Downstream of tyrosine kinase 1, 2, and 3 proteins phosphotyrosine-binding domain (PTBi).  The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology ...
CDD:269915	106	EUK	Invertebrates:16,Mammals:2,Primates:1,Rodents:1,Vertebrates:5	cd01204, PTB_IRS, Insulin receptor substrate phosphotyrosine-binding domain (PTBi).  Insulin receptor substrate (IRS) molecules are mediators in insulin signaling and play a role in maintaining basic cellular functions such as growth and metabolism. They act as docking proteins between the insulin receptor and a complex network of intracellular signaling molecules containing Src homology 2 (SH2) domains. Four ...
CDD:269916	101	EUK	Invertebrates:25,Plants:24,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd01205, EVH1_WASP-like, WASP family proteins EVH1 domain.  The Wiskott-Aldrich Syndrome Protein (WASP; also called Bee1p) and its homolog N (neuronal)-WASP are signal transduction proteins that promote actin polymerization in response to upstream intracellular signals. WAS is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or ...
CDD:269917	109	EUK	Invertebrates:13,Primates:1,Rodents:2,Vertebrates:3	cd01206, EVH1_Homer_Vesl, Homer/Vesl family proteins EVH1 domain.  Homer/Vesl proteins are synaptic scaffolding proteins, required for long-term potentiation, a form of synaptic plasticity thought to underlie memory formation. They contains an N-terminal EVH1 domain and bind to both neurotransmitter receptors, such as the metabotropic group 1 glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in ...
CDD:269918	108	EUK	Invertebrates:14,Primates:1,Rodents:1,Vertebrates:3	cd01207, EVH1_Ena_VASP-like, Enabled/VASP family EVH1 domain.  Ena/VASP family includes proteins such as: Vasodilator-stimulated phosphoprotein (VASP), enabled gene product from Drosophila (Ena), mammalian enabled (Mena) and Ena/VASP-Like protein (EVL) localize to focal adhesions and to sites of actin filament dynamics. These proteins share a common modular organization with a highly conserved N- and C-terminal domains, ...
CDD:269919	161	EUK	Invertebrates:13,Mammals:5,Primates:2,Rodents:3,Vertebrates:6	cd01208, PTB_X11, X11-like Phosphotyrosine-binding (PTB) domain.  The function of the neuronal protein X11 is unknown to date. X11 has a PTB domain followed by two PDZ domains. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more ...
CDD:269920	170	EUK	Invertebrates:17,Mammals:2,Primates:3,Rodents:4,Vertebrates:9	cd01209, PTB_Shc, Shc-like phosphotyrosine-binding (PTB) domain.  Shc is a substrate for receptor tyrosine kinases, which can interact with phosphoproteins at NPXY motifs. Shc contains an PTB domain followed by an SH2 domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements ...
CDD:269921	131	EUK	Invertebrates:16,Mammals:8,Primates:1,Rodents:3,Vertebrates:8	cd01210, PTB_EPS8, Epidermal growth factor receptor kinase substrate (EPS8)-like Phosphotyrosine-binding (PTB) domain.  EPS8 is a regulator of Rac signaling. It consists of a PTB and an SH3 domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the ...
CDD:269922	129	EUK	Invertebrates:18,Mammals:1,Primates:1,Vertebrates:6	cd01211, PTB_Rab6GAP, GTPase activating protein for Rab 6 Phosphotyrosine-binding (PTB) domain.  GAPCenA is a centrosome-associated GTPase activating protein (GAP) for Rab 6. It consists of an N-terminal PTB domain and a C-terminal TBC domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing ...
CDD:269923	149	EUK	Invertebrates:15,Mammals:1,Primates:1,Rodents:2,Vertebrates:5	cd01212, PTB_JIP, JNK-interacting protein-like (JIP) Phosphotyrosine-binding (PTB) domain.  JIP is a mitogen-activated protein kinase scaffold protein. JIP consists of a C-terminal SH3 domain, followed by a PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for ...
CDD:269924	136	EUK	Invertebrates:25,Mammals:3,Primates:3,Vertebrates:8	cd01213, PTB_tensin, Tensin Phosphotyrosine-binding (PTB) domain.  Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies ...
CDD:269925	125	EUK	Invertebrates:17,Mammals:1,Primates:1,Vertebrates:4	cd01214, PTB_FAM43A, Family with sequence similarity 43, member A (FAM43A) Phosphotyrosine-binding (PTB) domain.  The function of FAM43A is currently unknown. Human FAM43A is located on chromosome 3 at location 3q29. It encodes a 3182 base pair mRNA which possesses one Pleckstrin homology-like domain. The mRNA translates into LOC131583, a hydrophilic protein that is predicted to localize in the nucleus. The FAM43A gene is ...
CDD:269926	147	EUK	Invertebrates:13,Primates:1,Vertebrates:6	cd01215, PTB_Dab, Disabled (Dab) Phosphotyrosine-binding domain.  Dab is a cystosolic adaptor protein, which binds to the cytoplasmic tails of lipoprotein receptors, such as ApoER2 and VLDLR, via its PTB domain. The dab PTB domain has a preference for unphosphorylated tyrosine within an NPxY motif. Additionally, the Dab PTB domain, which is structurally similar to PH domains, binds to phosphatidlyinositol phosphate 4,5 bisphosphate in ...
CDD:269927	123	EUK	Invertebrates:13,Primates:1,Vertebrates:4	cd01218, PH_Phafin2-like, Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain.  Phafin2 is differentially expressed in the liver cancer cell and regulates the structure and function of the endosomes through Rab5-dependent processes. Phafin2 modulates the cell's response to extracellular stimulation by modulating the receptor density on the cell surface. Phafin2 contains a PH domain and a FYVE ...
CDD:269928	109	EUK	Invertebrates:11,Vertebrates:2	cd01220, PH1_FARP1-like, FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 1.  Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc finger FYVE domain-containing protein 24). They are members of the Dbl ...
CDD:269929	131	EUK	Invertebrates:16,Primates:1,Vertebrates:6	cd01221, PH_ephexin, Ephexin Pleckstrin homology (PH) domain.  Ephexin-1 (also called NGEF/ neuronal guanine nucleotide exchange factor) plays a role in the homeostatic modulation of presynaptic neurotransmitter release. Specific functions are still unknown for Ephexin-2 (also called RhoGEF19) and Ephexin-3 (also called Rho guanine nucleotide exchange factor 5/RhoGEF5, Transforming immortalized mammary oncogene/p60 TIM, and ...
CDD:269930	127	EUK	Invertebrates:11,Mammals:1,Primates:1,Vertebrates:4	cd01223, PH_Vav, Vav pleckstrin homology (PH) domain.  Vav acts as a guanosine nucleotide exchange factor (GEF) for Rho/Rac proteins. They control processes including T cell activation, phagocytosis, and migration of cells. The Vav subgroup of Dbl GEFs consists of three family members (Vav1, Vav2, and Vav3) in mammals. Vav1 is preferentially expressed in the hematopoietic system, while Vav2 and Vav3 are described by broader ...
CDD:269931	138	EUK	Invertebrates:15,Primates:1,Vertebrates:2	cd01224, PH_Collybistin_ASEF, Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain.  Collybistin (also called PEM2) is homologous to the Dbl proteins ASEF (also called ARHGEF4/RhoGEF4) and SPATA13 (Spermatogenesis-associated protein 13; also called ASEF2). It activates CDC42 specifically and not any other Rho-family GTPases. Collybistin consists of an SH3 domain, followed by a RhoGEF/DH and PH ...
CDD:269932	100	EUK	Invertebrates:6,Rodents:1,Vertebrates:4	cd01225, PH_Cool_Pix, Cloned out of library/PAK-interactive exchange factor pleckstrin homology (PH) domain.  There are two forms of Pix proteins: alpha Pix (also called Rho guanine nucleotide exchange factor (GEF) 6/90Cool-2) and beta Pix (GEF7/p85Cool-1). betaPix contains an N-terminal SH3 domain, a RhoGEF/DH domain, a PH domain, a GIT1 binding domain (GBD), and a C-terminal coiled-coil (CC) domain. alphaPix differs in that it contains ...
CDD:269933	115	EUK	Invertebrates:14,Plants:2,Rodents:1,Vertebrates:3	cd01226, PH_RalBD_exo84, Exocyst complex 84-kDa subunit Ral-binding domain/Pleckstrin Homology (PH) domain.  The Sec6/8 complex, also called the exocyst complex, forms an octameric protein (Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84) involved in the tethering of secretory vesicles to specific regions on the plasma membrane. The regulation of Sec6/8 complex differs between mammals and yeast. Mamalian Exo84 and Sec5 ...
CDD:269935	166	EUK	Invertebrates:8,Primates:1,Vertebrates:1	cd01228, PH_BCR-related, Breakpoint Cluster Region-related pleckstrin homology (PH) domain.  The BCR gene is one of the two genes in the BCR-ABL complex, which is associated with the Philadelphia chromosome, a product of a reciprocal translocation between chromosomes 22 and 9. BCR is a GTPase-activating protein (GAP) for RAC1 (primarily) and CDC42. The Dbl region of BCR has the most RhoGEF activity for Cdc42, and less activity towards ...
CDD:269936	180	EUK	Invertebrates:15,Primates:1,Vertebrates:3	cd01229, PH_Ect2, Epithelial cell transforming 2 (Ect2) pleckstrin homology (PH) domain.  Ect2, a mammalian ortholog of Drosophila pebble, plays a role in neuronal differentiation and brain development. Pebble and Ect2 have been identified as Rho-family guanine nucleotide exchange factors (GEF) that mediate activation of Rho during cytokinesis, but are proposed to play slightly different roles. PH domains have diverse functions, but in ...
CDD:269938	115	EUK	Invertebrates:9,Mammals:2,Primates:2,Rodents:1,Vertebrates:5	cd01231, PH_SH2B_family, SH2B adapter protein 1, 2, and 3 Pleckstrin homology (PH) domain.  SH2B family/APS proteins are a family of intracellular adaptor proteins that influences a variety of signaling pathways mediated by Janus kinase (JAK) and receptor tyrosine kinases (RTKs) including receptors for insulin, insulin-like growth factor-1, Janus kinase 2 (Jak2), platelet derived growth factor, fibroblast growth ...
CDD:269939	103	EUK	Invertebrates:10,Plants:16,Vertebrates:2	cd01233, PH_KIFIA_KIFIB, KIFIA and KIFIB protein pleckstrin homology (PH) domain.  The kinesin-3 family motors KIFIA (Caenorhabditis elegans homolog unc-104) and KIFIB transport synaptic vesicle precursors that contain synaptic vesicle proteins, such as synaptophysin, synaptotagmin and the small GTPase RAB3A, but they do not transport organelles that contain plasma membrane proteins. They have a N-terminal motor domain, followed by a ...
CDD:269940	122	EUK	Invertebrates:10,Rodents:1,Vertebrates:4	cd01234, PH_CADPS, Ca2+-dependent activator protein (also called CAPS) Pleckstrin homology (PH) domain.  CADPS/CAPS consists of two members, CAPS1 which regulates catecholamine release from neuroendocrine cells and CAPS2 which is involved in the release of two neurotrophins, brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) from cerebellar granule cells. CADPS plays an important role in vesicle exocytosis in neurons and ...
CDD:269941	106	EUK	Invertebrates:10,Vertebrates:3	cd01235, PH_Sbf1_hMTMR5, Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain.  Sbf1 is a myotubularin-related pseudo-phosphatase. Both Sbf1 and myotubularin interact with the SET domains of Hrx and other epigenetic regulatory proteins, but Sbf1 lacks phosphatase activity due to several amino acid changes in its structurally preserved catalytic pocket. It contains pleckstrin (PH), GEF, and myotubularin homology domains ...
CDD:269944	140	EUK	Invertebrates:16,Primates:1,Rodents:1,Vertebrates:7	cd01238, PH_Btk, Bruton's tyrosine kinase pleckstrin homology (PH) domain.  Btk is a member of the Tec family of cytoplasmic protein tyrosine kinases that includes BMX, IL2-inducible T-cell kinase (Itk) and Tec. Btk plays a role in the maturation of B cells. Tec proteins general have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. The Btk PH domain binds ...
CDD:269945	127	EUK	Invertebrates:18,Primates:2,Rodents:2,Vertebrates:4	cd01239, PH_PKD, Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain.  Protein Kinase C family is composed of three members, PKD1 (PKCmu), PKD2 and PKD3 (PKCnu). Like the C-type protein kinases (PKCs), PKDs are activated by diacylglycerol (DAG). They are involved in vesicular transport, cell proliferation, survival, migration and immune responses. PKD consists of tandem C1 domains, followed by a PH domain and a ...
CDD:269946	118	EUK	Invertebrates:10,Primates:1,Vertebrates:2	cd01240, PH_GRK2_subgroup, G Protein-Coupled Receptor Kinase 2 subgroup pleckstrin homology (PH) domain.  GRKs are a family of serine-threonine kinases which phosphorylates activated G-protein coupled receptors leading to the release of the previously bound heterotrimeric G protein agonist and thus signal termination. There are seven mammalian GRKs (GRK1-7) grouped into three subfamilies: GRK1 (GRK1 and 7), GRK2 (GRK2 and 3), and GRK4 ...
CDD:269947	107	EUK	Invertebrates:16,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd01241, PH_PKB, Protein Kinase B-like pleckstrin homology (PH) domain.  PKB (also called Akt), a member of the AGC kinase family, is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase which alters the activity of the targeted protein. The name AGC is based on the three proteins that it is most similar to cAMP-dependent protein kinase 1 (PKA; also known as PKAC), cGMP-dependent protein kinase (PKG; also ...
CDD:269948	110	EUK	Invertebrates:8,Primates:1,Vertebrates:3,nodiv:1	cd01242, PH_ROCK, Rho-associated coiled-coil containing protein kinase pleckstrin homology (PH) domain.  ROCK is a serine/threonine kinase that binds GTP-Rho. It consists of a kinase domain, a coiled coil region and a PH domain. The ROCK PH domain is interrupted by a C1 domain. ROCK plays a role in cellular functions, such as contraction, adhesion, migration, and proliferation and in the regulation of apoptosis. There are two ...
CDD:269949	135	EUK	Invertebrates:12,Primates:1,Vertebrates:2	cd01243, PH_MRCK, MRCK (myotonic dystrophy-related Cdc42-binding kinase) pleckstrin homology (PH) domain.  MRCK is thought to be coincidence detector of signaling by Cdc42 and phosphoinositides. It has been shown to promote cytoskeletal reorganization, which affects many biological processes. There are 2 members of this family: MRCKalpha and MRCKbeta. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH ...
CDD:269950	107	EUK	Invertebrates:7,Primates:1,Vertebrates:6	cd01244, PH_GAP1-like, RAS p21 protein activator (GTPase activating protein) family pleckstrin homology (PH) domain.  RASAL1, GAP1(m), GAP1(IP4BP), and CAPRI are all members of the GAP1 family of GTPase-activating proteins. They contain N-terminal SH2-SH3-SH2 domains, followed by two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. With the notable exception of GAP1(m), they all possess an arginine finger-dependent GAP ...
CDD:269952	108	EUK	Invertebrates:8,Plants:4,Primates:1	cd01248, PH_PLC_ELMO1, Phospholipase C and Engulfment and cell motility protein 1 pleckstrin homology domain.  The C-terminal region of ELMO1, the PH domain and Pro-rich sequences, binds the SH3-containing region of DOCK2 forming a intermolecular five-helix bundle allowing for DOCK mediated Rac1 activation. ELMO1, a mammalian homolog of C. elegans CED-12, contains an N-terminal RhoG-binding region, a ELMO domain, a PH domain, and a ...
CDD:269953	105	EUK	Invertebrates:17,Plants:1,Primates:2,Rodents:1,Vertebrates:3	cd01249, BAR-PH_GRAF_family, GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain.  This hierarchy contains GRAF family members: OPHN1/oligophrenin1, GRAF1 (also called ARHGAP26/Rho GTPase activating protein 26), GRAF2 (also called ARHGAP10/ARHGAP42), AK057372, and LOC129897, all of which are members of the APPL family. OPHN1 is a RhoGAP involved in X-linked mental ...
CDD:241281	114	EUK	Invertebrates:13,Vertebrates:3	cd01250, PH_AGAP, Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain.  AGAP (also called centaurin gamma; PIKE/Phosphatidylinositol-3-kinase enhancer) reside mainly in the nucleus and are known to activate phosphoinositide 3-kinase, a key regulator of cell proliferation, motility and vesicular trafficking. There are 3 isoforms of AGAP (PIKE-A, PIKE-L, and PIKE-S) the longest of which PIKE-L consists ...
CDD:241282	105	EUK	Invertebrates:15,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	cd01251, PH2_ADAP, ArfGAP with dual PH domains Pleckstrin homology (PH) domain, repeat 2.  ADAP (also called centaurin alpha) is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma ...
CDD:269954	119	EUK	Invertebrates:15,Primates:1,Rodents:1,Vertebrates:3	cd01252, PH_GRP1-like, General Receptor for Phosphoinositides-1-like Pleckstrin homology (PH) domain.  GRP1/cytohesin3 and the related proteins ARNO (ARF nucleotide-binding site opener)/cytohesin-2 and cytohesin-1 are ARF exchange factors that contain a pleckstrin homology (PH) domain thought to target these proteins to cell membranes through binding polyphosphoinositides. The PH domains of all three proteins exhibit ...
CDD:269955	113	EUK	Invertebrates:7,Mammals:1,Primates:2,Vertebrates:2	cd01253, PH_ARHGAP21-like, ARHGAP21 and related proteins pleckstrin homology (PH) domain.  ARHGAP family genes encode Rho/Rac/Cdc42-like GTPase activating proteins with a RhoGAP domain. These proteins functions as a GTPase-activating protein (GAP) for RHOA and CDC42. ARHGAP21 controls the Arp2/3 complex and F-actin dynamics at the Golgi complex by regulating the activity of the small GTPase Cdc42. It is recruited to the Golgi ...
CDD:269956	136	EUK	Invertebrates:14,Plants:18,Rodents:1,Vertebrates:4	cd01254, PH_PLD, Phospholipase D pleckstrin homology (PH) domain.  PLD hydrolyzes phosphatidylcholine to phosphatidic acid (PtdOH), which can bind target proteins. PLD contains a PH domain, a PX domain and four conserved PLD signature domains. The PLD PH domain is specific for bisphosphorylated inositides. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location ...
CDD:269958	112	EUK	Invertebrates:17,Mammals:1,Primates:1,Rodents:1,Vertebrates:5	cd01256, PH_dynamin, Dynamin pleckstrin homology (PH) domain.  Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain. Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains have ...
CDD:269959	106	EUK	Invertebrates:4,Rodents:1	cd01257, PH_IRS, Insulin receptor substrate (IRS) pleckstrin homology (PH) domain.  Insulin receptor substrate (IRS) molecules are mediators in insulin signaling and play a role in maintaining basic cellular functions such as growth and metabolism. They act as docking proteins between the insulin receptor and a complex network of intracellular signaling molecules containing Src homology 2 (SH2) domains. Four members (IRS-1, IRS-2, IRS-3, IRS-4) of ...
CDD:269960	89	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:7	cd01258, PHsplit_syntrophin, Syntrophin Split Pleckstrin homology (PH) domain.  Syntrophins are scaffold proteins that associate with associate with the Duchenne muscular dystrophy protein dystrophin and the dystrophin-related proteins, utrophin and dystrobrevin to form the dystrophin glycoprotein complex (DGC). There are 5 members: alpha, beta1, beta2, gamma1, and gamma2) all of which contains a split (also called joined) PH ...
CDD:269961	124	EUK	Invertebrates:23,Mammals:3,Primates:1,Vertebrates:4	cd01259, PH_APBB1IP, Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain.  APBB1IP consists of a Ras-associated (RA) domain, a PH domain, a family-specific BPS region, and a C-terminal SH2 domain. Grb7, Grb10 and Grb14 are paralogs that are also present in this hierarchy. These adapter proteins bind a variety of receptor tyrosine kinases, including the insulin ...
CDD:269963	109	EUK	Invertebrates:10,Primates:1	cd01261, PH_SOS, Son of Sevenless (SOS) Pleckstrin homology (PH) domain.  SOS is a Ras guanine nucleotide exchange factor. SOS is thought to transmit signals from activated receptor tyrosine kinases to the Ras signaling pathway. SOS contains a histone domain, Dbl-homology (DH), a PH domain, Rem domain, Cdc25 domain, and a Grb2 binding domain. The SOS PH domain binds to phosphatidylinositol-4,5-bisphosphate (PIP2) and phosphatidic acid (PA). SOS is ...
CDD:241293	107	EUK	Invertebrates:18,Mammals:1,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd01262, PH_PDK1, 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain.  PDK1 plays an important role in insulin and growth factor signalling cascades. It phosphorylates and activates many AGC (cAMP-dependent, cGMP-dependent, protein kinase C (PKC)) family of protein kinases members, including protein kinase B (PKB, also known as Akt), p70 ribosomal S6-kinase (S6K), serum and ...
CDD:269964	121	EUK	Invertebrates:25,Vertebrates:2	cd01263, PH_anillin, Anillin Pleckstrin homology (PH) domain.  Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin homology domain-containing family K) is an actin binding protein involved in cytokinesis. It interacts with GTP-bound Rho proteins and results in the inhibition of their GTPase activity. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Anillin proteins have a N-terminal HRI ...
CDD:269966	102	EUK	Invertebrates:10,Primates:1,Vertebrates:4	cd01265, PH_TBC1D2A, TBC1 domain family member 2A pleckstrin homology (PH) domain.  TBC1D2A (also called PARIS-1/Prostate antigen recognized and identified by SEREX 1 and ARMUS) contains a PH domain and a TBC-type GTPase catalytic domain. TBC1D2A integrates signaling between Arf6, Rac1, and Rab7 during junction disassembly. Activated Rac1 recruits TBC1D2A to locally inactivate Rab7 via its C-terminal TBC/RabGAP domain and facilitate ...
CDD:241298	135	EUK	Invertebrates:15,Primates:2,Rodents:1,Vertebrates:3	cd01268, PTB_Numb, Numb Phosphotyrosine-binding (PTB) domain.  Numb is a membrane associated adaptor protein which plays critical roles in cell fate determination. Numb proteins are involved in control of asymmetric cell division and cell fate choice, endocytosis, cell adhesion, cell migration, ubiquitination of specific substrates and a number of signaling pathways (Notch, Hedgehog, p53). Mutations in Numb plays a critical ...
CDD:269967	143	EUK	Invertebrates:13,Mammals:2,Primates:1,Rodents:3,Vertebrates:6	cd01269, PTB_TBC1D1_like, TBC1 domain family member 1  and related proteins Phosphotyrosine-binding (PTB) domain.  The TBC1D1-like members here include TBC1D1, TBC1D4 (also called Akt substrate of 160 kDa or AS160), and pollux (PLX), a calmodulin-binding protein, and are thought to have a role in regulating cell growth and differentiation. These proteins are thought to function as GTPase-activating protein for Rab ...
CDD:269968	179	EUK	Invertebrates:20,Mammals:1,Vertebrates:4	cd01270, PTB_CAPON-like, Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein (CAPON) Phosphotyrosine-binding (PTB) domain.  CAPON (also known as Nitric oxide synthase 1 adaptor protein, NOS1AP, encodes a cytosolic protein that binds to the signaling molecule, neuronal NOS (nNOS). It contains a N-terminal PTB domain that binds to the small monomeric G protein, Dexras1 and a C-terminal PDZ-binding domain that mediates ...
CDD:269969	127	EUK	Invertebrates:16,Mammals:1,Primates:1,Rodents:2,Vertebrates:7	cd01271, PTB2_Fe65, Fe65 C-terminal Phosphotyrosine-binding (PTB) domain.  The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains. The C-terminal PTB domain is responsible ...
CDD:269970	138	EUK	Invertebrates:7,Mammals:1,Primates:1,Vertebrates:1	cd01272, PTB1_Fe65, Fe65 N-terminal Phosphotyrosine-binding (PTB) domain.  The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains. The N-terminal PTB domain was shown to interact with ...
CDD:269971	144	EUK	Invertebrates:16,Mammals:1,Primates:1,Vertebrates:4,nodiv:1	cd01273, PTB_CED-6, Cell death protein 6 homolog (CED-6/GULP1) Phosphotyrosine-binding (PTB) domain.  CED6 (also known as GULP1: engulfment adaptor PTB domain containing 1) is an adaptor protein involved in the specific recognition and engulfment of apoptotic cells. CED6 has been shown to interact with the cytoplasmic tail of another protein involved in the engulfment of apoptotic cells, CED1. CED6 has a C-terminal ...
CDD:269972	146	EUK	Invertebrates:13,Primates:2,Rodents:1,Vertebrates:5	cd01274, PTB_Anks, Ankyrin repeat and sterile alpha motif (SAM) domain-containing (Anks) protein family Phosphotyrosine-binding (PTB) domain.  Both AIDA-1b (AbetaPP intracellular domain-associated protein 1b) and Odin (also known as ankyrin repeat and sterile alpha motif domain-containing 1A; ANKS1A) belong to the Anks protein family. Both of these family members interacts with the EphA8 receptor. Ank members consists of ...
CDD:238606	126	EUKprk	Bacteria:11,Environmental:1,Invertebrates:4,Plants:2,Primates:1	cd01275, FHIT, FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three  branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine ...
CDD:238607	104	EUKprk	Bacteria:27,Invertebrates:4,Mammals:1,Plants:1,Primates:1	cd01276, PKCI_related, Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
CDD:238608	103	EUKprk	Bacteria:13,Invertebrates:2,Plants:2	cd01277, HINT_subgroup, HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in ...
CDD:238609	104	EUK	Invertebrates:4,Plants:1,Primates:1,Vertebrates:1	cd01278, aprataxin_related, aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
CDD:133388	112	PRK	Bacteria:21	cd01282, HTH_MerR-like_sg3, Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily.  Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress ...
CDD:238610	112	EUKprk	Bacteria:18,Invertebrates:4,Plants:4,Primates:1,Rodents:2	cd01283, cytidine_deaminase, Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in ...
CDD:238611	115	EUKprk	Bacteria:18,Plants:2	cd01284, Riboflavin_deaminase-reductase, Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain ...
CDD:238612	109	EUKprk	Bacteria:35,Invertebrates:5,Plants:6,Primates:1,Vertebrates:1	cd01285, nucleoside_deaminase, Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. ...
CDD:238613	131	EUKprk	Bacteria:18,Invertebrates:2,Phages:1,Plants:2,Primates:1,Viruses:1	cd01286, deoxycytidylate_deaminase, Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP,  providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even ...
CDD:238614	150	miss	miss	cd01287, FabA, FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface.  Each active site is tunnel-shaped and completely inaccessible to solvent.  No metal ions or cofactors are required for ...
CDD:238615	131	miss	miss	cd01288, FabZ, FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
CDD:238616	138	miss	miss	cd01289, FabA_like, Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ.
CDD:211324	87	EUKprk	Bacteria:43,Invertebrates:9,Plants:13,Primates:1,Vertebrates:4	cd01291, PseudoU_synth, Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same ...
CDD:238617	275	EUKprk	Bacteria:19,Environmental:1,Invertebrates:1,Plants:2,Primates:1	cd01292, metallo-dependent_hydrolases, Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, ...
CDD:238618	398	EUKprk	Bacteria:18,Invertebrates:1,Plants:1	cd01293, Bact_CD, Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi, but not mammalian cells. The bacterial enzymes, but not the fungal enzymes, are related to the adenosine deaminases (ADA). The bacterial enzymes are iron dependent and ...
CDD:238619	335	EUKprk	Bacteria:2,Invertebrates:2,Plants:4,nodiv:1	cd01294, DHOase, Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is monofunctional and mainly dimeric.
CDD:238620	422	PRK	Bacteria:7	cd01295, AdeC, Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source in bacteria and archea.
CDD:238621	371	EUKprk	Bacteria:5,Invertebrates:1,Rodents:1,Vertebrates:1	cd01296, Imidazolone-5PH, Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria, the enzyme is part of histidine utilization (hut) operon.
CDD:238622	415	PRK	Bacteria:15	cd01297, D-aminoacylase, D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics.
CDD:238623	411	EUKprk	Bacteria:20,Plants:1	cd01298, ATZ_TRZ_like, TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are catalyzed by atrazine chlorohydrolase (AtzA), hydroxyatrazine ethylaminohydrolase (AtzB), and N-isopropylammelide N-isopropylaminohydrolase (AtzC). All three enzymes belong to the ...
CDD:238624	342	EUKprk	Bacteria:18,Plants:3	cd01299, Met_dep_hydrolase_A, Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a ...
CDD:238625	479	EUKprk	Bacteria:23,Environmental:1,Invertebrates:1,Plants:3	cd01300, YtcJ_like, YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling.
CDD:238626	309	EUKprk	Bacteria:17,Environmental:1,Invertebrates:1,Plants:1,nodiv:1	cd01301, rDP_like, renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
CDD:238627	337	PRK	Bacteria:4	cd01302, Cyclic_amidohydrolases, Cyclic amidohydrolases, including hydantoinase, dihydropyrimidinase, allantoinase, and dihydroorotase, are involved in the metabolism of pyrimidines and purines, sharing the property of hydrolyzing the cyclic amide bond of each substrate to the corresponding N-carbamyl amino acids. Allantoinases catalyze the degradation of purines, while dihydropyrimidinases and hydantoinases, a microbial counterpart of dihydropyrimidinase, are ...
CDD:238628	429	EUKprk	Bacteria:4,Invertebrates:3,Plants:2,Primates:1	cd01303, GDEase, Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and therefore can play a role in the regulation of cellular GTP and the guanylate nucleotide pool.
CDD:238630	263	PRK	Bacteria:2	cd01305, archeal_chlorohydrolases, Predicted chlorohydrolases. These metallo-dependent hydrolases from archea are part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. They have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a ...
CDD:238631	325	PRK	Bacteria:5	cd01306, PhnM, PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage of alkylphosphonates, which are utilized as sole phosphorus sources by many bacteria.
CDD:238632	338	PRK	Bacteria:4,nodiv:1	cd01307, Met_dep_hydrolase_B, Metallo-dependent hydrolases, subgroup B is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water ...
CDD:238634	359	EUKprk	Bacteria:7,Plants:1	cd01309, Met_dep_hydrolase_C, Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a ...
CDD:238635	251	EUKprk	Bacteria:42,Invertebrates:4,Plants:2,Primates:1	cd01310, TatD_DNAse, TatD like proteins;  E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
CDD:238636	263	EUKprk	Bacteria:4,Plants:2,nodiv:1	cd01311, PDC_hydrolase, 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most important intermediate metabolites in the bacterial pathways for various phenolic compounds, including lignin, which is the most abundant aromatic material in nature.
CDD:238639	447	EUKprk	Bacteria:12,Invertebrates:3,Plants:4,Rodents:1,Vertebrates:2	cd01314, D-HYD, D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine or hydantoin. The hydrolysis of dihydropyrimidines is the second step of reductive catabolism of pyrimidines in human. The hydrolysis of ...
CDD:238640	447	EUKprk	Bacteria:4,Invertebrates:3,Plants:2	cd01315, L-HYD_ALN, L-Hydantoinases (L-HYDs) and Allantoinase (ALN); L-Hydantoinases are a member of the dihydropyrimidinase family, which catalyzes the reversible hydrolytic ring opening of dihydropyrimidines and hydantoins (five-membered cyclic diamides used in biotechnology). But L-HYDs differ by having an L-enantio specificity and by lacking activity on possible natural substrates such as dihydropyrimidines. Allantoinase catalyzes the ...
CDD:238642	374	EUKprk	Bacteria:20,Invertebrates:1	cd01317, DHOase_IIa, Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C.elegans protein involved in axon growth.
CDD:238643	361	PRK	Bacteria:7	cd01318, DHOase_IIb, Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family.
CDD:238645	325	EUKprk	Bacteria:11,Invertebrates:2,Mammals:1,Plants:1	cd01320, ADA, Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in the purine pathway. Low, as well as high levels of ADA activity have been linked to several diseases.
CDD:238646	345	EUK	Invertebrates:6,Plants:2,Primates:1,Vertebrates:1	cd01321, ADGF, Adenosine deaminase-related growth factors (ADGF), a novel family of secreted growth-factors with sequence similarty to adenosine deaminase.
CDD:238647	48	PRK	Bacteria:22,nodiv:1	cd01324, cbb3_Oxidase_CcoQ, Cytochrome cbb oxidase CcoQ.  Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a ...
CDD:238648	45	miss	miss	cd01327, KAZAL_PSTI, Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins, including the second domain of the ovomucoid turkey inhibitor and the C-terminal domain of the esophagus cancer-related gene-2 protein (ECRG-2), are members of the superfamily of kazal-type proteinase inhibitors and follistatin-like proteins.
CDD:238650	54	miss	miss	cd01330, KAZAL_SLC21, The kazal-type serine protease inhibitor domain has been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The KAZAL_SLC21 domain is a member of the superfamily of kazal-like proteinase inhibitors and follistatin-like proteins.
CDD:176461	325	EUKprk	Bacteria:115,Environmental:4,Invertebrates:12,Plants:13,Primates:1,Vertebrates:6,nodiv:1	cd01334, Lyase_I, Lyase class I family; a group of proteins which catalyze similar beta-elimination reactions.  The Lyase class I family contains class II fumarase, aspartase, adenylosuccinate lyase (ASL), argininosuccinate lyase (ASAL), prokaryotic-type 3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and related proteins. It belongs to the Lyase_I superfamily. Proteins of this ...
CDD:100105	204	EUKprk	Bacteria:28,Invertebrates:1,Primates:1	cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a ...
CDD:133421	325	EUK	Invertebrates:13,Plants:5,Vertebrates:3	cd01336, MDH_cytoplasmic_cytosolic, Cytoplasmic and cytosolic Malate dehydrogenases.  MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are eukaryotic MDHs localized to the cytoplasm and cytosol. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which ...
CDD:133422	310	EUKprk	Bacteria:2,Invertebrates:14,Mammals:1,Plants:18,Primates:1,Vertebrates:3	cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and mitochondrial malate dehydrogenases.  MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are localized to the glycosome and mitochondria. MDHs are part of the NAD(P)-binding ...
CDD:133423	322	EUKprk	Bacteria:24,Invertebrates:4,Plants:3	cd01338, MDH_choloroplast_like, Chloroplast-like malate dehydrogenases.  MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are bacterial MDHs, and plant MDHs localized to the choloroplasts. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a ...
CDD:133424	300	EUKprk	Bacteria:47,Invertebrates:11,Plants:1	cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate dehydrogenase proteins.  Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted ...
CDD:238651	137	EUKprk	Bacteria:1,Invertebrates:1,Phages:1,Plants:2,Primates:1,Vertebrates:2	cd01341, ADP_ribosyl, ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 ...
CDD:238652	83	EUKprk	Bacteria:222,Environmental:6,Invertebrates:44,Mammals:2,Plants:44,Primates:1,Rodents:2,Vertebrates:5,nodiv:3	cd01342, Translation_Factor_II_like, Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G ...
CDD:238653	233	miss	miss	cd01343, PL1_Passenger_AT, Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
CDD:238654	188	miss	miss	cd01344, PL2_Passenger_AT, Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43, AIDA-1 and IcsA, as well as, the less characterized ShdA, MisL, and BapA autotransporters.
CDD:238656	392	PRK	Bacteria:16	cd01346, Maltoporin-like, The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-barrel (18,22). Loop 3 folds into the core to constrict pore size. Long irregular loops are found on the extracelllular side, while short turns are in the periplasm.Tightly-bound water ...
CDD:238657	635	PRK	Bacteria:30	cd01347, ligand_gated_channel, TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel.   Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which ...
CDD:153129	389	EUKprk	Bacteria:3,Mammals:1,Primates:1	cd01351, Aconitase, Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle.  Aconitase catalytic domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle.  Cis-aconitate is formed as an intermediate product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to ...
CDD:153130	389	EUKprk	Bacteria:6,Plants:2,nodiv:1	cd01355, AcnX, Putative Aconitase X catalytic domain.  Putative Aconitase X catalytic domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution.
CDD:238658	123	PRK	Bacteria:5,nodiv:1	cd01356, AcnX_swivel, Putative Aconitase X swivel domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution.
CDD:176462	450	miss	miss	cd01357, Aspartase, Aspartase.  This subgroup contains Escherichia coli aspartase (L-aspartate ammonia-lyase), Bacillus aspartase and related proteins. It is a member of the Lyase class I family, which includes both aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins ...
CDD:176463	435	miss	miss	cd01359, Argininosuccinate_lyase, Argininosuccinate lyase (argininosuccinase, ASAL).  This group contains ASAL and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues ...
CDD:176464	387	miss	miss	cd01360, Adenylsuccinate_lyase_1, Adenylsuccinate lyase (ASL)_subgroup 1.  This subgroup contains bacterial and archeal proteins similar to ASL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by ...
CDD:176465	455	miss	miss	cd01362, Fumarase_classII, Class II fumarases.  This subgroup contains Escherichia coli fumarase C, human mitochondrial fumarase, and related proteins.  It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each ...
CDD:238660	352	EUK	Invertebrates:6,Plants:6,Vertebrates:2	cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the ...
CDD:238661	356	EUK	Invertebrates:5,Plants:2,Primates:1,Rodents:1,Vertebrates:1	cd01365, KISc_KIF1A_KIF1B, Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve  terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in ...
CDD:238662	329	EUK	Invertebrates:6,Plants:7,Primates:1,Rodents:1,Vertebrates:3	cd01366, KISc_C_terminal, Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins ...
CDD:238663	322	EUK	Invertebrates:9,Plants:6,Rodents:1,Vertebrates:1	cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in ...
CDD:238664	345	EUK	Invertebrates:4,Plants:1,Primates:1,Vertebrates:1	cd01368, KISc_KIF23_like, Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type ...
CDD:238665	325	EUK	Invertebrates:8,Plants:5,Vertebrates:1	cd01369, KISc_KHC_KIF5, Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the ...
CDD:238666	338	EUK	Invertebrates:4,Plants:4,Primates:1,Vertebrates:2	cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus ...
CDD:238668	341	EUK	Invertebrates:4,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd01372, KISc_KIF4, Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular ...
CDD:238670	321	EUK	Invertebrates:2,Plants:6,Vertebrates:1	cd01374, KISc_CENP_E, Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus ...
CDD:238673	693	EUK	Invertebrates:10,Mammals:1,Plants:3,Primates:1,Vertebrates:5	cd01377, MYSc_type_II, Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is ...
CDD:238674	674	EUK	Invertebrates:5,Plants:2,Primates:1,Vertebrates:3	cd01378, MYSc_type_I, Myosin motor domain, type I myosins. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important ...
CDD:238676	691	EUK	Invertebrates:4,Plants:6,Primates:1	cd01380, MYSc_type_V, Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a ...
CDD:238684	72	miss	miss	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
CDD:238685	77	miss	miss	cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
CDD:238686	66	miss	miss	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in ...
CDD:107248	269	EUKprk	Bacteria:73,Invertebrates:2,Mammals:1,Primates:1,Rodents:2,Vertebrates:3	cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic binding fold superfamily.  Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including ...
CDD:143331	52	EUKprk	Bacteria:421,Environmental:1,Plants:3,nodiv:1	cd01392, HTH_LacI, Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators.  HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features ...
CDD:238687	226	miss	miss	cd01393, recA_like, RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57.  Archaea have the RecA-like homologs radA and radB.
CDD:238689	60	miss	miss	cd01395, HMT_MBD, Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to ...
CDD:238690	77	miss	miss	cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form ...
CDD:238692	213	EUKprk	Bacteria:61,Environmental:3,Invertebrates:5,Plants:11,Vertebrates:3	cd01398, RPI_A, RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the conversion of phosphosugars into glycolysis intermediates, which are precursors for the synthesis of amino acids, vitamins, nucleotides, and ...
CDD:238693	232	EUKprk	Bacteria:53,Invertebrates:10,Plants:4,Primates:1,Vertebrates:3	cd01399, GlcN6P_deaminase, GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or deamination. It is the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate (GlcNAc6P). GlcN6P deaminase is a ...
CDD:238694	219	EUKprk	Bacteria:107,Environmental:1,Invertebrates:13,Plants:11,Primates:1,Vertebrates:4	cd01400, 6PGL, 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard against the accumulation of the delta form of the lactone, which may be toxic through its reaction with endogenous cellular nucleophiles.
CDD:238695	377	miss	miss	cd01401, PncB_like, Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
CDD:238697	242	miss	miss	cd01406, SIR2-like, Sir2-like: Prokaryotic group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines; and are members of the SIR2 superfamily of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation.
CDD:238698	218	miss	miss	cd01407, SIR2-fam, SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene ...
CDD:238699	235	miss	miss	cd01408, SIRT1, SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by ...
CDD:238700	260	miss	miss	cd01409, SIRT4, SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
CDD:238701	206	miss	miss	cd01410, SIRT7, SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
CDD:238703	224	miss	miss	cd01412, SIRT5_Af1_CobB, SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that ...
CDD:238704	222	miss	miss	cd01413, SIR2_Af2, SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus ...
CDD:133469	279	EUKprk	Bacteria:51,Environmental:4,Plants:12,nodiv:1	cd01414, SAICAR_synt_Sc, non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase.  Eukaryotic, bacterial, and archaeal group of SAICAR synthetases represented by the Saccharomyces cerevisiae (Sc) enzyme, mostly absent in metazoans. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts ...
CDD:133470	230	PRK	Bacteria:48,Environmental:1	cd01415, SAICAR_synt_PurC, bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase.  A subfamily of SAICAR synthetases represented by the Thermotoga maritima (Tm) enzyme and E. coli PurC. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into ...
CDD:133471	252	EUKprk	Bacteria:3,Invertebrates:10,Vertebrates:3,nodiv:1	cd01416, SAICAR_synt_Ade5, Ade5_like 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase.  Eukaryotic group of SAICAR synthetases represented by the Drosophila melanogaster, N-terminal, SAICAR synthetase domain of bifunctional Ade5. The Ade5 gene product (CAIR-SAICARs) catalyzes the sixth and seventh steps of the de novo biosynthesis of purine nucleotides (also reported as seventh and eighth steps). ...
CDD:238705	164	miss	miss	cd01417, Ribosomal_L19e_E, Ribosomal protein L19e, eukaryotic.  L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit.  The other exposed end is involved in ...
CDD:238706	145	miss	miss	cd01418, Ribosomal_L19e_A, Ribosomal protein L19e, archaeal.  L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit.  The other exposed end is involved in ...
CDD:238708	140	miss	miss	cd01420, MoaC_PE, MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
CDD:238709	187	EUKprk	Bacteria:21,Environmental:1,Invertebrates:3,Plants:2,Primates:1,Vertebrates:1	cd01421, IMPCH, Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal  ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. ...
CDD:238710	115	PRK	Bacteria:11	cd01422, MGS, Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of ...
CDD:238711	116	EUKprk	Bacteria:1,Invertebrates:5,Plants:3,Vertebrates:3	cd01423, MGS_CPS_I_III, Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
CDD:238712	110	EUKprk	Bacteria:42,Plants:3	cd01424, MGS_CPS_II, Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding ...
CDD:100106	193	EUKprk	Bacteria:53,Environmental:2,Invertebrates:25,Plants:37,Primates:1,Vertebrates:3	cd01425, RPS2, Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the ...
CDD:119389	139	EUKprk	Bacteria:198,Environmental:3,Invertebrates:13,Plants:13,Primates:1,Rodents:1,Vertebrates:1,nodiv:2	cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a ...
CDD:238713	194	EUKprk	Bacteria:48,Environmental:1,Invertebrates:18,Mammals:2,Plants:14,Primates:1,Vertebrates:6	cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
CDD:238714	112	EUKprk	Bacteria:22,Invertebrates:31,Plants:42,Primates:1,Vertebrates:3,nodiv:1	cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation ...
CDD:238715	116	EUKprk	Bacteria:37,Environmental:1,Invertebrates:3,Plants:8,nodiv:2	cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G.  Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein ...
CDD:259844	779	EUK	Invertebrates:29,Plants:32,Primates:1,Vertebrates:3,nodiv:1	cd01435, RNAP_I_RPA1_N, Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain.  RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial ...
CDD:238717	347	EUK	Invertebrates:2,Plants:5,Primates:1,Rodents:1,Vertebrates:4	cd01437, parp_like, Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins,  which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have ...
CDD:238719	121	EUKprk	Invertebrates:1,Phages:1,Primates:1,Rodents:1,Vertebrates:2	cd01439, TCCD_inducible_PARP_like, Poly(ADP-ribose) polymerases catalyse the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. ...
CDD:238720	113	EUK	Invertebrates:2,Plants:3	cd01443, Cdc25_Acr2p, Cdc25 enzymes are members of the Rhodanese Homology Domain (RHOD) superfamily. Also included in this CD are eukaryotic arsenate resistance proteins such as Saccharomyces cerevisiae Acr2p and similar proteins. Cdc25 phosphatases activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. ...
CDD:238721	96	EUKprk	Bacteria:14,Invertebrates:1,nodiv:2	cd01444, GlpE_ST, GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.
CDD:238723	132	EUK	Invertebrates:2,Plants:2,Primates:1,Rodents:2,Vertebrates:4	cd01446, DSP_MapKP, N-terminal regulatory rhodanese domain of dual specificity phosphatases (DSP), such as Mapk Phosphatase. This domain is believed to determine substrate specificity by binding the substrate, such as ERK2, and activating the C-terminal catalytic domain by inducing a conformational change. This domain has homology to the Rhodanese Homology Domain.
CDD:238725	122	EUKprk	Bacteria:34,Invertebrates:2,Mammals:1,Plants:2,Vertebrates:2	cd01448, TST_Repeat_1, Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.
CDD:238726	118	EUKprk	Bacteria:13,Invertebrates:1,Plants:3,Vertebrates:1	cd01449, TST_Repeat_2, Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
CDD:238727	161	EUKprk	Bacteria:1,Invertebrates:7,Mammals:1,Primates:1,Rodents:2,Vertebrates:8	cd01450, vWFA_subfamily_ECM, Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement ...
CDD:238728	178	EUKprk	Bacteria:9,Environmental:1,Plants:1	cd01451, vWA_Magnesium_chelatase, Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding ...
CDD:238730	183	EUK	Invertebrates:4,Plants:3,Rodents:1,Vertebrates:1	cd01453, vWA_transcription_factor_IIH_type, Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA ...
CDD:238731	174	PRK	Bacteria:19	cd01454, vWA_norD_type, norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role  in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3-  ------> NO2- ------> NO -------> N2O ---------> N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have ...
CDD:238733	206	PRK	Bacteria:8	cd01456, vWA_ywmD_type, VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These ...
CDD:238735	218	EUK	Invertebrates:3,Plants:3,Rodents:1,Vertebrates:2	cd01458, vWA_ku, Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that ...
CDD:238736	254	EUK	Invertebrates:3,Plants:2,Primates:1,Vertebrates:1	cd01459, vWA_copine_like, VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in ...
CDD:238737	266	EUK	Invertebrates:5,Plants:2,Primates:1	cd01460, vWA_midasin, VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this ...
CDD:238738	171	EUKprk	Bacteria:3,Mammals:1,Plants:3,Primates:1,Rodents:2	cd01461, vWA_interalpha_trypsin_inhibitor, vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although ...
CDD:238739	152	PRK	Bacteria:5	cd01462, VWA_YIEM_type, VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. ...
CDD:238740	190	EUK	Invertebrates:3,Rodents:1	cd01463, vWA_VGCC_like, VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or ...
CDD:238741	176	PRK	Bacteria:7	cd01464, vWA_subfamily, VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. ...
CDD:238742	170	PRK	Bacteria:9	cd01465, vWA_subgroup, VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These ...
CDD:238743	155	EUK	Plants:4	cd01466, vWA_C3HC4_type, VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. ...
CDD:238744	180	PRK	Bacteria:9	cd01467, vWA_BatA_type, VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. ...
CDD:238745	239	EUK	Invertebrates:2,Plants:5,Primates:1	cd01468, trunk_domain, trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family ...
CDD:238746	177	EUK	Primates:1,Rodents:2	cd01469, vWA_integrins_alpha_subunit, Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta ...
CDD:238747	198	miss	miss	cd01470, vWA_complement_factors, Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation ...
CDD:238749	164	miss	miss	cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins.  This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In ...
CDD:238750	192	miss	miss	cd01473, vWA_CTRP, CTRP for  CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino ...
CDD:238753	163	miss	miss	cd01476, VWA_integrin_invertebrates, VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in  cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest  any immunological ...
CDD:238754	193	miss	miss	cd01477, vWA_F09G8-8_type, VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. ...
CDD:238756	244	miss	miss	cd01479, Sec24-like, Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several ...
CDD:238757	186	miss	miss	cd01480, vWA_collagen_alpha_1-VI-type, VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far.  Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement ...
CDD:238759	164	miss	miss	cd01482, vWA_collagen_alphaI-XII-like, Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as ...
CDD:238760	143	EUKprk	Bacteria:24,Invertebrates:1,Plants:2,Primates:1	cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, ...
CDD:238763	307	EUK	Invertebrates:4,Plants:4,Primates:1	cd01486, Apg7, Apg7 is an E1-like protein, that activates two different ubiquitin-like proteins, Apg12 and Apg8, and assigns them to specific E2 enzymes, Apg10 and Apg3, respectively. This leads to the covalent conjugation of Apg8 with phosphatidylethanolamine, an important step in autophagy. Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole.
CDD:238767	435	EUK	Invertebrates:6,Plants:4,Primates:1,Vertebrates:3	cd01490, Ube1_repeat2, Ubiquitin activating enzyme (E1), repeat 2. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and ...
CDD:238768	286	EUK	Plants:1,Primates:1,Vertebrates:1	cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a ...
CDD:238769	197	EUK	Invertebrates:1,Plants:5,Primates:1,Vertebrates:1	cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and ...
CDD:238770	425	EUK	Invertebrates:4,Plants:6,Primates:1,Vertebrates:2	cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, ...
CDD:99742	170	EUKprk	Bacteria:6,Mammals:1,Primates:1,nodiv:1	cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH ...
CDD:238771	102	EUKprk	Bacteria:1,Mammals:1	cd01513, Translation_factor_III, Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ...
CDD:238772	79	EUKprk	Bacteria:64,Environmental:1,Invertebrates:19,Plants:20,Primates:1,Vertebrates:2	cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small ...
CDD:238773	257	PRK	Bacteria:5	cd01515, Arch_FBPase_1, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family (FBPase class IV). These are Mg++ dependent phosphatases. Members in this family may have both fructose-1,6-bisphosphatase and inositol-monophosphatase activity. In hyperthermophilic archaea, inositol monophosphatase is thought to play a role in the biosynthesis of di-myo-inositol-1,1'-phosphate, an osmolyte unique to hyperthermophiles.
CDD:238774	309	PRK	Bacteria:10	cd01516, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core structure around the active site is well preserved. In E. coli, FBPase II is part of the glp regulon, which mediates growth on glycerol or sn-glycerol 3-phosphate as the sole carbon source.
CDD:238775	274	EUKprk	Bacteria:11,Plants:12	cd01517, PAP_phosphatase, PAP-phosphatase_like domains. PAP-phosphatase is a member of the inositol monophosphatase family, and catalyses the hydrolysis of 3'-phosphoadenosine-5'-phosphate (PAP) to AMP. In Saccharomyces cerevisiae, HAL2 (MET22) is involved in methionine biosynthesis and provides increased salt tolerance when over-expressed. Bacterial members of this domain family may differ in their substrate specificity and dephosphorylate different ...
CDD:238776	101	EUKprk	Bacteria:9,Invertebrates:1,Plants:2,Primates:1	cd01518, RHOD_YceA, Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
CDD:238777	106	EUK	Invertebrates:2,Plants:8,Primates:1	cd01519, RHOD_HSP67B2, Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.
CDD:238778	128	PRK	Bacteria:3	cd01520, RHOD_YbbB, Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.
CDD:238780	117	PRK	Bacteria:7	cd01522, RHOD_1, Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.
CDD:238782	90	PRK	Bacteria:5	cd01524, RHOD_Pyr_redox, Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.
CDD:238784	122	EUK	Invertebrates:1,Plants:5,Vertebrates:1	cd01526, RHOD_ThiF, Member of the Rhodanese Homology Domain superfamily. This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.
CDD:238786	101	EUKprk	Bacteria:5,Plants:1	cd01528, RHOD_2, Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
CDD:238788	121	EUK	Invertebrates:7,Plants:9,Primates:1,Vertebrates:1	cd01530, Cdc25, Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The ...
CDD:107249	267	PRK	Bacteria:90	cd01536, PBP1_ABC_sugar_binding_like, Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily.  Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The ...
CDD:107250	264	PRK	Bacteria:8	cd01537, PBP1_Repressors_Sugar_Binding_like, Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems.  Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, ...
CDD:107251	288	PRK	Bacteria:39	cd01538, PBP1_ABC_xylose_binding, Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily.  Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta ...
CDD:107252	303	PRK	Bacteria:18	cd01539, PBP1_GGBP, Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species.  Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily ...
CDD:107254	273	PRK	Bacteria:21	cd01541, PBP1_AraR, Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type ...
CDD:107255	259	PRK	Bacteria:17	cd01542, PBP1_TreR_like, Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type ...
CDD:107256	265	PRK	Bacteria:12	cd01543, PBP1_XylR, Ligand-binding domain of DNA transcription repressor specific for xylose (XylR).  Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR ...
CDD:107257	270	PRK	Bacteria:21	cd01544, PBP1_GalR, Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism.  Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors ...
CDD:107258	270	PRK	Bacteria:14,Environmental:1	cd01545, PBP1_SalR, Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic ...
CDD:238796	400	PRK	Bacteria:25	cd01555, UdpNAET, UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine = phosphate + UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine. This enzyme is of interest as a potential target for anti-bacterial agents. The only other known enolpyruvyl transferase is the related ...
CDD:238797	409	EUKprk	Bacteria:50,Plants:4	cd01556, EPSP_synthase, EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form 5-enolpyruvylshkimate-3-phosphate (EPSP), an intermediate in the shikimate pathway leading to aromatic amino acid biosynthesis. The reaction is phosphoenolpyruvate + 3-phosphoshikimate = phosphate + ...
CDD:238798	279	miss	miss	cd01557, BCAT_beta_family, BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids  leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and alpha-ketoisovalerate. The enzyme requires pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze the reaction. It has been found that mammals have two foms of the enzyme - mitochondrial and cytosolic forms ...
CDD:238799	270	miss	miss	cd01558, D-AAT_like, D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and D-glutamate in addition to other D-amino acids. The enzyme like other members of this superfamily requires PLP as a cofactor. Members of this subgroup are found in all three forms of life.
CDD:238800	249	miss	miss	cd01559, ADCL_like, ADCL_like: 4-Amino-4-deoxychorismate lyase:  is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate.  Based on the information available from the crystal structure, most members of this subgroup are likely to function as dimers.  The enzyme from E.Coli, the structure of which is available, is a homodimer that is folded into a small and a larger domain. The coenzyme ...
CDD:107203	460	miss	miss	cd01560, Thr-synth_2, Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
CDD:107204	291	miss	miss	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the ...
CDD:107205	304	miss	miss	cd01562, Thr-dehyd, Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly converted into NH4+. The direct deamination is catalyzed by threonine dehydratase, in which pyridoxal phosphate (PLP) is the prosthetic group. Threonine dehydratase is widely distributed in all three major ...
CDD:107206	324	miss	miss	cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of  threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants, OPH is an intermediate between the methionine and threonine/isoleucine pathways. Thus threonine synthase competes for OPH with cystathionine-gamma-synthase, the first enzyme in the methionine pathway. ...
CDD:238801	343	miss	miss	cd01567, NAPRTase_PncB, Nicotinate phosphoribosyltransferase (NAPRTase) family. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
CDD:238802	269	miss	miss	cd01568, QPRTase_NadC, Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, ...
CDD:238803	407	miss	miss	cd01569, PBEF_like, pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general, nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the ...
CDD:238804	327	miss	miss	cd01570, NAPRTase_A, Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi).
CDD:238805	302	miss	miss	cd01571, NAPRTase_B, Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
CDD:238806	268	miss	miss	cd01572, QPRTase, Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each ...
CDD:238807	272	miss	miss	cd01573, modD_like, ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
CDD:107259	264	PRK	Bacteria:22	cd01574, PBP1_LacI, Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains ...
CDD:107260	268	PRK	Bacteria:40,nodiv:1	cd01575, PBP1_GntR, Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators.  This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ...
CDD:238809	91	EUKprk	Bacteria:18,Plants:5	cd01577, IPMI_Swivel, Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo ...
CDD:238812	171	EUKprk	Bacteria:5,Invertebrates:4,Plants:2,Vertebrates:2	cd01580, AcnA_IRP_Swivel, Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other ...
CDD:153133	382	EUKprk	Bacteria:16,Plants:2	cd01583, IPMI, 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate.  Aconatase-like catalytic domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and ...
CDD:153136	404	EUKprk	Bacteria:2,Invertebrates:3,Plants:1,Rodents:1,Vertebrates:1	cd01586, AcnA_IRP, Aconitase A catalytic domain.  Aconitase A catalytic domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydrolyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals ...
CDD:176466	231	PRK	Bacteria:1	cd01594, Lyase_I_like, Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions.  Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I ...
CDD:176467	381	miss	miss	cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase (ASL)_like.  This group contains ASL, prokaryotic-type 3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and related proteins. These proteins are members of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active ...
CDD:176468	450	miss	miss	cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes.  This group contains aspartase (L-aspartate ammonia-lyase), fumarase class II enzymes, and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four ...
CDD:176469	437	miss	miss	cd01597, pCLME, prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like.  This subgroup contains pCLME and related proteins, and belongs to the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from ...
CDD:176470	425	miss	miss	cd01598, PurB, PurB_like adenylosuccinases (adenylsuccinate lyase, ASL).  This subgroup contains EcASL, the product of the purB gene in Escherichia coli, and related proteins. It is a member of the Lyase class I family of the Lyase_I superfamily. Members of the Lyase class I family function as homotetramers to catalyze similar beta-elimination reactions in which a Calpha-N or Calpha-O bond is cleaved with the subsequent release of fumarate as one of the products. The ...
CDD:259845	659	EUKprk	Bacteria:25,Environmental:3,Invertebrates:2,Plants:2	cd01609, RNAP_beta'_N, Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain.  Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase ...
CDD:238813	122	EUKprk	Bacteria:225,Environmental:1,Invertebrates:17,Mammals:1,Plants:34,Primates:1,Rodents:2,Vertebrates:5,nodiv:2	cd01610, PAP2_like, PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly ...
CDD:176355	112	miss	miss	cd01611, GABARAP, Ubiquitin domain of GABA-receptor-associated protein.  GABARAP  (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion.  GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1.  Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8).  ATG8 is a ...
CDD:176356	87	miss	miss	cd01612, APG12_C, Ubiquitin-like domain of APG12.  APG12_C    The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.
CDD:133473	83	PRK	Bacteria:50,Environmental:1	cd01614, EutN_CcmL, Ethanolamine utilisation protein and carboxysome structural protein domain family.  Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various ...
CDD:119367	78	EUK	Invertebrates:8,Mammals:2,Primates:1,Rodents:2,Vertebrates:5	cd01615, CIDE_N, CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the ...
CDD:133435	60	EUKprk	Bacteria:4,Primates:1	cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely ...
CDD:176357	80	miss	miss	cd01617, DCX, Ubiquitin-like domain of DCX.  DCX   The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein.  Doublecortin is expressed in migrating neurons.  Mutations in the gene encoding doublecortin cause lissencephaly in males and  'double-cortex syndrome' in females.
CDD:240620	323	PRK	Bacteria:14	cd01619, LDH_like, D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains.  D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the ...
CDD:240621	317	EUKprk	Bacteria:5,Invertebrates:1,Plants:2	cd01620, Ala_dh_like, Alanine dehydrogenase and related dehydrogenases.  Alanine dehydrogenase/Transhydrogenase, such as the hexameric L-alanine dehydrogenase of Phormidium lapideum, contain 2 Rossmann fold-like domains linked by an alpha helical region. Related proteins include Saccharopine Dehydrogenase (SDH), bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase enzyme, N(5)-(carboxyethyl)ornithine synthase, and ...
CDD:99959	229	EUKprk	Bacteria:61,Environmental:2,Mammals:1,Plants:3,Primates:1	cd01635, Glycosyltransferase_GTB_type, Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The ...
CDD:238814	184	EUKprk	Bacteria:4,Mammals:1,Primates:1	cd01636, FIG, FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule ...
CDD:238815	238	PRK	Bacteria:22	cd01637, IMPase_like, Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1,6-bisphosphate, inositol poly- and monophosphates, PAP and PAPS, sedoheptulose-1,7-bisphosphate and probably others.
CDD:238816	242	PRK	Bacteria:39	cd01638, CysQ, CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine biosynthesis (a principal route of sulfur assimilation).
CDD:238817	244	EUKprk	Bacteria:37,Invertebrates:4,Plants:9,Primates:1,Vertebrates:2	cd01639, IMPase, IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be recycled into inositol lipids; in eukaryotes IMPase plays a vital role in intracellular signaling. IMPase is one of the proposed targets of Li+ ...
CDD:238818	293	EUK	Invertebrates:5,Primates:1,Rodents:1,Vertebrates:3	cd01640, IPPase, IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also exhibit 3'-phosphoadenosine 5'-phosphate phosphatase activity, and they all appear to be inhibited by lithium. IPPase is one of the proposed targets of ...
CDD:238819	248	EUKprk	Bacteria:11,Plants:1	cd01641, Bacterial_IMPase_like_1, Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate,  or similar substrates.
CDD:238820	244	PRK	Bacteria:2	cd01642, Arch_FBPase_2, Putative fructose-1,6-bisphosphatase or related enzymes of inositol monophosphatase family. These are Mg++ dependent phosphatases. Members in this family may have fructose-1,6-bisphosphatase and/or inositol-monophosphatase activity. Fructose-1,6-bisphosphatase catalyzes the hydrolysis of fructose-1,6-biphosphate  into fructose-6-phosphate and is critical in gluconeogenesis pathway.
CDD:238821	242	PRK	Bacteria:9,nodiv:1	cd01643, Bacterial_IMPase_like_2, Bacterial family of Mg++ dependent phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate inositol monophosphate or similar substrates.
CDD:238822	213	EUKprk	Bacteria:1,Invertebrates:7,Vertebrates:2	cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
CDD:238823	213	EUKprk	Mammals:1,Primates:1,Rodents:1,Vertebrates:2,Viruses:9	cd01645, RT_Rtv, RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA ...
CDD:238824	158	PRK	Bacteria:53	cd01646, RT_Bac_retron_I, RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
CDD:238825	177	EUKprk	Bacteria:1,Invertebrates:11,Mammals:1,Plants:20,Primates:1,Vertebrates:1	cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in ...
CDD:238826	119	EUK	Invertebrates:13,Plants:16,Primates:1,Vertebrates:3	cd01648, TERT, TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid ...
CDD:238827	220	EUKprk	Bacteria:1,Invertebrates:28,Plants:13,Primates:1,Vertebrates:3,Viruses:1	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed ...
CDD:238828	226	EUKprk	Bacteria:64,Plants:24	cd01651, RT_G2_intron, RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
CDD:153210	115	EUKprk	Bacteria:342,Environmental:11,Invertebrates:24,Plants:42,Primates:1,Vertebrates:5,nodiv:3	cd01653, GATase1, Type 1 glutamine amidotransferase (GATase1)-like domain.  Type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4 ...
CDD:100099	159	miss	miss	cd01657, Ribosomal_L7_archeal_euk, Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome.  The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs.  L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
CDD:100100	54	miss	miss	cd01658, Ribosomal_L30, Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome.  The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs.  L30 is closely related to the ...
CDD:238829	69	EUKprk	Bacteria:24,Invertebrates:2,Mammals:2,Plants:4,Primates:1,Rodents:2,Vertebrates:1	cd01659, TRX_superfamily, Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include ...
CDD:238830	473	miss	miss	cd01660, ba3-like_Oxidase_I, ba3-like heme-copper oxidase subunit I.  The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea which catalyze the reduction of O2 and simultaneously pump protons across the membrane.  It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria.  The ba3 family contains oxidases that lack the conserved residues ...
CDD:238831	493	miss	miss	cd01661, cbb3_Oxidase_I, Cytochrome cbb3 oxidase subunit I.  Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  Found mainly in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized ...
CDD:238832	501	miss	miss	cd01662, Ubiquinol_Oxidase_I, Ubiquinol oxidase subunit I.  Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits in ubiquinol oxidase varies from two to five. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) ...
CDD:238833	488	miss	miss	cd01663, Cyt_c_Oxidase_I, Cytochrome C oxidase subunit I.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian ...
CDD:238834	243	miss	miss	cd01665, Cyt_c_Oxidase_III, Cytochrome c oxidase subunit III.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. CcO catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian ...
CDD:133436	75	EUKprk	Bacteria:21,Invertebrates:14,Plants:9,Primates:1,Vertebrates:3	cd01666, TGS_DRG_C, TGS_DRG_C:   DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG ...
CDD:133437	61	EUKprk	Bacteria:70,Environmental:1,Invertebrates:13,Mammals:1,Plants:9,Primates:1,Vertebrates:4,nodiv:1	cd01667, TGS_ThrRS_N, TGS _ThrRS_N:  ThrRS (threonyl-tRNA Synthetase)  is a class II tRNA synthetase that couples threonine to its cognate tRNA.  In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along ...
CDD:133438	60	EUKprk	Bacteria:35,Plants:2	cd01668, TGS_RelA_SpoT, TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs.  The function of the TGS domain is unknown.
CDD:133439	76	PRK	Bacteria:9,Environmental:1	cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. ...
CDD:260017	79	EUK	Invertebrates:26,Mammals:3,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	cd01670, Death, Death Domain: a protein-protein interaction domain.  Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and ...
CDD:260018	79	EUK	Invertebrates:24,Mammals:2,Primates:1,Rodents:1,Vertebrates:8,nodiv:2	cd01671, CARD, Caspase activation and recruitment domain: a protein-protein interaction domain.  Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor ...
CDD:238835	200	PRK	Bacteria:52,Phages:1,nodiv:1	cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
CDD:238836	193	EUKprk	Bacteria:17,Environmental:2,Invertebrates:6,Mammals:1,Plants:2,Primates:1,Rodents:2,Synthetic:1,Vertebrates:4,Viruses:7,nodiv:1	cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key ...
CDD:153084	555	PRK	Bacteria:8	cd01675, RNR_III, Class III ribonucleotide reductase.  Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and ...
CDD:153086	781	PRK	Bacteria:13	cd01677, PFL2_DhaB_BssA, Pyruvate formate lyase 2 and related enzymes.  This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
CDD:153088	460	EUKprk	Bacteria:18,Invertebrates:6,Plants:4,Primates:1,Vertebrates:3	cd01679, RNR_I, Class I ribonucleotide reductase.  Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and many viruses, use a diiron-tyrosyl radical. Class II ...
CDD:238838	116	PRK	Bacteria:7	cd01680, EFG_like_IV, Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P ...
CDD:238839	177	EUKprk	Bacteria:5,Invertebrates:17,Plants:12,Primates:1,Vertebrates:2	cd01681, aeEF2_snRNP_like_IV, This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P ...
CDD:238840	178	miss	miss	cd01683, EF2_IV_snRNP, EF-2_domain IV_snRNP domain is a part of 116kD U5-specific protein of the U5 small nucleoprotein (snRNP) particle, essential component of the spliceosome. The protein is structurally closely related to the eukaryotic translational elongation factor EF2. This domain has been also identified in 114kD U5-specific protein of  Saccharomyces cerevisiae and may play an important role either in splicing process itself or the recycling of spliceosomal snRNP.
CDD:238841	115	PRK	Bacteria:7	cd01684, Tet_like_IV, EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by ...
CDD:238842	120	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:1	cd01693, mtEFG2_like_IV, mtEF-G2 domain IV. This subfamily is a part the of mitochondrial transcriptional elongation factor, mtEF-G2. Mitochondrial translation is crucial for maintaining mitochondrial function and mutations in this system lead to a breakdown in the respiratory chain-oxidative phosphorylation system and to impaired maintenance of mitochondrial DNA. In complex with GTP, EF-G promotes the translocation step of ...
CDD:238843	278	EUKprk	Plants:2,Viruses:62,nodiv:1	cd01699, RNA_dep_RNAP, RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D ...
CDD:176454	344	PRK	Bacteria:43,Environmental:1	cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V.  umuC subunit of Pol V.   Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits.  Translesion synthesis is a process that allows the bypass of a variety of DNA lesions.  TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides ...
CDD:176455	404	EUK	Invertebrates:5,Plants:7,Primates:1,Vertebrates:1	cd01701, PolY_Rev1, DNA polymerase Rev1.  Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes.  Translesion synthesis is a process that allows the bypass of a variety of DNA lesions.  TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions.  Rev1 has both structural and enzymatic roles.  Structurally, ...
CDD:176456	359	EUK	Invertebrates:3,Plants:7,Primates:1,Vertebrates:2	cd01702, PolY_Pol_eta, DNA Polymerase eta.  Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase.  Translesion synthesis is a process that allows the bypass of a variety of DNA lesions.  TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions.  Unlike other Y-family members, Pol eta can efficiently ...
CDD:238844	346	EUK	Plants:9	cd01709, RT_like_1, RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA ...
CDD:238845	177	PRK	Bacteria:18,Environmental:1	cd01712, ThiI, ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide.
CDD:238846	173	EUKprk	Bacteria:58,Environmental:2,Invertebrates:6,Phages:4,Plants:12,Primates:1,Vertebrates:1,nodiv:1	cd01713, PAPS_reductase, This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in ...
CDD:238847	202	EUKprk	Bacteria:33,Environmental:1,Invertebrates:2,Plants:3,Primates:1,Vertebrates:2	cd01714, ETF_beta, The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria.  The ...
CDD:238848	168	EUKprk	Bacteria:34,Invertebrates:3,Plants:10,Primates:1,Vertebrates:2	cd01715, ETF_alpha, The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria.  The homologous pair of ...
CDD:212463	60	PRK	Bacteria:33	cd01716, Hfq, bacterial Hfq-like.  Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotropic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in ...
CDD:212464	80	EUK	Invertebrates:23,Plants:17,Primates:1,Vertebrates:3	cd01717, Sm_B, Sm protein B.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212465	79	EUK	Invertebrates:25,Plants:13,Primates:1,Rodents:1,Vertebrates:3	cd01718, Sm_E, Sm protein E.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns ...
CDD:212466	70	EUK	Invertebrates:24,Plants:13,Vertebrates:3	cd01719, Sm_G, Sm protein G.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of ...
CDD:212467	89	EUK	Invertebrates:24,Plants:11,Primates:2,Vertebrates:2	cd01720, Sm_D2, Sm protein D2.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212468	70	EUK	Invertebrates:26,Plants:16,Primates:1,Vertebrates:2	cd01721, Sm_D3, Sm protein D3.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212469	69	EUK	Invertebrates:24,Plants:13,Primates:1,Vertebrates:2	cd01722, Sm_F, Sm protein F.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212470	76	EUK	Invertebrates:21,Plants:17,Vertebrates:3	cd01723, LSm4, Like-Sm protein 4.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is ...
CDD:212471	92	EUK	Invertebrates:22,Plants:11,Primates:1,Vertebrates:3	cd01724, Sm_D1, Sm protein D1.  The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212472	89	EUK	Invertebrates:22,Plants:13,Vertebrates:2	cd01725, LSm2, Like-Sm protein 2.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is ...
CDD:212473	68	EUKprk	Bacteria:10,Invertebrates:18,Plants:16,Primates:1,Vertebrates:2	cd01726, LSm6, Like-Sm protein 6.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ...
CDD:212474	91	EUK	Invertebrates:26,Plants:37,Vertebrates:3	cd01727, LSm8, Like-Sm protein 8.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is ...
CDD:212475	74	EUK	Invertebrates:18,Plants:13,Primates:2,Vertebrates:3	cd01728, LSm1, Like-Sm protein 1.  The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the ...
CDD:212476	89	EUK	Invertebrates:21,Plants:16,Primates:1,Vertebrates:3	cd01729, LSm7, Like-Sm protein 7.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. ...
CDD:212477	82	EUK	Invertebrates:22,Plants:14,Rodents:1,Vertebrates:3	cd01730, LSm3, Like-Sm protein 3.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. ...
CDD:212478	69	EUKprk	Bacteria:21,Environmental:1,Invertebrates:2	cd01731, archaeal_Sm1, archaeal Sm protein 1.  The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ...
CDD:212479	76	EUK	Invertebrates:20,Plants:12,Primates:2,Vertebrates:3	cd01732, LSm5, Like-Sm protein 5.  The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. ...
CDD:212480	78	EUK	Invertebrates:17,Plants:5,Vertebrates:3,nodiv:1	cd01733, LSm10, Like-Sm protein 10.  The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. ...
CDD:212481	72	PRK	Bacteria:206,Environmental:5	cd01734, YlxS_C, Bacillus subtilis YxlS-like, C-terminal domain.  YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
CDD:212482	61	EUK	Invertebrates:7,Vertebrates:4	cd01735, LSm12_N, Like-Sm protein 12, N-terminal domain.  LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel ...
CDD:212483	74	EUK	Invertebrates:11,Plants:9,Primates:1,Vertebrates:2	cd01736, LSm14_N, Like-Sm protein 14, N-terminal domain.  LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a ...
CDD:212484	65	EUK	Invertebrates:8,Plants:3,Vertebrates:3	cd01737, LSm16_N, Like-Sm protein 16, N-terminal domain.  LSm16 (also known as enhancer of decapping-3 or EDC3) has been shown to be associated with an mRNA-decapping complex Dcp1-Dcp2, required for removal of the 5-prime cap from mRNA prior to its degradation from the 5-prime end. EDC3 is believed to be a scaffold for decapping complex formation. It belongs to a family of Sm-like proteins that associate with RNA to form complexes involved ...
CDD:212485	63	EUK	Invertebrates:11,Plants:2,Vertebrates:3	cd01739, LSm11_M, Like-Sm protein 11, middle domain.  The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel ...
CDD:153211	238	miss	miss	cd01740, GATase1_FGAR_AT, Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase.  Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT). FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine ...
CDD:153212	188	miss	miss	cd01741, GATase1_1, Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain.  This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the ...
CDD:153213	181	miss	miss	cd01742, GATase1_GMP_Synthase, Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase.  Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase. GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. Glutamine amidotransferase (GATase) activity catalyse the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate.  GMP synthetase catalyses the amination of the ...
CDD:153214	184	miss	miss	cd01743, GATase1_Anthranilate_Synthase, Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase.  Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase (ASase). This group contains proteins similar to para-aminobenzoate (PABA) synthase and ASase.  These enzymes catalyze similar reactions and produce similar products, PABA and ortho-aminobenzoate (anthranilate). Each enzyme is composed of non-identical subunits: a ...
CDD:153215	178	miss	miss	cd01744, GATase1_CPSase, Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II.  This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II.  CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete ...
CDD:153216	189	miss	miss	cd01745, GATase1_2, Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain.  This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the ...
CDD:153217	235	miss	miss	cd01746, GATase1_CTP_Synthase, Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase.  Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase (CTP). CTP is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. CTPs produce CTP from UTP and glutamine and regulate intracellular CTP levels through interactions with four ribonucleotide triphosphates. The enzyme exists as a dimer of ...
CDD:153218	273	miss	miss	cd01747, GATase1_Glutamyl_Hydrolase, Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase.  Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. GATase activity involves the removal of the ammonia group from a ...
CDD:153219	198	miss	miss	cd01748, GATase1_IGP_Synthase, Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS).  Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS). IGPS incorporates ammonia derived from glutamine into N1-[(5'-phosphoribulosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to form 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR) and imidazole ...
CDD:153220	183	miss	miss	cd01749, GATase1_PB, Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis.  Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis. Glutamine amidotransferase (GATase) activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate.  This group contains proteins like Bacillus subtilus YaaE  and Plasmodium ...
CDD:153221	194	miss	miss	cd01750, GATase1_CobQ, Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ).  Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ).  CobQ plays a role in cobalamin biosythesis.   CobQ catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin.  CobQ belongs to the triad family of amidotransferases.  Two of the three residues of the catalytic ...
CDD:238849	137	EUK	Plants:11	cd01751, PLAT_LH2, PLAT/ LH2 domain of plant lipoxygenase related proteins. Lipoxygenases are nonheme, nonsulfur iron dioxygenases that act on lipid substrates containing one or more (Z,Z)-1,4-pentadiene moieties. In plants, the immediate products are involved in defense mechanisms against pathogens and may be precursors of metabolic regulators. The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
CDD:238850	120	EUK	Invertebrates:2,Primates:1,Vertebrates:2	cd01752, PLAT_polycystin, PLAT/LH2 domain of polycystin-1 like proteins.  Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant ...
CDD:238851	113	EUK	Primates:1,Rodents:2,Vertebrates:4	cd01753, PLAT_LOX, PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
CDD:238853	120	EUK	Invertebrates:1,Mammals:2,Primates:1,Vertebrates:5	cd01755, PLAT_lipase, PLAT/ LH2 domain present in connection with a lipase domain. This family contains two major subgroups, the  lipoprotein lipase (LPL) and the pancreatic triglyceride lipase.  LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs). The central role of triglyceride lipases is in energy production. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or ...
CDD:238854	120	EUK	Invertebrates:1,Mammals:1,Primates:2,Vertebrates:3	cd01756, PLAT_repeat, PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.
CDD:238856	137	miss	miss	cd01758, PLAT_LPL, PLAT/ LH2 domain present in lipoprotein lipase (LPL).  LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs) and has therefeore has a profound influence on triglyceride and high-density lipoprotein (HDL) cholesterol levels in the blood. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or membrane bound proteins.
CDD:176358	72	miss	miss	cd01760, RBD, Ubiquitin-like domain of RBD-like S/T kinases.  The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
CDD:176359	87	miss	miss	cd01763, Sumo, Small ubiquitin-related modifier (SUMO).  Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability.  SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) ...
CDD:176360	94	miss	miss	cd01764, Urm1, Urm1-like ubuitin domain.  Urm1 (Ubiquitin-Related Modifier1)  The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast.  The Urm1 fold is found only in eukaryotes.
CDD:176362	77	miss	miss	cd01767, UBX, UBX (ubiquitin regulatory X) domain.  The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome ...
CDD:176363	87	miss	miss	cd01768, RA, RA (Ras-associating) ubiquitin domain.  The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
CDD:176364	69	miss	miss	cd01769, UBL, Ubiquitin-like domain of UBL.  UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also ...
CDD:176365	79	miss	miss	cd01770, p47_UBX, p47-like ubiquitin domain.  p47_UBX  p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events.  p47 has carboxy-terminal SEP and UBX domains.  The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus ...
CDD:176400	77	miss	miss	cd01805, RAD23_N, Ubiquitin-like domain of RAD23.  RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
CDD:176404	72	miss	miss	cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein.  Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus.  Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
CDD:176407	71	miss	miss	cd01812, BAG1_N, Ubiquitin-like domain of BAG1.  BAG1_N  N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein.  This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
CDD:132836	155	EUKprk	Bacteria:1,Invertebrates:1,Plants:2,Primates:1	cd01819, Patatin_and_cPLA2, Patatins and Phospholipases.  Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have ...
CDD:238858	214	EUKprk	Bacteria:8,Invertebrates:5,Mammals:1,Primates:1,Vertebrates:2	cd01820, PAF_acetylesterase_like, PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like ...
CDD:238859	198	EUKprk	Bacteria:22,Plants:6	cd01821, Rhamnogalacturan_acetylesterase_like, Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted ...
CDD:238860	177	PRK	Bacteria:73,Environmental:1	cd01822, Lysophospholipase_L1_like, Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.
CDD:238861	259	EUKprk	Bacteria:20,Invertebrates:1,Plants:9	cd01823, SEST_like, SEST_like. A family of secreted SGNH-hydrolases similar to Streptomyces scabies esterase (SEST), a causal agent of the potato scab disease, which hydrolyzes a specific ester bond in suberin, a plant lipid. The tertiary fold of this enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles two of the three components of ...
CDD:238862	288	EUK	Invertebrates:5,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd01824, Phospholipase_B_like, Phospholipase-B_like. This subgroup of the SGNH-family of lipolytic enzymes may have both esterase and phospholipase-A/lysophospholipase activity.  It's members may be involved in the conversion of phosphatidylcholine to fatty acids and glycerophosphocholine, perhaps in the context of dietary lipid uptake. Members may be membrane proteins. The tertiary fold of the SGNH-hydrolases is ...
CDD:238863	189	PRK	Bacteria:14	cd01825, SGNH_hydrolase_peri1, SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238866	169	PRK	Bacteria:12,nodiv:1	cd01828, sialate_O-acetylesterase_like2, sialate_O-acetylesterase_like subfamily of the SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238867	200	PRK	Bacteria:21,nodiv:1	cd01829, SGNH_hydrolase_peri2, SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238868	204	EUKprk	Bacteria:18,Plants:4	cd01830, XynE_like, SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the ...
CDD:238869	169	EUKprk	Bacteria:16,Invertebrates:2,Plants:6	cd01831, Endoglucanase_E_like, Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
CDD:238870	185	PRK	Bacteria:23	cd01832, SGNH_hydrolase_like_1, Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. Myxobacterial members of this subfamily have been reported to be involved in ...
CDD:238871	157	EUKprk	Bacteria:10,Plants:7	cd01833, XynB_like, SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238872	191	PRK	Bacteria:16	cd01834, SGNH_hydrolase_like_2, SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238873	193	PRK	Bacteria:13	cd01835, SGNH_hydrolase_like_3, SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238874	191	PRK	Bacteria:25	cd01836, FeeA_FeeB_like, SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it turn are loaded onto the acyl carrier protein FeeL. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the ...
CDD:238875	315	EUK	Plants:13	cd01837, SGNH_plant_lipase_like, SGNH_plant_lipase_like, a plant specific subfamily of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238876	199	EUKprk	Bacteria:6,Invertebrates:2,Plants:14,Primates:1,Vertebrates:2	cd01838, Isoamyl_acetate_hydrolase_like, Isoamyl-acetate hydrolyzing esterase-like proteins. SGNH_hydrolase subfamily similar to the Saccharomyces cerevisiae IAH1. IAH1 may be the major esterase that hydrolyses isoamyl acetate in sake mash.  The SGNH-family of hydrolases is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase ...
CDD:238877	208	EUKprk	Bacteria:14,Invertebrates:2,nodiv:1	cd01839, SGNH_arylesterase_like, SGNH_hydrolase subfamily, similar to arylesterase (7-aminocephalosporanic acid-deacetylating enzyme) of A. tumefaciens. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine ...
CDD:238878	150	PRK	Bacteria:29	cd01840, SGNH_hydrolase_yrhL_like, yrhL-like subfamily of SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in ...
CDD:238879	174	EUKprk	Bacteria:11,Plants:1	cd01841, NnaC_like, NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases. E. coli NnaC appears to be involved in polysaccharide synthesis.
CDD:238881	177	PRK	Bacteria:12	cd01844, SGNH_hydrolase_like_6, SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
CDD:238882	270	EUKprk	Bacteria:33,Invertebrates:1,Plants:7	cd01846, fatty_acyltransferase_like, Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Might catalyze fatty acid transfer between phosphatidylcholine ...
CDD:238883	281	PRK	Bacteria:18,nodiv:1	cd01847, Triacylglycerol_lipase_like, Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Members of this subfamily might hydrolyze triacylglycerol into diacylglycerol ...
CDD:206746	146	EUKprk	Bacteria:3,Invertebrates:4,Plants:3,Primates:1	cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related GTPases.  These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.
CDD:206649	275	EUK	Invertebrates:5,Plants:16,Primates:1,Vertebrates:3	cd01850, CDC_Septin, CDC/Septin GTPase family.  Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and ...
CDD:206650	224	EUK	Invertebrates:9,Plants:11,Primates:1,Vertebrates:4	cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal domain).  Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity ...
CDD:206651	201	EUK	Plants:3,Primates:1,Rodents:2,Vertebrates:2	cd01852, AIG1, AvrRpt2-Induced Gene 1 (AIG1).  This group represents Arabidoposis protein AIG1 (avrRpt2-induced gene 1) that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This ...
CDD:206652	248	EUK	Invertebrates:1,Plants:6	cd01853, Toc34_like, Translocon at the Outer-envelope membrane of Chloroplasts 34-like (Toc34-like).  The Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts) family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five ...
CDD:206747	211	EUKprk	Bacteria:388,Environmental:3,Invertebrates:2,Plants:7	cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases.  YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be ...
CDD:206748	191	EUKprk	Bacteria:5,Invertebrates:8,Plants:8,Primates:1	cd01855, YqeH, Circularly permuted YqeH GTPase.  YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs ...
CDD:206749	171	EUKprk	Bacteria:40,Invertebrates:7,Plants:14,Primates:1,Vertebrates:2	cd01856, YlqF, Circularly permuted YlqF GTPase.  Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including ...
CDD:206750	140	EUK	Invertebrates:9,Plants:5,Primates:1,Vertebrates:2	cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras GTPases.  Human HSR1 is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 ...
CDD:206751	157	EUK	Invertebrates:17,Plants:12,Vertebrates:2	cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases.  Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand ...
CDD:206752	157	PRK	Bacteria:10,Environmental:1	cd01859, MJ1464, An uncharacterized, circularly permuted subfamily of the Ras GTPases.  This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.
CDD:206653	163	EUK	Invertebrates:16,Plants:10,Primates:1,Rodents:1,Vertebrates:4	cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion.  The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early ...
CDD:206654	161	EUK	Invertebrates:12,Plants:6,Primates:1,Vertebrates:2	cd01861, Rab6, Rab GTPase family 6 (Rab6).  Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through ...
CDD:206655	172	EUK	Invertebrates:11,Plants:6,Primates:1,Rodents:1,Vertebrates:3	cd01862, Rab7, Rab GTPase family 7 (Rab7).  Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration ...
CDD:206656	161	EUK	Invertebrates:8,Plants:3,Vertebrates:3	cd01863, Rab18, Rab GTPase family 18 (Rab18).  Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase ...
CDD:206659	167	EUK	Invertebrates:7,Plants:6,Primates:1,Rodents:1,Vertebrates:4	cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13).  Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation ...
CDD:206660	165	EUK	Invertebrates:14,Plants:10,Vertebrates:3	cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25.  Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi ...
CDD:206665	170	EUKprk	Bacteria:26,Environmental:1,Invertebrates:7,Plants:7,Primates:1	cd01876, YihA_EngB, YihA (EngB) GTPase family.  The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be ...
CDD:206666	204	EUKprk	Bacteria:61,Environmental:2,Invertebrates:2,Plants:2,Vertebrates:2	cd01878, HflX, HflX GTPase family.  HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.
CDD:206667	159	PRK	Bacteria:69,Environmental:2	cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.  Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron ...
CDD:206668	167	EUKprk	Bacteria:1,Invertebrates:2	cd01881, Obg_like, Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1.  The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the ...
CDD:206670	219	EUKprk	Bacteria:1,Environmental:2,Invertebrates:15,Plants:14,Primates:1,Vertebrates:3,nodiv:1	cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein family.  EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This ...
CDD:206671	195	EUKprk	Bacteria:10,Invertebrates:5,Mammals:1,Plants:8,Primates:1	cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.  EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from ...
CDD:206672	218	EUKprk	Bacteria:2,Invertebrates:4,Plants:2	cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.  Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast ...
CDD:206673	270	EUKprk	Bacteria:7,Invertebrates:4,Plants:5	cd01886, EF-G, Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis.  Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, ...
CDD:206674	169	EUKprk	Bacteria:18,Invertebrates:6,Mammals:1,Plants:5,Rodents:1	cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family.  IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including ...
CDD:206675	197	EUKprk	Bacteria:1,Invertebrates:1,Plants:2	cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2 gamma).  eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the ...
CDD:206676	192	EUKprk	Bacteria:2,Invertebrates:5,Vertebrates:1	cd01889, SelB_euk, SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with ...
CDD:206677	179	EUKprk	Bacteria:4,Invertebrates:3,Plants:1,Vertebrates:1	cd01890, LepA, LepA also known as Elongation Factor 4 (EF4).  LepA (also known as elongation factor 4, EF4) belongs to the GTPase family and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic ...
CDD:206678	194	EUKprk	Bacteria:13,Invertebrates:3	cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases.  BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since ...
CDD:206679	180	EUK	Invertebrates:2,Mammals:1,Plants:13,Primates:1,Rodents:1,Vertebrates:4	cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.  Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho ...
CDD:206680	168	EUK	Invertebrates:1,Plants:2,Primates:1,Vertebrates:1	cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.  Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial ...
CDD:206681	157	EUKprk	Bacteria:36,Environmental:2,Invertebrates:4,Plants:1	cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.  This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. ...
CDD:206682	174	EUKprk	Bacteria:14,Invertebrates:1	cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.  This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact ...
CDD:206683	233	EUKprk	Bacteria:4,Invertebrates:5,Plants:8,Primates:1,Vertebrates:2	cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).  The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various ...
CDD:206684	167	EUKprk	Bacteria:12,Invertebrates:9,Plants:5,Primates:1,Vertebrates:2	cd01897, NOG, Nucleolar GTP-binding protein (NOG).  NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell ...
CDD:206685	170	EUKprk	Bacteria:32,Environmental:3,Invertebrates:9,Mammals:1,Plants:10,Primates:1,Vertebrates:3	cd01898, Obg, Obg GTPase.  The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the ...
CDD:206686	318	EUKprk	Bacteria:3,Invertebrates:5,Plants:4	cd01899, Ygr210, Ygr210 GTPase.  Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, ...
CDD:206687	274	EUKprk	Bacteria:21,Invertebrates:4,Plants:10,Primates:1,Vertebrates:3	cd01900, YchF, YchF GTPase.  YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and ...
CDD:238884	164	EUKprk	Bacteria:144,Environmental:3,Invertebrates:35,Mammals:1,Plants:23,Primates:1,Vertebrates:9,nodiv:1	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, ...
CDD:238885	291	miss	miss	cd01902, Ntn_CGH, Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile.  CGH is present in a number of probiotic microbial organisms that inhabit the gut.  CGH has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which CGH belongs.
CDD:238886	231	miss	miss	cd01903, Ntn_AC_NAAA, AC_NAAA This conserved domain includes two closely related proteins, acid ceramidase (AC, also known as N-acylsphingosine amidohydrolase), and N-acylethanolamine-hydrolyzing acid amidase (NAAA).  AC catalyzes the hydrolysis of ceramide to sphingosine and fatty acid. Ceramide is required for the biosynthesis of most sphingolipids and plays an important role in many signal transduction pathways by inducing apoptosis and/or arresting cell growth. An ...
CDD:238887	182	miss	miss	cd01906, proteasome_protease_HslV, proteasome_protease_HslV. This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their ...
CDD:238888	249	miss	miss	cd01907, GlxB, Glutamine amidotransferases class-II (Gn-AT)_GlxB-type.  GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases including glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase),  asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and ...
CDD:238889	257	miss	miss	cd01908, YafJ, Glutamine amidotransferases class-II (Gn-AT)_YafJ-type.  YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea.  YafJ has a conserved structural fold similar to those of other class II glutamine amidotransferases including lucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase),  asparagine synthetase B (AsnB), beta lactam ...
CDD:238891	224	miss	miss	cd01910, Wali7, This domain is present in Wali7, a protein of unknown function, expressed in wheat and induced by aluminum.  Wali7 has a single domain similar to the glutamine amidotransferase domain of glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase),  asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS).  The Wali7 domain is also somewhat similar ...
CDD:238892	209	EUKprk	Bacteria:2,Mammals:1	cd01911, proteasome_alpha, proteasome alpha subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:238893	189	EUKprk	Bacteria:1,Mammals:1,Plants:1	cd01912, proteasome_beta, proteasome beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal ...
CDD:238894	171	PRK	Bacteria:1	cd01913, protease_HslV, Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases.  HslV has a ...
CDD:238895	423	EUKprk	Bacteria:15,Invertebrates:2,nodiv:1	cd01914, HCP, Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a central beta-sheet flanked by alpha-helices. HCP contains two iron-sulfur clusters, one of which is a [Fe4-S4] cubane cluster similar to that of carbon monoxide dehydrogenase ...
CDD:238896	613	PRK	Bacteria:14	cd01915, CODH, Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to that of hybrid cluster protein (HCP) and a Ni-Fe-S center (C-cluster) where carbon monoxide oxidation occurs.  Bifunctional CODH forms a heterotetramer with acetyl-CoA synthase (ACS) consisting of two ...
CDD:238899	149	PRK	Bacteria:15	cd01918, HprK_C, HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase ...
CDD:238902	166	EUK	Invertebrates:3,Plants:6,Primates:1,Vertebrates:1	cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM). This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The ...
CDD:238905	176	EUKprk	Bacteria:3,Invertebrates:1,Plants:2	cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40.  Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator ...
CDD:238907	164	EUKprk	Bacteria:3,Invertebrates:12,Mammals:1,Plants:8,Primates:1,Rodents:1,Vertebrates:3	cd01926, cyclophilin_ABH_like, cyclophilin_ABH_like: Cyclophilin  A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline ...
CDD:238910	229	miss	miss	cd01935, Ntn_CGH_like, Choloylglycine hydrolase (CGH)_like. This family of choloylglycine hydrolase-like proteins includes conjugated bile acid hydrolase (CBAH), penicillin V acylase (PVA), acid ceramidase (AC), and N-acylethanolamine-hydrolyzing acid amidase (NAAA) which cleave non-peptide carbon-nitrogen bonds in bile salt constituents.  These enzymes have an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which they belong.  This ...
CDD:238911	469	miss	miss	cd01936, Ntn_CA, Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively.  While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the ...
CDD:238912	254	PRK	Bacteria:3,Environmental:1	cd01937, ribokinase_group_D, Ribokinase-like subgroup D.  Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily.  Its oligomerization state is unknown at this time.
CDD:238913	445	EUKprk	Bacteria:3,Invertebrates:3,Primates:1,Vertebrates:2	cd01938, ADPGK_ADPPFK, ADP-dependent glucokinase (ADPGK) and phosphofructokinase (ADPPFK). ADPGK and ADPPFK are proteins that rely on ADP rather than ATP to donate a phosphoryl group.  They are found in certain hyperthermophilic archaea and in higher eukaryotes.  A functional ADPGK has been characterized in mouse and is assumed to be desirable during ischemia/hypoxia.  ADPGK and ADPPFK contain a large and a small domain ...
CDD:238914	290	EUK	Invertebrates:2,Plants:3,Primates:1,Vertebrates:2	cd01939, Ketohexokinase, Ketohexokinase (fructokinase, KHK) catalyzes the phosphorylation of fructose to fructose-1-phosphate (F1P), the first step in the metabolism of dietary fructose.  KHK can also phosphorylate several other furanose sugars.  It is found in higher eukaryotes where it is believed to function as a dimer and requires K(+) and ATP to be active.  In humans, hepatic KHK deficiency causes fructosuria, a benign ...
CDD:238915	264	PRK	Bacteria:3	cd01940, Fructoselysine_kinase_like, Fructoselysine kinase-like.  Fructoselysine is a fructoseamine formed by glycation, a non-enzymatic reaction of glucose with a primary amine followed by an Amadori rearrangement, resulting in a protein that is modified at the amino terminus and at the lysine side chains. Fructoseamines are typically metabolized by fructoseamine-3-kinase, especially in higher eukaryotes. In E. coli, fructoselysine kinase has been shown in vitro to ...
CDD:238916	288	EUKprk	Bacteria:7,Invertebrates:2,Plants:7,Vertebrates:1	cd01941, YeiC_kinase_like, YeiC-like sugar kinase.  Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time.
CDD:238917	279	PRK	Bacteria:16,nodiv:1	cd01942, ribokinase_group_A, Ribokinase-like subgroup A.  Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily.  Its oligomerization state is unknown at this time.
CDD:238918	328	EUK	Plants:11	cd01943, MAK32, MAK32 kinase.  MAK32 is a protein found primarily in fungi that is necessary for the structural stability of L-A particles.  The L-A virus particule is a specialized compartment for the transcription and replication of double-stranded RNA, known to infect yeast and other fungi.  MAK32 is part of the host machinery used by the virus to multiply.
CDD:238920	284	EUKprk	Bacteria:10,Plants:2	cd01945, ribokinase_group_B, Ribokinase-like subgroup B.  Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily.  Its oligomerization state is unknown at this time. .
CDD:238922	265	PRK	Bacteria:5	cd01947, Guanosine_kinase_like, Guanosine kinase-like sugar kinases.  Found in bacteria and archaea, the guanosine kinase-like group is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time.
CDD:238923	240	PRK	Bacteria:102,nodiv:2	cd01948, EAL, EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2).  The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.
CDD:143635	158	PRK	Bacteria:178,Environmental:5,nodiv:1	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain.  Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with ...
CDD:173886	223	EUKprk	Bacteria:25,Invertebrates:1,Mammals:1,Plants:6	cd01951, lectin_L-type, legume lectins.  The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind.  This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor.  L-type lectins have a dome-shaped beta-barrel ...
CDD:238924	85	EUK	Plants:8	cd01958, HPS_like, HPS_like: Hydrophobic Protein from Soybean (HPS)-like subfamily; composed of proteins with similarity to HPS, a small hydrophobic protein with unknown function related to cereal-type alpha-amylase inhibitors and lipid transfer proteins. In addition to HPS, members of this subfamily include a hybrid proline-rich protein (HyPRP) from maize, a dark-inducible protein (LeDI-2) from Lithospermum erythrorhizon, maize ZRP3 protein, and rice RcC3 protein. ...
CDD:238925	66	EUK	Plants:11	cd01959, nsLTP2, nsLTP2: Non-specific lipid-transfer protein type 2 (nsLTP2) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular weight, and ...
CDD:238926	89	EUK	Invertebrates:1,Plants:37	cd01960, nsLTP1, nsLTP1: Non-specific lipid-transfer protein type 1 (nsLTP1) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular ...
CDD:238927	428	miss	miss	cd01965, Nitrogenase_MoFe_beta_like, Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia.  This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent  nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase ...
CDD:238928	417	miss	miss	cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE.  NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it ...
CDD:238929	406	miss	miss	cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like: Nitrogenase MoFe protein, alpha subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia.  Three genetically distinct types of nitrogenase systems are known to exist: a molybdenum-dependent  nitrogenase (Mo-nitrogenase), a vanadium dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component ...
CDD:238930	410	miss	miss	cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN.  NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it ...
CDD:238934	435	miss	miss	cd01974, Nitrogenase_MoFe_beta, Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems.  Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2).  MoFe is an alpha2beta2 tetramer. This group contains the beta subunit of the MoFe protein. Each ...
CDD:238939	430	miss	miss	cd01981, Pchlide_reductase_B, Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR).  Angiosperms contain only LPOR, cyanobacteria, ...
CDD:238941	99	EUKprk	Bacteria:288,Environmental:6,Invertebrates:17,Phages:2,Plants:21,Primates:1,Rodents:1,Vertebrates:5,nodiv:2	cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
CDD:238942	86	EUKprk	Bacteria:5,Vertebrates:1	cd01984, AANH_like, Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide.
CDD:238943	181	miss	miss	cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria.  The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The alpha ...
CDD:238944	103	EUKprk	Bacteria:8,Plants:3	cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which  binds to Adenosine group..
CDD:238945	124	miss	miss	cd01987, USP_OKCHK, USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the ...
CDD:238946	132	miss	miss	cd01988, Na_H_Antiporter_C, The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this ...
CDD:238947	146	miss	miss	cd01989, STK_N, The N-terminal domain of Eukaryotic Serine Threonine  kinases. The Serine Threonine  kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain  is predicted to be involved in ATP binding.
CDD:238948	202	PRK	Bacteria:20	cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.
CDD:238949	269	EUKprk	Bacteria:58,Environmental:2,Invertebrates:5,Plants:9,Primates:1,Vertebrates:2,Viruses:1,nodiv:1	cd01991, Asn_Synthase_B_C, The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B  catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. The three-dimensional architecture ...
CDD:238950	185	EUKprk	Bacteria:80,Plants:10,Synthetic:1,nodiv:2	cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This domain has  a strongly conserved ...
CDD:238951	185	EUKprk	Bacteria:24,Invertebrates:7,Plants:5	cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins is predicted to  bind ATP. This domainhas  a strongly conserved motif SGGKD at the N terminus.
CDD:238952	194	EUKprk	Bacteria:14,Invertebrates:4,Plants:4,Primates:1,Vertebrates:1	cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins is predicted to  bind ATP. This domainhas  a strongly conserved motif SGGKD at the N terminus.
CDD:238953	169	PRK	Bacteria:27,Environmental:1,Phages:2	cd01995, ExsB, ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, ...
CDD:238954	154	PRK	Bacteria:13,Environmental:2	cd01996, Alpha_ANH_like_III, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins is predicted to  bind ATP. This domain has  a strongly conserved motif SGGKD at the N terminus.
CDD:238955	295	EUKprk	Bacteria:17,Environmental:2,Invertebrates:3,Plants:2,Vertebrates:1	cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched between helical layers. It has a signature nucleotide-binding motif, or P-loop, at the end of the first-beta strand.The dimerization ...
CDD:238956	349	EUKprk	Bacteria:41,Invertebrates:4,Plants:9,Primates:1,Vertebrates:2	cd01998, tRNA_Me_trans, tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. This family of enzyme only presents in bacteria and eukaryote. The  archaeal counterpart of this enzyme performs same function, but is ...
CDD:238957	385	EUKprk	Bacteria:30,Environmental:1,Invertebrates:1,Plants:4,Primates:1,Vertebrates:2	cd01999, Argininosuccinate_Synthase, Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate .  In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting ...
CDD:238958	293	EUKprk	Bacteria:73,Environmental:1,Invertebrates:9,Plants:10,Primates:1,Vertebrates:3	cd02000, TPP_E1_PDC_ADC_BCADC, Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). PDC catalyzes the irreversible ...
CDD:238960	178	EUKprk	Bacteria:28,Environmental:1,Plants:3	cd02002, TPP_BFDC, Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors.
CDD:238961	205	PRK	Bacteria:12	cd02003, TPP_IolD, Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism.
CDD:238962	172	EUKprk	Bacteria:19,Invertebrates:6,Plants:7,Primates:1,Vertebrates:3,nodiv:1	cd02004, TPP_BZL_OCoD_HPCL, Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as ...
CDD:238963	183	EUKprk	Bacteria:20,Invertebrates:2,Plants:17	cd02005, TPP_PDC_IPDC, Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of pyruvate to acetaldehyde and CO2. It is able to utilize other 2-oxo acids as substrates. In plants and various plant-associated bacteria, IPDC plays a role in the ...
CDD:238965	195	EUKprk	Bacteria:15,Environmental:1,Invertebrates:1,Plants:3	cd02007, TPP_DXS, Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS catalyzes a transketolase-type condensation of pyruvate with D-glyceraldehyde-3-phosphate to form ...
CDD:238966	178	PRK	Bacteria:25	cd02008, TPP_IOR_alpha, Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
CDD:238967	175	EUKprk	Bacteria:24,Plants:2	cd02009, TPP_SHCHC_synthase, Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal ...
CDD:238968	177	PRK	Bacteria:7	cd02010, TPP_ALS, Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2 molecules of pyruvate to acetolactate and carbon dioxide. ALS does not contain FAD, and requires TPP and a divalent metal cation for activity.
CDD:238970	255	EUKprk	Bacteria:41,Invertebrates:11,Plants:8,Vertebrates:3,nodiv:1	cd02012, TPP_TK, Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. In addition, the enzyme plays a ...
CDD:238972	178	PRK	Bacteria:20	cd02014, TPP_POX, Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. It requires FAD in addition to TPP and a divalent cation as cofactors.
CDD:238973	186	EUKprk	Bacteria:41,Plants:7	cd02015, TPP_AHAS, Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate. 2-Acetolactate is the precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to ...
CDD:238974	265	EUKprk	Bacteria:10,Invertebrates:10,Plants:3,Primates:1,Vertebrates:3	cd02016, TPP_E1_OGDC_like, Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle.
CDD:238975	386	EUKprk	Bacteria:16,Environmental:1,Invertebrates:1	cd02017, TPP_E1_EcPDC_like, Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative decarboxylation of pyruvate and the subsequent acetylation of coenzyme A to acetyl-CoA. The E1 component of PDC catalyzes the first step of the multistep process, ...
CDD:238977	69	EUKprk	Bacteria:3,Plants:7,Primates:1	cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of ...
CDD:238978	147	PRK	Bacteria:38,Environmental:1,Synthetic:1	cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
CDD:238979	150	EUKprk	Bacteria:17,Invertebrates:2,Plants:11,Synthetic:1,Vertebrates:1,nodiv:1	cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
CDD:238980	179	EUKprk	Bacteria:60,Environmental:3,Invertebrates:4,Plants:10,Primates:1,Synthetic:1,Vertebrates:4,nodiv:2	cd02022, DPCK, Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
CDD:238981	198	EUKprk	Bacteria:9,Invertebrates:5,Plants:5,Vertebrates:3	cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the ...
CDD:238982	187	EUK	Invertebrates:3,Plants:13,Primates:1,Rodents:2,Vertebrates:5	cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the ...
CDD:238983	220	PRK	Bacteria:2	cd02025, PanK, Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
CDD:238984	273	EUKprk	Bacteria:5,Invertebrates:1,Plants:10	cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
CDD:238985	149	EUKprk	Bacteria:44,Environmental:2,Invertebrates:2,Plants:13,Primates:1,Synthetic:1,Vertebrates:5,nodiv:1	cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.
CDD:238986	179	EUKprk	Bacteria:10,Invertebrates:2,Plants:3	cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
CDD:238991	116	miss	miss	cd02034, CooC, The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are ...
CDD:238992	217	miss	miss	cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is ...
CDD:238993	179	miss	miss	cd02036, MinD, Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related ...
CDD:238994	169	miss	miss	cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
CDD:238995	139	miss	miss	cd02038, FleN-like, FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
CDD:185678	143	PRK	Bacteria:6	cd02039, cytidylyltransferase_like, Cytidylyltransferase-like domain.  Cytidylyltransferase-like domain. Many of these proteins are known to use CTP or ATP and release pyrophosphate. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the ...
CDD:238996	270	miss	miss	cd02040, NifH, NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 ...
CDD:238997	104	miss	miss	cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds ...
CDD:239004	364	PRK	Bacteria:9	cd02049, bacterial_SERPIN, SERine Proteinase INhibitors (serpins), prokaryotic subgroup. Little information about specific functions is available for this subgroup, most likely they are inhibitory members of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors.
CDD:239011	361	EUK	Primates:1,Rodents:2,Vertebrates:5	cd02056, alpha-1-antitrypsin_like, alpha-1-antitrypsin_like. This family contains a variety of different members of clade A of the serpin superfamily. They include the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and noninhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational ...
CDD:239015	122	EUKprk	Bacteria:52,Environmental:2,Invertebrates:1,Primates:1	cd02062, Nitro_FMN_reductase, Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer,  utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH ...
CDD:185679	180	EUKprk	Bacteria:69,Environmental:1,Plants:1	cd02064, FAD_synthetase_N, FAD synthetase, N-terminal domain of the bifunctional enzyme.  FAD synthetase_N.  N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities.  The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain ...
CDD:239016	125	EUKprk	Bacteria:66,Invertebrates:1,Primates:1,Rodents:1,Vertebrates:1	cd02065, B12-binding_like, B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the ...
CDD:239017	72	EUKprk	Bacteria:39,Invertebrates:16,Plants:22,Primates:2,Rodents:2,Vertebrates:5	cd02066, GRX_family, Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular ...
CDD:239018	119	miss	miss	cd02067, B12-binding, B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away ...
CDD:239019	127	miss	miss	cd02068, radical_SAM_B12_BD, B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
CDD:239020	213	miss	miss	cd02069, methionine_synthase_B12_BD, B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
CDD:239021	201	miss	miss	cd02070, corrinoid_protein_B12-BD, B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
CDD:239022	122	miss	miss	cd02071, MM_CoA_mut_B12_BD, methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to ...
CDD:259797	110	EUKprk	Bacteria:9,Invertebrates:1,Plants:2,Primates:1,Rodents:2	cd02106, SPFH_like, core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster ...
CDD:239026	185	miss	miss	cd02108, bact_SO_family_Moco, bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of ...
CDD:239027	180	PRK	Bacteria:1	cd02109, arch_bact_SO_family_Moco, bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ...
CDD:239028	317	miss	miss	cd02110, SO_family_Moco_dimer, Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). .
CDD:239029	365	miss	miss	cd02111, eukary_SO_Moco, molybdopterin binding domain of sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Common features of all known members of the sulfite oxidase (SO) family of molybdopterin binding domains are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the ...
CDD:239033	248	EUKprk	Bacteria:11,Invertebrates:1,Plants:2,Primates:1	cd02115, AAK, Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that phosphorylate a variety of amino acid substrates. These kinases catalyze the formation of phosphoric anhydrides, generally with a carboxylate, and use ATP as the ...
CDD:153139	60	EUKprk	Bacteria:348,Environmental:8,Invertebrates:11,Mammals:1,Plants:33,Primates:1,Vertebrates:3,nodiv:1	cd02116, ACT, ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme.  Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has ...
CDD:239034	212	miss	miss	cd02117, NifH_like, This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the  protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
CDD:239035	126	EUKprk	Bacteria:14,Plants:9	cd02120, PA_subtilisin_like, PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a ...
CDD:239036	220	EUKprk	Bacteria:5,Invertebrates:3,Plants:14,Primates:1,Vertebrates:3	cd02121, PA_GCPII_like, PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like. This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or ...
CDD:239037	138	EUK	Invertebrates:6,Primates:1,Rodents:1,Vertebrates:5	cd02122, PA_GRAIL_like, PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like. This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, ...
CDD:239038	153	EUK	Invertebrates:8,Mammals:1,Plants:2,Primates:1,Rodents:1,Vertebrates:3	cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger ...
CDD:239039	129	EUK	Plants:11	cd02124, PA_PoS1_like, PA_PoS1_like: Protease-associated (PA) domain PoS1-like. This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the ...
CDD:239041	126	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd02126, PA_EDEM3_like, PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In ...
CDD:239043	183	EUK	Mammals:1,Primates:1,Vertebrates:3	cd02128, PA_TfR, PA_TfR: Protease-associated domain containing proteins like transferrin receptor (TfR). This group contains various PA domain-containing proteins similar to human TfR1 and TfR2. TfR1 and TfR2 are type II membrane proteins, belonging to the peptidase M28 family. TfR1 is homodimeric, widely expressed, and a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and this ...
CDD:239044	120	EUK	Invertebrates:1,Primates:1,Vertebrates:4	cd02129, PA_hSPPL_like, PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like. This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha ...
CDD:239045	122	EUK	Plants:15	cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. ...
CDD:239048	143	PRK	Bacteria:25	cd02133, PA_C5a_like, PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. ...
CDD:239049	61	PRK	Bacteria:36	cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is ...
CDD:239050	160	PRK	Bacteria:45,nodiv:1	cd02135, Arsenite_oxidase, Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-proteobacterial strain is able to oxidize arsenite to arsenate.
CDD:239051	178	PRK	Bacteria:32,Environmental:1,nodiv:1	cd02136, Nitroreductase, Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source of reducing equivalents in an obligatory two-election transfer mechanism.  The enzyme is typically a homodimer. Members of this family are also called NADH ...
CDD:239052	148	PRK	Bacteria:34	cd02137, Nitroreductase_1, Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a homodimer. Members of this family are ...
CDD:239053	181	PRK	Bacteria:15,nodiv:1	cd02138, Nitroreductase_2, Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a homodimer. Members of this ...
CDD:239054	164	PRK	Bacteria:14	cd02139, Nitroreductase_3, Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a homodimer. Members of this family are ...
CDD:239055	192	EUKprk	Bacteria:20,Invertebrates:1,Plants:9,nodiv:1	cd02140, Nitroreductase_4, Nitroreductase-like family 4.  A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a ...
CDD:239056	180	EUKprk	Bacteria:49,Environmental:1,Invertebrates:1,Plants:1,nodiv:1	cd02142, mcbC-like_oxidoreductase, This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin biosynthesis pathway, mtsD, part of the myxothiozol biosynthesis pathway; indC, part of the indigoidine biosynthesis pathway ...
CDD:239057	147	EUKprk	Bacteria:11,Invertebrates:1	cd02143, NADH_nitroreductase, Nitroreductase family. Members of this family utilize FMN as a cofactor. This family is involved in the reduction of flavin or nitroaromatic compounds by using NAD(P)H as electron donor in a obligatory two-electron transfer. Nitrogenase is homodimer. Each subunit contains one FMN molecule. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
CDD:239058	193	EUKprk	Bacteria:5,Invertebrates:3,Vertebrates:3	cd02144, iodotyrosine_dehalogenase, Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney,  using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
CDD:239059	196	EUKprk	Bacteria:24,Invertebrates:1	cd02145, BluB, Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor.
CDD:239060	229	EUKprk	Bacteria:41,Plants:1	cd02146, NfsA_FRP, This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as an electron donor. Oxygen-insensitive nitroreductase, such as NfsA protein in Escherichia coli, catalyzes reduction of nitrocompounds using NADPH as electron donor.
CDD:239061	185	PRK	Bacteria:10,nodiv:1	cd02148, Nitroreductase_5, Nitroreductase-like family 5.  A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a homodimer. Members of this ...
CDD:239062	157	PRK	Bacteria:33,nodiv:1	cd02149, NfsB_like_nitroreductase, NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use ...
CDD:239063	166	PRK	Bacteria:19	cd02150, NADPH_oxidoreductase_1, NAD(P)H:flavin oxidoreductase-like family 1.  A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically a homodimer. ...
CDD:239064	162	EUKprk	Bacteria:7,Invertebrates:1	cd02151, NADPH_oxidoreductase_2, NAD(P)H:flavin oxidoreductase-like family 2.  A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor.  The enzyme is typically ...
CDD:239065	390	EUKprk	Bacteria:88,Environmental:3,Invertebrates:1,Plants:9	cd02152, OAT, Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in the arginine biosynthetic pathway. Members of this family may experience feedback inhibition by L-arginine. The active enzyme is a heterotetramer of two ...
CDD:239066	99	EUKprk	Bacteria:65,Invertebrates:6,Plants:6,Primates:1,Vertebrates:3	cd02153, tRNA_bindingDomain, The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human ...
CDD:173914	153	PRK	Bacteria:45,Environmental:2	cd02163, PPAT, Phosphopantetheine adenylyltransferase.  Phosphopantetheine adenylyltransferase (PPAT). PPAT is an essential enzyme in bacteria, responsible for catalyzing the rate-limiting step in coenzyme A (CoA) biosynthesis.  The dinucleotide-binding fold of PPAT is homologous to class I aminoacyl-tRNA synthetases. CoA has been shown to inhibit PPAT and competes with ATP, PhP, and dPCoA. PPAT is a homohexamer in E. coli.
CDD:173915	143	EUKprk	Bacteria:3,Invertebrates:2,Plants:4,Primates:1	cd02164, PPAT_CoAS, phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes.  The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form ...
CDD:185680	192	EUKprk	Bacteria:43,Plants:11	cd02165, NMNAT, Nicotinamide/nicotinate mononucleotide adenylyltransferase.  Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT).  NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide.  It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the ...
CDD:173917	163	PRK	Bacteria:7	cd02166, NMNAT_Archaea, Nicotinamide/nicotinate mononucleotide adenylyltransferase, archaeal.  This family of archaeal proteins exhibits nicotinamide-nucleotide adenylyltransferase (NMNAT) activity utilizing the salvage pathway to synthesize NAD. In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a number of ...
CDD:173919	181	PRK	Bacteria:3	cd02168, NMNAT_Nudix, Nicotinamide/nicotinate mononucleotide adenylyltransferase of bifunctional proteins, also containing a Nudix hydrolase domain.  N-terminal NMNAT (Nicotinamide/nicotinate mononucleotide adenylyltransferase) domain of a novel bifunctional enzyme endowed with NMN adenylyltransferase and Nudix hydrolase activities.  This domain is highly homologous to the archeal NMN adenyltransferase that catalyzes NAD synthesis from NMN and ATP.  NMNAT is an ...
CDD:173920	297	PRK	Bacteria:15	cd02169, Citrate_lyase_ligase, Citrate lyase ligase.  Citrate lyase ligase, also known as [Citrate (pro-3S)-lyase] ligase, is responsible for acetylation of the (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) prosthetic group of the gamma subunit of citrate lyase, converting the inactive thiol form of this enzyme to the active form. The acetylation of 1 molecule of deacetyl-citrate lyase to enzymatically active citrate lyase requires 6 molecules of ATP. The ...
CDD:173921	136	EUKprk	Bacteria:5,Invertebrates:2,Primates:1	cd02170, cytidylyltransferase, cytidylyltransferase.  The cytidylyltransferase family includes cholinephosphate cytidylyltransferase (CCT), glycerol-3-phosphate cytidylyltransferase, RafE and  phosphoethanolamine cytidylyltransferase (ECT). All enzymes catalyze the transfer of a cytidylyl group from CTP to various substrates.
CDD:173924	152	EUK	Invertebrates:7,Plants:5,Vertebrates:2	cd02173, ECT, CTP:phosphoethanolamine cytidylyltransferase (ECT).  CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP-ethanolamine biosynthesis pathway.  ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECTs, including yeast and human ECT, have large repetitive ...
CDD:173925	150	EUK	Invertebrates:7,Plants:7,Rodents:1,Vertebrates:2	cd02174, CCT, CTP:phosphocholine cytidylyltransferase.  CTP:phosphocholine cytidylyltransferase (CCT) catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway. CCT is unique in that its enzymatic activity is regulated by the extent of its association with membrane structures. A current model posts that the elastic stress of the bilayer curvature ...
CDD:185684	212	EUKprk	Bacteria:17,Plants:1	cd02175, GH16_lichenase, lichenase, member of glycosyl hydrolase family 16.  Lichenase, also known as 1,3-1,4-beta-glucanase, is a member of glycosyl hydrolase family 16, that specifically cleaves 1,4-beta-D-glucosidic bonds in mixed-linked beta glucans that also contain 1,3-beta-D-glucosidic linkages.  Natural substrates of beta-glucanase are beta-glucans from grain endosperm cell walls or lichenan from the Islandic moss, Cetraria islandica.  This ...
CDD:185685	263	EUK	Plants:7	cd02176, GH16_XET, Xyloglucan endotransglycosylase, member of glycosyl hydrolase family 16.  Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Xyloglucan is a soluble hemicellulose with a backbone of beta-1,4-linked glucose units, partially substituted with alpha-1,6-linked xylopyranose branches. It binds noncovalently to cellulose, cross-linking the adjacent cellulose microfibrils, ...
CDD:185687	258	PRK	Bacteria:14	cd02178, GH16_beta_agarase, Beta-agarase, member of glycosyl hydrolase family 16.  Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms ...
CDD:185688	321	EUK	Invertebrates:12	cd02179, GH16_beta_GRP, beta-1,3-glucan recognition protein, member of glycosyl hydrolase family 16.  Beta-GRP (beta-1,3-glucan recognition protein) is one of several pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. They are present in insects and lack all catalytic residues. This ...
CDD:185689	295	EUK	Plants:11	cd02180, GH16_fungal_KRE6_glucanase, Saccharomyces cerevisiae KRE6 and related glucanses, member of glycosyl hydrolase family 16.  KRE6 is a Saccharomyces cerevisiae glucanase that participates in the synthesis of beta-1,6-glucan, a major structural component of the cell wall.  It is a golgi membrane protein required for normal beta-1,6-glucan levels in the cell wall.  KRE6 is closely realted to laminarinase, a glycosyl hydrolase family 16 member that hydrolyzes ...
CDD:185690	293	EUK	Plants:30	cd02181, GH16_fungal_Lam16A_glucanase, fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A.  Group of fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Lam16A belongs to the 'nonspecific' 1,3(4)-beta-glucanase subfamily, although beta-1,6 branching and beta-1,4 bonds specifically define where Lam16A hydrolyzes its substrates, like curdlan (beta-1,3-glucan), lichenin (beta-1,3-1,4-mixed ...
CDD:185691	259	EUKprk	Bacteria:5,Plants:10	cd02182, GH16_Strep_laminarinase_like, Streptomyces laminarinase-like, member of glycosyl hydrolase family 16.  Proteins similar to Streptomyces sioyaensis beta-1,3-glucanase (laminarinase) present in Actinomycetales as well as Peziomycotina. Laminarinases belong to glycosyl hydrolase family 16 and hydrolyze the glycosidic bond of the 1,3-beta-linked glucan, a major component of fungal and plant cell walls and the structural and storage polysaccharides ...
CDD:185692	203	EUK	Plants:36	cd02183, GH16_fungal_CRH1_transglycosylase, glycosylphosphatidylinositol-glucanosyltransferase.  Group of fungal GH16 members related to Saccharomyces cerevisiae Crh1p. Chr1p and Crh2p are transglycosylases that are required for the linkage of chitin to beta(1-3)glucose branches of beta(1-6)glucan, an important step in the assembly of new cell wall. Both have been shown to be glycosylphosphatidylinositol (GPI)-anchored. A third homologous protein, Crr1p, functions in ...
CDD:100026	117	PRK	Bacteria:45	cd02185, AroH, Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme.  The AroH domain forms a ...
CDD:100015	434	EUK	Invertebrates:21,Mammals:1,Plants:14,Vertebrates:3	cd02186, alpha_tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly.  The delta- and epsilon-tubulins are widespread but ...
CDD:100016	425	EUK	Invertebrates:20,Mammals:1,Plants:15,Vertebrates:3	cd02187, beta_tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly.  The delta- and epsilon-tubulins are widespread but unlike ...
CDD:100017	431	EUK	Invertebrates:13,Plants:11,Vertebrates:2	cd02188, gamma_tubulin, Gamma-tubulin is a ubiquitous phylogenetically conserved member of tubulin superfamily.  Gamma is a low abundance protein present within the cells in both various types of microtubule-organizing centers and cytoplasmic protein complexes.  Gamma-tubulin recruits the alpha/beta-tubulin dimers that form the minus ends of microtubules and is thought to be involved in microtubule nucleation and capping.
CDD:100018	446	EUK	Invertebrates:14,Plants:1,Vertebrates:3	cd02189, delta_tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly.  The delta- and epsilon-tubulins are widespread but unlike the ...
CDD:100019	379	EUK	Invertebrates:8,Plants:1,Vertebrates:3	cd02190, epsilon_tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The epsilon-tubulins which are widespread but not ubiquitous among eukaryotes play a role in basal body/centriole morphogenesis.
CDD:100028	283	PRK	Bacteria:23	cd02192, PurM-like3, AIR synthase (PurM) related protein, subgroup 3 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
CDD:100030	291	PRK	Bacteria:163	cd02194, ThiL, ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the conversion of this intermediate to thiamine pyrophosphate. The N-terminal domain of ThiL binds ATP and is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR ...
CDD:100031	287	EUKprk	Bacteria:54,Invertebrates:5,Plants:1,Primates:1,Vertebrates:3	cd02195, SelD, Selenophosphate synthetase  (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The N-terminal domain of SelD is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, and FGAM synthase ...
CDD:100032	297	EUKprk	Bacteria:72,Environmental:4,Invertebrates:7,Plants:5,Primates:1,Vertebrates:3	cd02196, PurM, PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis. The N-terminal domain of PurM is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR ...
CDD:100033	293	PRK	Bacteria:75	cd02197, HypE, HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis.  HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the ATP-binding domains of the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP.
CDD:100005	111	miss	miss	cd02198, YjgH_like, YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA ...
CDD:100006	142	miss	miss	cd02199, YjgF_YER057c_UK114_like_1, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic ...
CDD:100021	304	EUKprk	Bacteria:62,Environmental:1,Invertebrates:2,Plants:10	cd02201, FtsZ_type1, FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes.  FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
CDD:100022	349	PRK	Bacteria:8,Environmental:1	cd02202, FtsZ_type2, FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes.  FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
CDD:100034	313	EUKprk	Bacteria:68,Environmental:3,Invertebrates:3,Plants:4	cd02203, PurL_repeat1, PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL ...
CDD:100035	264	EUKprk	Bacteria:25,Invertebrates:1,Plants:1	cd02204, PurL_repeat2, PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL gene as a ...
CDD:239067	113	EUKprk	Bacteria:175,Environmental:2,Invertebrates:9,Plants:10,Primates:1,Vertebrates:3	cd02205, CBS_pair, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd ...
CDD:239068	210	EUK	Invertebrates:44,Mammals:1,Plants:10,Primates:1,Rodents:1,Vertebrates:6,nodiv:1	cd02248, Peptidase_C1A, Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates ...
CDD:239069	46	EUK	Invertebrates:3,Plants:6,Primates:1,Rodents:1,Vertebrates:3	cd02249, ZZ, Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ...
CDD:239070	260	PRK	Bacteria:26	cd02252, nylC_like, nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly-polymerized 6-aminohexanoate oligomers. Together with other nylon degradation enzymes, such as 6-aminohexanoate cyclic dimer hydrolase (EI) and 6-aminohexanoate dimer hydrolase (EII), EIII plays a ...
CDD:239071	339	EUKprk	Bacteria:24,Plants:2,nodiv:1	cd02253, DmpA, L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active heterodimeric form. The cleavage results in two polypeptide chains, with one chain containing an N-terminal nucleophile. This group represents one of the rare aminopeptidases that are not ...
CDD:239072	255	EUKprk	Bacteria:1,Invertebrates:18,Mammals:1,Plants:22,Primates:2,Rodents:1,Vertebrates:4	cd02257, Peptidase_C19, Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could ...
CDD:199210	382	PRK	Bacteria:26,Environmental:2	cd02258, Peptidase_C25_N, Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins.  Peptidase family C25 is a unique class of cysteine proteases, exemplified by gingipain, which is produced by Porphyromonas gingivalis. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease that is also associated with other diseases such as diabetes and cardiovascular ...
CDD:239073	122	PRK	Bacteria:22	cd02259, Peptidase_C39_like, Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial ...
CDD:100064	59	EUKprk	Bacteria:114,Invertebrates:25,Mammals:1,Plants:44,Primates:2,Rodents:1,Vertebrates:5	cd02325, R3H, R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a ...
CDD:239074	49	EUK	Invertebrates:4,Mammals:1,Primates:1,Vertebrates:5	cd02334, ZZ_dystrophin, Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
CDD:239075	49	EUK	Invertebrates:9,Plants:10,Primates:1,Vertebrates:4	cd02335, ZZ_ADA2, Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
CDD:239076	45	EUK	Plants:15	cd02336, ZZ_RSC8, Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
CDD:239078	49	EUK	Invertebrates:4,Mammals:1,Plants:3,Primates:1,Vertebrates:3	cd02338, ZZ_PCMF_like, Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1  and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
CDD:239080	43	EUK	Invertebrates:6,Mammals:1,Plants:7,Primates:1,Vertebrates:2	cd02340, ZZ_NBR1_like, Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 ...
CDD:239081	48	EUK	Invertebrates:2,Plants:2,Vertebrates:1	cd02341, ZZ_ZZZ3, Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
CDD:239086	61	miss	miss	cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and ...
CDD:239087	62	miss	miss	cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like.  The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development ...
CDD:239088	120	miss	miss	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, ...
CDD:239089	65	miss	miss	cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two ...
CDD:239091	115	EUKprk	Bacteria:7,Invertebrates:11,Plants:7,Primates:1,Vertebrates:3	cd02407, PTH2_family, Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes.
CDD:239092	68	EUKprk	Bacteria:58,Environmental:3,Invertebrates:12,Mammals:1,Plants:25,Primates:1,Vertebrates:4,nodiv:1	cd02409, KH-II, KH-II  (K homology RNA-binding domain, type II).  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins  (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but ...
CDD:239093	145	miss	miss	cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH).  The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In ...
CDD:239094	85	miss	miss	cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3  is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.   The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA ...
CDD:239095	109	miss	miss	cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3  is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA or ...
CDD:239096	81	miss	miss	cd02413, 40S_S3_KH, K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3  is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH binds single-stranded RNA or ...
CDD:239097	77	miss	miss	cd02414, jag_KH, jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins ...
CDD:239098	121	PRK	Bacteria:16	cd02417, Peptidase_C39_likeA, A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases.  Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are ...
CDD:239099	136	PRK	Bacteria:25	cd02418, Peptidase_C39B, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit ...
CDD:239100	127	PRK	Bacteria:12,nodiv:2	cd02419, Peptidase_C39C, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that ...
CDD:239102	124	PRK	Bacteria:13,nodiv:1	cd02421, Peptidase_C39_likeD, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria ...
CDD:239103	129	PRK	Bacteria:15	cd02423, Peptidase_C39G, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit ...
CDD:239104	129	PRK	Bacteria:5	cd02424, Peptidase_C39E, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit ...
CDD:239105	126	PRK	Bacteria:14	cd02425, Peptidase_C39F, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit ...
CDD:239107	116	miss	miss	cd02429, PTH2_like, Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported  to encode such activity, Pth present in bacteria and eukaryotes and  Pth2 present in archaea and eukaryotes. There is no functional information for this eukaryote-specific subgroup.
CDD:239108	115	miss	miss	cd02430, PTH2, Peptidyl-tRNA hydrolase, type 2 (PTH2). Peptidyl-tRNA hydrolase (PTH) activity releases tRNA from the premature translation termination product peptidyl-tRNA, therefore allowing the tRNA and peptide to be reused in protein synthesis. PTH2 is present in archaea and eukaryotes.
CDD:153122	149	miss	miss	cd02431, Ferritin_CCC1_C, CCC1-related domain of ferritin.  Ferritin_CCC1_like_C: The proteins of this family contain two domains. This is the C-terminal domain that is closely related to the CCC1, a vacuole transmembrane protein functioning as an iron and manganese transporter. The N-terminal domain is similar to ferritin-like diiron-carboxylate proteins, which are involved in a variety of iron ion related functions, such as iron storage and regulation, ...
CDD:153123	218	miss	miss	cd02432, Nodulin-21_like_1, Nodulin-21 and CCC1-related protein family.  Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. .
CDD:153125	225	miss	miss	cd02434, Nodulin-21_like_3, Nodulin-21 and CCC1-related protein family.  Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. .
CDD:153126	241	miss	miss	cd02435, CCC1, CCC1.  CCC1: This domain is present in the CCC1, an iron and manganese transporter of Saccharomyces cerevisiae. CCC1 is a transmembrane protein that is located in the vacuole and transfers the iron and manganese ions from the cytosol to the vacuole. This domain may be unique to certain fungi and plants.
CDD:153128	175	miss	miss	cd02437, CCC1_like_1, CCC1-related protein family.  CCC1_like_1: This is a protein family closely related to CCC1, a family of proteins involved in iron and manganese transport. Yeast CCC1 is a vacuole transmembrane protein responsible for the iron and manganese accumulation in vacuole.   .
CDD:143332	315	EUKprk	Bacteria:108,Plants:1	cd02439, DMB-PRT_CobT, Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT.  Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT/CobT, not to be confused with the CobT subunit of cobaltochelatase, which does not belong to this group) catalyzes the synthesis of alpha-ribazole-5'-phosphate, from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is ...
CDD:100107	107	EUKprk	Bacteria:42,Invertebrates:1,Plants:8,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	cd02440, AdoMet_MTases, S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within ...
CDD:133000	181	PRK	Bacteria:97	cd02503, MobA, MobA catalyzes the formation of molybdopterin guanine dinucleotide.  The prokaryotic enzyme molybdopterin-guanine dinucleotide biosynthesis protein A (MobA). All mononuclear molybdoenzymes bind molybdenum in complex with an organic cofactor termed molybdopterin (MPT). In many bacteria, including Escherichia coli, molybdopterin can be further modified by attachment of a GMP group to the terminal phosphate of molybdopterin to form molybdopterin guanine ...
CDD:133001	216	EUK	Invertebrates:14,Plants:11,Primates:1,Vertebrates:3	cd02507, eIF-2B_gamma_N_like, The N-terminal of eIF-2B_gamma_like is predicted to have glycosyltransferase activity.  N-terminal domain of eEIF-2B epsilon and gamma, subunits of eukaryotic translation initiators, is a subfamily of glycosyltranferase 2 and is predicted to have glycosyltranferase activity. eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for ...
CDD:133002	200	EUKprk	Bacteria:32,Plants:2	cd02508, ADP_Glucose_PP, ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch.  ADP-glucose pyrophosphorylase (glucose-1-phosphate adenylyltransferase) catalyzes a very important step in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants: synthesis of the activated glucosyl donor, ADP-glucose, from glucose-1-phosphate and ATP.  ADP-glucose pyrophosphorylase is a tetrameric allosterically ...
CDD:133003	274	EUKprk	Bacteria:49,Environmental:1,Invertebrates:1,Plants:1	cd02509, GDP-M1P_Guanylyltransferase, GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose.  GDP-mannose-1-phosphate guanylyltransferase, also called GDP-mannose pyrophosphorylase (GDP-MP), catalyzes the formation of GDP-Mannose from mannose-1-phosphate and GTP. Mannose is a key monosaccharide for glycosylation of proteins and lipids. GDP-Mannose is the activated donor for mannosylation of various ...
CDD:133004	299	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd02510, pp-GalNAc-T, pp-GalNAc-T initiates the formation of mucin-type O-linked glycans.  UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to hydroxyl groups of Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These enzymes are type II ...
CDD:133005	229	PRK	Bacteria:55	cd02511, Beta4Glucosyltransferase, UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide.  UDP-glucose: lipooligosaccharide (LOS)  beta-1-4-glucosyltransferase catalyzes the addition of the first residue, glucose, of the lacto-N-neotetrase structure to HepI of the LOS inner core.  LOS is the major constituent of the outer leaflet of the outer membrane of gram-positive bacteria. It consists of a short oligosaccharide chain ...
CDD:133006	223	EUKprk	Bacteria:88,Environmental:2,Invertebrates:3,Rodents:1,Vertebrates:3	cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety.  CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc synthetase) or acylneuraminate cytidylyltransferase catalyzes the transfer the CMP moiety of CTP to the anomeric hydroxyl group of NeuAc in the presence of Mg++. It is the second to last step in the sialylation of the oligosaccharide component of ...
CDD:133007	334	EUK	Invertebrates:6,Mammals:1,Plants:2,Primates:1,Vertebrates:2	cd02514, GT13_GLCNAC-TI, GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides.  Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GLCNAC-T I , GNT-I)  transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide, an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The ...
CDD:133008	271	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:4	cd02515, Glyco_transf_6, Glycosyltransferase family 6 comprises enzymes responsible for the production of the human ABO blood group antigens.  Glycosyltransferase family 6, GT_6, comprises enzymes with three known activities: alpha-1,3-galactosyltransferase, alpha-1,3 N-acetylgalactosaminyltransferase, and alpha-galactosyltransferase. UDP-galactose:beta-galactosyl alpha-1,3-galactosyltransferase (alpha3GT) catalyzes the transfer of ...
CDD:133009	218	EUKprk	Bacteria:98,Environmental:1,Plants:2,Primates:1,Vertebrates:3	cd02516, CDP-ME_synthetase, CDP-ME synthetase is involved in mevalonate-independent isoprenoid production.  4-diphosphocytidyl-2-methyl-D-erythritol synthase (CDP-ME), also called  2C-methyl-d-erythritol 4-phosphate cytidylyltransferase catalyzes the third step in the alternative (non-mevalonate) pathway of Isopentenyl diphosphate (IPP) biosynthesis: the formation of 4-diphosphocytidyl-2C-methyl-D-erythritol from ...
CDD:133010	239	EUKprk	Bacteria:66,Plants:3	cd02517, CMP-KDO-Synthetase, CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide.  CMP-KDO Synthetase: 3-Deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) catalyzes the conversion of CTP and 3-deoxy-D-manno-octulosonate into CMP-3-deoxy-D-manno-octulosonate (CMP-KDO) and pyrophosphate. KDO is an essential component of the lipopolysaccharide found in the outer surface of ...
CDD:133011	233	PRK	Bacteria:41	cd02518, GT2_SpsF, SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat.  Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat.  SpsF gene mutation ...
CDD:133012	196	EUKprk	Bacteria:12,Invertebrates:4,Plants:4,Primates:1,Vertebrates:2	cd02520, Glucosylceramide_synthase, Glucosylceramide synthase catalyzes the first glycosylation step of glycosphingolipid synthesis.  UDP-glucose:N-acylsphingosine D-glucosyltransferase (glucosylceramide synthase or ceramide glucosyltransferase) catalyzes the first glycosylation step of glycosphingolipid synthesis. Its product, glucosylceramide, serves as the core of more than 300 glycosphingolipids (GSL). GSLs ...
CDD:133013	221	EUKprk	Bacteria:36,Plants:3	cd02522, GT_2_like_a, GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function.  Glycosyltransferase family 2 (GT-2) subfamily of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of ...
CDD:133014	229	PRK	Bacteria:45,Environmental:2	cd02523, PC_cytidylyltransferase, Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline.  This family contains proteins similar to prokaryotic phosphocholine (P-cho) cytidylyltransferases. Phosphocholine (PC) cytidylyltransferases catalyze the transfer of a cytidine monophosphate from CTP to phosphocholine to form CDP-choline. PC is the most abundant phospholipid in eukaryotic membranes and it is also important in prokaryotic ...
CDD:133015	253	PRK	Bacteria:32	cd02524, G1P_cytidylyltransferase, G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose.  Alpha-D-Glucose-1-phosphate Cytidylyltransferase catalyzes the production of CDP-D-Glucose from alpha-D-Glucose-1-phosphate and MgCTP as substrate. CDP-D-Glucose is the precursor  for synthesizing four of the five naturally occurring 3,6-dideoxy sugars-abequose (3,6-dideoxy-D-Xylo-hexose), ascarylose (3,6-dideoxy-L-arabino-hexose), paratose ...
CDD:133016	249	PRK	Bacteria:20,Environmental:1	cd02525, Succinoglycan_BP_ExoA, ExoA is involved in the biosynthesis of succinoglycan.  Succinoglycan Biosynthesis Protein ExoA catalyzes the formation of a beta-1,3 linkage of the second sugar (glucose) of the succinoglycan with the galactose on the lipid carrie. Succinoglycan is an acidic exopolysaccharide that is important for invasion of the nodules. Succinoglycan is a high-molecular-weight polymer composed of repeating octasaccharide units. ...
CDD:133017	237	PRK	Bacteria:28	cd02526, GT2_RfbF_like, RfbF is a putative dTDP-rhamnosyl transferase.  Shigella flexneri RfbF protein is a putative dTDP-rhamnosyl transferase. dTDP rhamnosyl  transferases of Shigella flexneri  add rhamnose sugars to N-acetyl-glucosamine in the O-antigen tetrasaccharide repeat. Lipopolysaccharide O antigens are important virulence determinants for many bacteria. The variations of sugar composition, the sequence of the sugars and the linkages in the O antigen ...
CDD:133018	240	EUKprk	Bacteria:2,Invertebrates:7,Plants:14,Vertebrates:3	cd02537, GT8_Glycogenin, Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen.  Glycogenin initiates the biosynthesis of glycogen by incorporating glucose residues through a self-glucosylation reaction at a Tyr residue, and then acts as substrate for chain elongation by glycogen synthase and branching enzyme. It contains a conserved DxD motif and an N-terminal beta-alpha-beta Rossmann-like fold that ...
CDD:133019	240	EUKprk	Bacteria:22,Invertebrates:1	cd02538, G1P_TT_short, G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase.  This family is the short form of glucose-1-phosphate thymidylyltransferase.  Glucose-1-phosphate thymidylyltransferase catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate. It is the first enzyme in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.There are two forms of   ...
CDD:133020	229	PRK	Bacteria:72,Environmental:1	cd02540, GT2_GlmU_N_bac, N-terminal domain of bacterial GlmU.  The N-terminal domain of N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU). GlmU is an essential bacterial enzyme with both an acetyltransferase and an uridyltransferase activity which have been mapped to the C-terminal and N-terminal domains, respectively. This family represents the N-terminal uridyltransferase. GlmU performs the last two steps in the synthesis of ...
CDD:133021	267	EUKprk	Bacteria:29,Plants:1	cd02541, UGPase_prokaryotic, Prokaryotic UGPase catalyses the synthesis of UDP-glucose.  Prokaryotic UDP-Glucose Pyrophosphorylase (UGPase) catalyzes a reversible production of UDP-Glucose  and pyrophosphate (PPi) from glucose-1-phosphate and UTP.  UDP-glucose plays pivotal roles in galactose utilization, in glycogen synthesis, and in the synthesis of the carbohydrate moieties of glycolipids , glycoproteins , and proteoglycans. UGPase is found in both ...
CDD:239109	141	EUKprk	Bacteria:24,Invertebrates:1	cd02549, Peptidase_C39A, A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of ...
CDD:211325	154	miss	miss	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family.  This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors.  E. coli RluC for example makes psi955, 2504 ...
CDD:211326	232	miss	miss	cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD family.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 ...
CDD:211327	167	EUKprk	Bacteria:34,Invertebrates:1,Rodents:1,nodiv:1	cd02553, PseudoU_synth_RsuA, Pseudouridine synthase, Escherichia coli RsuA like.  This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
CDD:211328	164	PRK	Bacteria:11	cd02554, PseudoU_synth_RluF, Pseudouridine synthase, Escherichia coli RluF like.  This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that ...
CDD:211330	167	EUKprk	Bacteria:6,Environmental:1,Invertebrates:1	cd02556, PseudoU_synth_RluB, Pseudouridine synthase, Escherichia coli RluB like.  This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RluB makes psi2605 in 23S RNA.  psi2605 has been detected in eubacteria but, not in eukarya and ...
CDD:211331	213	EUK	Invertebrates:7,Plants:10,Primates:1,Vertebrates:2	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2.  Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes ...
CDD:211332	246	PRK	Bacteria:13	cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family.  This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
CDD:211333	223	PRK	Bacteria:10	cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C.  Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. TruC makes psi65 in tRNAs.  This psi residue is not universally conserved.
CDD:211335	245	EUK	Invertebrates:14,Plants:11,Primates:1,Vertebrates:2	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like.  This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p,  S.  cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. cerevisiae Pus1p ...
CDD:211336	256	EUK	Invertebrates:5,Plants:6,Primates:1,Vertebrates:3	cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like.  This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse ...
CDD:211337	239	EUKprk	Bacteria:106,Environmental:2,Invertebrates:3,Plants:1,Primates:1,Vertebrates:1	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E.  coli TruA.  This group consists of eukaryotic and bacterial pseudouridine synthases similar to E.  coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines ...
CDD:211338	182	EUKprk	Bacteria:6,Invertebrates:9,Plants:6,Vertebrates:2	cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human dyskerin like.  This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein).  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactor is required. S. ...
CDD:211339	213	PRK	Bacteria:91,nodiv:1	cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia coli TruB like.  This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  E. coli TruB and M.  tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved.  E. coli ...
CDD:211340	253	miss	miss	cd02575, PseudoU_synth_EcTruD, Pseudouridine synthase, similar to Escherichia coli TruD.  This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
CDD:211341	371	miss	miss	cd02576, PseudoU_synth_ScPUS7, Pseudouridine synthase, TruD family.  This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in ...
CDD:211342	319	miss	miss	cd02577, PSTD1, Pseudouridine synthase, a subgroup of the TruD family.  This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  The TruD family is comprised of proteins related to Escherichia coli TruD.
CDD:259846	861	PRK	Bacteria:14,Environmental:2	cd02582, RNAP_archeal_A', A' subunit of archaeal RNA polymerase (RNAP).  A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different ...
CDD:259847	816	EUK	Invertebrates:26,Plants:22,Primates:1,Vertebrates:3	cd02583, RNAP_III_RPC1_N, Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain.  Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. ...
CDD:132720	410	EUK	Invertebrates:16,Plants:16,Primates:1,Vertebrates:1	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain.  RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest ...
CDD:239110	223	EUKprk	Bacteria:18,Invertebrates:3,Plants:2	cd02619, Peptidase_C1, C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage ...
CDD:239111	236	EUK	Invertebrates:24,Mammals:1,Plants:2,Primates:1,Vertebrates:4	cd02620, Peptidase_C1A_CathepsinB, Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme ...
CDD:239112	243	EUK	Invertebrates:5,Vertebrates:3	cd02621, Peptidase_C1A_CathepsinC, Cathepsin C; also known as Dipeptidyl Peptidase I (DPPI), an atypical papain-like cysteine peptidase with chloride dependency and dipeptidyl aminopeptidase activity, resulting from its tetrameric structure which limits substrate access. Each subunit of the tetramer is composed of three peptides: the heavy and light chains, which together adopts the papain fold and forms the catalytic domain; and the residual ...
CDD:100066	65	miss	miss	cd02637, R3H_PARN, R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
CDD:100068	60	miss	miss	cd02639, R3H_RRM, R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The ...
CDD:100070	60	miss	miss	cd02641, R3H_Smubp-2_like, R3H domain of Smubp-2_like proteins.  Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
CDD:100071	63	miss	miss	cd02642, R3H_encore_like, R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The ...
CDD:100072	74	miss	miss	cd02643, R3H_NF-X1, R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H ...
CDD:100073	67	miss	miss	cd02644, R3H_jag, R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
CDD:100074	60	miss	miss	cd02645, R3H_AAA, R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
CDD:100075	58	miss	miss	cd02646, R3H_G-patch, R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
CDD:239113	312	EUKprk	Bacteria:7,Invertebrates:1,Plants:2	cd02647, nuc_hydro_TvIAG, nuc_hydro_ TvIAG:  Nucleoside hydrolases similar to the Inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax.   Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. Nucleoside hydrolases vary in their substrate specificity. This group contains eukaryotic and bacterial proteins similar to the purine specific ...
CDD:239115	306	EUKprk	Bacteria:5,Invertebrates:7,Vertebrates:3	cd02649, nuc_hydro_CeIAG, nuc_hydro_CeIAG: Nucleoside hydrolases similar to the inosine-adenosine-guanosine-preferring nucleoside hydrolase from Caenorhabditis elegans.  Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal proteins similar to the purine-preferring nucleoside ...
CDD:239116	304	EUKprk	Bacteria:11,Plants:3,nodiv:1	cd02650, nuc_hydro_CaPnhB, NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. .
CDD:239117	302	EUKprk	Bacteria:19,Invertebrates:1,Plants:9,nodiv:2	cd02651, nuc_hydro_IU_UC_XIUA, nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases.  Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains proteins similar to nucleoside hydrolases which hydrolyze both ...
CDD:239118	293	EUKprk	Bacteria:5,Plants:1	cd02652, nuc_hydro_2, NH_2: A subgroup of nucleoside hydrolases. This group contains eukaryotic and bacterial proteins similar to nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  .
CDD:239119	320	PRK	Bacteria:9	cd02653, nuc_hydro_3, NH_3: A subgroup of nucleoside hydrolases. This group contains eukaryotic and bacterial proteins similar to nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  .
CDD:132721	204	EUKprk	Bacteria:20,Invertebrates:4,Plants:15	cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain.  Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers ...
CDD:239121	75	EUK	Invertebrates:8,Plants:2,Primates:1,Rodents:1,Vertebrates:1	cd02656, MIT, MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
CDD:239122	305	miss	miss	cd02657, Peptidase_C19A, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239123	311	miss	miss	cd02658, Peptidase_C19B, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239124	334	miss	miss	cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239125	328	miss	miss	cd02660, Peptidase_C19D, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239126	304	miss	miss	cd02661, Peptidase_C19E, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239127	240	miss	miss	cd02662, Peptidase_C19F, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239128	300	miss	miss	cd02663, Peptidase_C19G, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239129	327	miss	miss	cd02664, Peptidase_C19H, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239131	343	miss	miss	cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239132	279	miss	miss	cd02667, Peptidase_C19K, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239133	324	miss	miss	cd02668, Peptidase_C19L, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239134	440	miss	miss	cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239137	268	miss	miss	cd02672, Peptidase_C19P, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:239139	230	miss	miss	cd02674, Peptidase_C19R, A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as ...
CDD:259861	136	EUK	Invertebrates:16,Primates:1,Rodents:1	cd02675, Ephrin_ectodomain, Ectodomain of Ephrins.  Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin (Eph) ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, depending on Eph ...
CDD:239140	75	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:4	cd02677, MIT_SNX15, MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
CDD:239141	75	EUK	Invertebrates:5,Plants:8,Primates:1,Vertebrates:3	cd02678, MIT_VPS4, MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
CDD:239142	79	EUK	Invertebrates:3,Plants:3,Primates:1,Vertebrates:4	cd02679, MIT_spastin, MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
CDD:239148	148	EUKprk	Bacteria:6,Invertebrates:6,Primates:1,Vertebrates:4	cd02685, MIT_C, MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown.
CDD:199878	82	EUKprk	Bacteria:23,Plants:5,Primates:1	cd02688, E_set, Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus.  The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose ...
CDD:193493	252	EUKprk	Bacteria:40,Environmental:1,Invertebrates:2,Plants:3,Primates:1	cd02690, M28, M28 Zn-peptidases include aminopeptidases and carboxypeptidases.  Peptidase M28 family (also called aminopeptidase Y family) contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions.  The aminopeptidases in this family are also ...
CDD:119407	172	PRK	Bacteria:296,Environmental:5,Phages:1	cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this ...
CDD:188992	230	EUKprk	Bacteria:91,Invertebrates:1,Plants:5	cd02699, M4, Peptidase M4 family includes thermolysin, pseudolysin, aureolysin, neutral protease and bacillolysin.  M4 Peptidase family belong to the Glu-zincins family and includes numerous zinc-dependent metallopeptidases that hydrolyze peptide bonds such as thermolysin (EC 3.4.24.27), pseudolysin (the extracellullar elastase of Pseudomonas aeruginosa), aureolysin (the extracellular metalloproteinase from Staphylococcus aureus), ...
CDD:259848	751	EUK	Invertebrates:24,Plants:17,Primates:1,Vertebrates:2,nodiv:1	cd02733, RNAP_II_RPB1_N, Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain.  The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two ...
CDD:132722	309	EUK	Invertebrates:10,Plants:5,Primates:1,Vertebrates:1	cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain.  RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies ...
CDD:132723	300	EUK	Invertebrates:10,Plants:3,Primates:1,Vertebrates:2	cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain.  Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal ...
CDD:132724	381	EUK	Plants:8	cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain.  Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous ...
CDD:119331	303	EUKprk	Bacteria:7,Primates:1	cd02742, GH20_hexosaminidase, Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes ...
CDD:239150	147	EUKprk	Bacteria:8,Invertebrates:4,Plants:2,Primates:1	cd02749, Macro, Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in ...
CDD:239151	461	miss	miss	cd02750, MopB_Nitrate-R-NarG-like, Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the ...
CDD:239152	609	miss	miss	cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; ...
CDD:239153	649	miss	miss	cd02752, MopB_Formate-Dh-Na-like, Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a  ...
CDD:239154	512	miss	miss	cd02753, MopB_Formate-Dh-H, Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a  Mo active site region and a [4Fe-4S] center. Members of the MopB_Formate-Dh-H CD belong to the molybdopterin_binding (MopB) superfamily ...
CDD:239155	565	miss	miss	cd02754, MopB_Nitrate-R-NapA-like, Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239156	454	miss	miss	cd02755, MopB_Thiosulfate-R-like, The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) ...
CDD:239159	735	miss	miss	cd02758, MopB_Tetrathionate-Ra, The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239160	477	miss	miss	cd02759, MopB_Acetylene-hydratase, The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239162	415	miss	miss	cd02761, MopB_FmdB-FwdB, The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239167	501	miss	miss	cd02766, MopB_3, The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239168	574	miss	miss	cd02767, MopB_ydeP, The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239169	386	miss	miss	cd02768, MopB_NADH-Q-OR-NuoG2, MopB_NADH-Q-OR-NuoG2: The NuoG/Nad11/75-kDa subunit (second domain) of the NADH-quinone oxidoreductase (NADH-Q-OR)/respiratory complex I/NADH dehydrogenase-1 (NDH-1). The NADH-Q-OR is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump that uses the redox energy to translocate H+ ions across the membrane, ...
CDD:239170	609	miss	miss	cd02769, MopB_DMSOR-BSOR-TMAOR, The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the ...
CDD:239171	617	miss	miss	cd02770, MopB_DmsA-EC, This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a  predicted N-terminal iron-sulfur [4Fe-4S] cluster  binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
CDD:239172	472	miss	miss	cd02771, MopB_NDH-1_NuoG2-N7, MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, ...
CDD:239173	414	miss	miss	cd02772, MopB_NDH-1_NuoG2, MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit ...
CDD:239174	375	miss	miss	cd02773, MopB_Res-Cmplx1_Nad11, MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump ...
CDD:239175	366	miss	miss	cd02774, MopB_Res-Cmplx1_Nad11-M, MopB_Res_Cmplx1_Nad11_M: Mitochondrial-encoded NADH-quinone oxidoreductase/respiratory complex I, the second domain of the Nad11/75-kDa subunit of some protists. NADH-quinone oxidoreductase is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The nad11 gene codes ...
CDD:239176	101	PRK	Bacteria:39,Environmental:1,nodiv:2	cd02775, MopB_CT, Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase ...
CDD:239177	141	miss	miss	cd02776, MopB_CT_Nitrate-R-NarG-like, Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains ...
CDD:239178	127	miss	miss	cd02777, MopB_CT_DMSOR-like, The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the ...
CDD:239179	123	miss	miss	cd02778, MopB_CT_Thiosulfate-R-like, The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large ...
CDD:239181	143	miss	miss	cd02780, MopB_CT_Tetrathionate_Arsenate-R, This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
CDD:239182	130	miss	miss	cd02781, MopB_CT_Acetylene-hydratase, The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:239183	129	miss	miss	cd02782, MopB_CT_1, The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:239186	124	miss	miss	cd02785, MopB_CT_4, The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:239187	116	miss	miss	cd02786, MopB_CT_3, The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:239188	112	miss	miss	cd02787, MopB_CT_ydeP, The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:239189	96	PRK	Bacteria:1	cd02788, MopB_CT_NDH-1_NuoG2-N7, MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy ...
CDD:239191	116	miss	miss	cd02790, MopB_CT_Formate-Dh_H, Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a  Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal ...
CDD:239192	122	miss	miss	cd02791, MopB_CT_Nitrate-R-NapA-like, Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not ...
CDD:239193	122	miss	miss	cd02792, MopB_CT_Formate-Dh-Na-like, Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a  ...
CDD:239194	129	miss	miss	cd02793, MopB_CT_DMSOR-BSOR-TMAOR, The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in ...
CDD:239195	121	miss	miss	cd02794, MopB_CT_DmsA-EC, The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a  predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
CDD:271143	124	EUKprk	Bacteria:26,Invertebrates:1,Plants:6	cd02795, CBM6-CBM35-CBM36_like, Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily.  Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, ...
CDD:239196	103	EUKprk	Bacteria:19,Environmental:1,Invertebrates:1	cd02796, tRNA_bind_bactPheRS, tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain.  PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe).  PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs.  This domain has general tRNA binding properties and is believed to ...
CDD:239197	107	EUKprk	Bacteria:1,Invertebrates:1	cd02798, tRNA_bind_CsaA, tRNA-binding-domain-containing CsaA-like proteins.  CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain.
CDD:239198	105	EUK	Invertebrates:4,Plants:3,Primates:1	cd02799, tRNA_bind_EMAP-II_like, tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2.  CeMetRS and hTyrRS aminoacylate their cognate tRNAs.  Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA ...
CDD:239199	105	PRK	Bacteria:5	cd02800, tRNA_bind_EcMetRS_like, tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins.  This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties.  MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The ...
CDD:239200	231	EUKprk	Bacteria:84,Environmental:1,Invertebrates:18,Plants:15,Primates:1,Vertebrates:4	cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently ...
CDD:239201	327	EUKprk	Bacteria:66,Environmental:2,Invertebrates:1,Plants:2	cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic ...
CDD:239202	392	EUKprk	Bacteria:61,Invertebrates:2,Plants:5,nodiv:1	cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain.  GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out  L-glutamine ...
CDD:239203	299	EUKprk	Bacteria:90,Environmental:1,Invertebrates:8,Plants:10,Primates:1,Rodents:1,Vertebrates:4	cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is ...
CDD:239204	289	EUKprk	Bacteria:9,Invertebrates:1,Mammals:1,Rodents:1	cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain.  DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and ...
CDD:239205	326	EUKprk	Bacteria:31,Environmental:4,Invertebrates:2	cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.
CDD:239206	219	PRK	Bacteria:12,Environmental:1	cd02812, PcrB_like, PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either ...
CDD:239207	115	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Plants:1,Primates:1	cd02825, PAZ, PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. ...
CDD:239208	393	EUKprk	Bacteria:4,Invertebrates:2,Primates:1	cd02826, Piwi-like, Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two ...
CDD:239211	117	EUK	Invertebrates:12,Mammals:1,Primates:1,Rodents:1,Vertebrates:2	cd02845, PAZ_piwi_like, PAZ domain,  Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named ...
CDD:239212	114	EUK	Invertebrates:6,Plants:12,Rodents:1,Vertebrates:4	cd02846, PAZ_argonaute_like, PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the ...
CDD:199879	62	EUKprk	Bacteria:52,Invertebrates:1	cd02847, E_set_Chitobiase_C, C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase).  E or "early" set domains are associated with the catalytic domain of chitobiase at the C-terminus. Chitobiase digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons. It is thought ...
CDD:199880	105	EUKprk	Bacteria:13,Invertebrates:1	cd02848, E_set_Chitinase_N, N-terminal Early set domain associated with the catalytic domain of chitinase.  E or "early" set domains are associated with the catalytic domain of chitinase at the N-terminal end. Chitinases hydrolyze the abundant natural biopolymer chitin, producing smaller chito-oligosaccharides. Chitin consists of multiple N-acetyl-D-glucosamine (NAG) residues connected via beta-1,4-glycosidic linkages and is an important ...
CDD:199881	86	EUKprk	Bacteria:129,Environmental:2,Invertebrates:1	cd02850, E_set_Cellulase_N, N-terminal Early set domain associated with the catalytic domain of cellulase.  E or "early" set domains are associated with the catalytic domain of cellulases at the N-terminal end. Cellulases are O-glycosyl hydrolases (GHs) that hydrolyze beta 1-4 glucosidic bonds in cellulose. They are usually categorized into either exoglucanases, which sequentially release terminal sugar units from the cellulose ...
CDD:199882	103	EUKprk	Bacteria:35,Plants:29	cd02851, E_set_GO_C, C-terminal Early set domain associated with the catalytic domain of galactose oxidase.  E or "early" set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates and possesses a unique mononuclear copper site essential for catalyzing a two-electron ...
CDD:199883	84	PRK	Bacteria:142	cd02853, E_set_MTHase_like_N, N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins.  E or "early" set domains are associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (MTHase) and similar proteins at the N-terminal end. This subfamily also includes bacterial alpha amylases and 1,4-alpha-glucan branching enzymes ...
CDD:199884	95	EUKprk	Bacteria:24,Environmental:1,Invertebrates:25,Plants:13,Vertebrates:4,nodiv:1	cd02854, E_set_GBE_euk_N, N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme).  This subfamily is composed of predominantly eukaryotic 1,4 alpha glucan branching enzymes, also called glycogen branching enzymes or starch binding enzymes in plants. E or "early" set domains are associated with the ...
CDD:199885	105	EUKprk	Bacteria:208,Environmental:1,Invertebrates:2,nodiv:1	cd02855, E_set_GBE_prok_N, N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme.  This subfamily is composed of predominantly prokaryotic 1,4 alpha glucan branching enzymes, also called glycogen branching enzymes. E or "early" set domains are associated with the catalytic domain of glycogen branching enzymes at the N-terminal end. Glycogen branching enzyme catalyzes the ...
CDD:199886	130	EUKprk	Bacteria:166,Plants:14	cd02856, E_set_GDE_Isoamylase_N, N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase).  E or "early" set domains are associated with the catalytic domain of the glycogen debranching enzyme at the N-terminal end. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase, it ...
CDD:199887	109	PRK	Bacteria:174	cd02857, E_set_CDase_PDE_N, N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes.  E or "early" set domains are associated with the catalytic domain of the cyclomaltodextrinase (CDase) and pullulan-degrading enzymes at the N-terminal end. Members of this subgroup include CDase, maltogenic amylase, and neopullulanase, all of which are capable of hydrolyzing all or two of the following three types of ...
CDD:199888	78	PRK	Bacteria:20,Environmental:1	cd02858, E_set_Esterase_N, N-terminal Early set domain associated with the catalytic domain of esterase.  E or "early" set domains are associated with the catalytic domain of esterase at the N-terminal end. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term esterase can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the first class of ...
CDD:199889	80	EUKprk	Bacteria:32,Invertebrates:30,Plants:65,Primates:1,Vertebrates:3,nodiv:1	cd02859, E_set_AMPKbeta_like_N, N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit.  E or "early" set domains are associated with the catalytic domain of AMP-activated protein kinase beta subunit glycogen binding domain at the N-terminal end. AMPK is a metabolic stress sensing protein that senses AMP/ATP and has ...
CDD:199890	97	EUKprk	Bacteria:191,Plants:8	cd02860, E_set_Pullulanase, Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase).  E or "early" set domains are associated with the catalytic domain of pullulanase at either the N-terminal or C-terminal end, and in a few instances at both ends. Pullulanase is an enzyme with activity similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, ...
CDD:199891	88	PRK	Bacteria:10	cd02861, E_set_pullulanase_like, Early set domain associated with the catalytic domain of pullulanase-like proteins.  E or "early" set domains are associated with the catalytic domain of pullulanase at either the N-terminal or C-terminal end, and in a few instances at both ends. Pullulanase (also called dextrinase or alpha-dextrin endo-1,6-alpha glucosidase) is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, ...
CDD:239213	186	miss	miss	cd02862, NorE_like, NorE_like subfamily of heme-copper oxidase subunit III.  Heme-copper oxidases include cytochrome c and ubiquinol oxidases.  Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of nitric oxide reductase (NOR). Based on this and on its similarity to subunit III of cytochrome c oxidase (CcO) and ubiquinol oxidase, NorE has been speculated to be a subunit of NOR.
CDD:239214	186	miss	miss	cd02863, Ubiquinol_oxidase_III, Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  Ubiquinol oxidases feature four subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of bovine CcO are encoded ...
CDD:239216	184	miss	miss	cd02865, Heme_Cu_Oxidase_III_2, Heme-copper oxidase subunit III subfamily.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types.  This superfamily includes cytochrome c and ubiquinol oxidases.  Bacterial ...
CDD:211344	312	EUK	Plants:7,Primates:1	cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.  This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
CDD:211346	185	EUKprk	Bacteria:119,Environmental:1,Invertebrates:12,Plants:7,Primates:1,Rodents:1,Vertebrates:3	cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family.  This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA.  Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines ...
CDD:211347	146	PRK	Bacteria:47,Environmental:2	cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases, RsuA subfamily.  Pseudouridine synthases  are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
CDD:119350	312	EUKprk	Bacteria:19,Plants:1	cd02871, GH18_chitinase_D-like, GH18 domain of Chitinase D (ChiD).  ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins.  The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18 (GH18) domain, a chitin-binding domain, and a fibronectin type III domain. The chitin-binding and fibronectin type III domains are located either N-terminal or C-terminal to ...
CDD:119351	362	EUK	Invertebrates:24,Mammals:3,Primates:1,Rodents:1,Vertebrates:6	cd02872, GH18_chitolectin_chitotriosidase, This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases.  The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases.  ...
CDD:119352	413	EUK	Invertebrates:9	cd02873, GH18_IDGF, The IDGF's (imaginal disc growth factors) are a family of growth factors identified in insects that include at least five members, some of which are encoded by genes in a tight cluster. The IDGF's have an eight-stranded alpha/beta barrel fold and are related to the glycosyl hydrolase family 18 (GH18) chitinases, but they have an amino acid substitution known to abolish chitinase catalytic activity. IDGFs may have evolved from chitinases to ...
CDD:119353	313	PRK	Bacteria:20	cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in  bacterial endospore germination.  CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells.  SleB translocates across the forespore inner membrane and is deposited as a mature enzyme in the cortex layer of the spore.  As part of a sensory mechanism capable of initiating germination, CFLE degrades a ...
CDD:119355	318	EUK	Invertebrates:10,Plants:5,Vertebrates:3	cd02876, GH18_SI-CLP, Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome.  SI-CLP has a glycosyl hydrolase family 18 (GH18) domain but lacks a chitin-binding domain. The catalytic amino acids of the GH18 domain are not conserved in SI-CLP, similar to the chitolectins ...
CDD:119356	280	EUK	Invertebrates:1,Plants:37	cd02877, GH18_hevamine_XipI_class_III, This conserved domain family includes xylanase inhibitor Xip-I, and the class III plant chitinases such as hevamine, concanavalin B, and PPL2, all of which have a glycosyl hydrolase family 18 (GH18) domain. Hevamine is a class III endochitinase that hydrolyzes the linear polysaccharide chains of chitin and peptidoglycan and is important for defense against pathogenic bacteria and fungi.  PPL2 (Parkia platycephala ...
CDD:119357	345	EUK	Plants:14	cd02878, GH18_zymocin_alpha, Zymocin, alpha subunit.  Zymocin is a heterotrimeric enzyme that inhibits yeast cell cycle progression. The zymocin alpha subunit has a chitinase activity that is essential for holoenzyme action from the cell exterior while the gamma subunit contains the intracellular toxin responsible for G1 phase cell cycle arrest.  The zymocin alpha and beta subunits are thought to act from the cell's exterior by docking to the cell wall-associated ...
CDD:119358	299	EUK	Plants:8	cd02879, GH18_plant_chitinase_class_V, The class V plant chitinases have a glycosyl hydrolase family 18 (GH18) domain, but lack the chitin-binding domain present in other GH18 enzymes.  The GH18 domain of the class V chitinases has endochitinase activity in some cases and no catalytic activity in others.  Included in this family is a lectin found in black locust (Robinia pseudoacacia) bark, which binds chitin but lacks chitinase activity.  Also included is a ...
CDD:239217	123	EUKprk	Bacteria:105,Invertebrates:6,Plants:8,Primates:1,Vertebrates:1	cd02883, Nudix_Hydrolase, Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, ...
CDD:239218	165	EUKprk	Bacteria:30,Invertebrates:8,Plants:8,Primates:1,Vertebrates:3	cd02885, IPP_Isomerase, Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP ...
CDD:153089	464	PRK	Bacteria:12	cd02888, RNR_II_dimer, Class II ribonucleotide reductase, dimeric form.  Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, ...
CDD:239219	348	miss	miss	cd02889, SQCY, Squalene cyclase (SQCY) domain; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. Bacterial SQCY catalyzes the convertion of squalene to hopene or diplopterol. Eukaryotic OSQCY transforms the 2,3-epoxide of squalene to compounds such as, ...
CDD:239220	286	miss	miss	cd02890, PTase, Protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). The protein prenyltransferase family of lipid-modifying enzymes includes protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II). They catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein ...
CDD:239221	282	miss	miss	cd02891, A2M_like, Proteins similar to alpha2-macroglobulin (alpha (2)-M).  Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor.  The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of proteases. This group contains another broadly specific proteinase inhibitor:  pregnancy zone protein (PZP).  PZP is a trace protein in the plasma of non-pregnant females and males which is elevated in ...
CDD:239222	634	miss	miss	cd02892, SQCY_1, Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY)  and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. This group contains bacterial SQCY which catalyzes the convertion of squalene to hopene or diplopterol and eukaryotic OSQCY which transforms ...
CDD:239223	299	miss	miss	cd02893, FTase, Protein farnesyltransferase (FTase)_like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). FTases are a subgroup of PTase family of lipid-modifying enzymes. PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. These proteins are heterodimers of alpha ...
CDD:239224	287	miss	miss	cd02894, GGTase-II, Geranylgeranyltransferase type II (GGTase-II)_like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). GGTase-IIs are a subgroup of the protein prenyltransferase family of lipid-modifying enzymes. PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. ...
CDD:239225	307	miss	miss	cd02895, GGTase-I, Geranylgeranyltransferase types I (GGTase-I)-like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). GGTase-I s are a subgroup of the protein prenyltransferase family of lipid-modifying enzymes PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. ...
CDD:239226	297	miss	miss	cd02896, complement_C3_C4_C5, Proteins similar to C3, C4 and C5 of vertebrate complement.  The vertebrate complement system, comprised of a large number of distinct plasma proteins, is an effector of both the acquired and innate immune systems.  The point of convergence of the classical, alternative and lectin pathways of the complement system is the proteolytic activation of C3. C4 plays a key role in propagating the classical and lectin pathways. C5 participates in the ...
CDD:239227	292	miss	miss	cd02897, A2M_2, Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP).  Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of proteases.  PZP is a trace protein in the plasma of non-pregnant females and males which is elevated in pregnancy. Alpha (2)-M and PZ bind ...
CDD:239229	186	EUKprk	Bacteria:3,Plants:5	cd02900, Macro_Appr_pase, Macro domain, Appr-1"-pase family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. The yeast protein Ymx7 and related proteins in this family contain a stand-alone macro domain and may be specific ...
CDD:239230	140	EUKprk	Bacteria:18,Invertebrates:4,Plants:8,Primates:1,Vertebrates:3	cd02901, Macro_Poa1p_like, Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p ...
CDD:239231	137	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:4	cd02903, Macro_BAL_like, Macro domain, BAL_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases).  Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) ...
CDD:239235	175	EUKprk	Bacteria:2,Mammals:1,Vertebrates:1	cd02907, Macro_Af1521_BAL_like, Macro domain, Af1521- and BAL-like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases).  Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as an Appr-1"-p (ADP-ribose-1"-monophosphate) processing ...
CDD:239236	165	EUKprk	Bacteria:37,Invertebrates:6,Plants:5,Primates:1,Vertebrates:2	cd02908, Macro_Appr_pase_like, Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p ...
CDD:239237	233	PRK	Bacteria:10	cd02911, arch_FMN, Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown.
CDD:239238	344	EUK	Plants:14	cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.  FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one ...
CDD:239239	370	PRK	Bacteria:9	cd02929, TMADH_HD_FMN, Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain.  TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a symetrical dimer with each subunit containing one 4Fe-4S cluster and one FMN cofactor.  It contains a unique flavin, in the form of a 6-S-cysteinyl FMN  which is bent by ~25 degrees along the N5-N10 ...
CDD:239240	353	EUKprk	Bacteria:14,Invertebrates:2	cd02930, DCR_FMN, 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain.  DCR in E. coli  is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the ...
CDD:239242	336	EUKprk	Bacteria:52,Invertebrates:1,Plants:11	cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or ...
CDD:239243	338	EUKprk	Bacteria:79,Invertebrates:4,Plants:21,nodiv:1	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  ...
CDD:239244	299	EUKprk	Bacteria:7,Invertebrates:5,Mammals:1,Plants:2,Primates:1,Vertebrates:3	cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain.  DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a ...
CDD:239245	93	EUKprk	Bacteria:159,Environmental:1,Invertebrates:29,Plants:36,Primates:1,Rodents:1,Vertebrates:4,nodiv:2	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, ...
CDD:239246	102	EUK	Invertebrates:4,Plants:1,Primates:1,Vertebrates:1	cd02948, TRX_NDPK, TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: ...
CDD:239248	142	EUKprk	Bacteria:9,Plants:2	cd02950, TxlA, TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation  of the structure and function of photosynthetic ...
CDD:239249	125	PRK	Bacteria:17	cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to ...
CDD:239250	119	EUK	Invertebrates:4,Plants:2,Rodents:1,Vertebrates:2	cd02952, TRP14_like, Human TRX-related protein 14 (TRP14)-like family; composed of proteins similar to TRP14, a 14kD cytosolic protein that shows disulfide reductase activity in vitro with a different substrate specificity compared with another human cytosolic protein, TRX1. TRP14 catalyzes the reduction of small disulfide-containing peptides but does not reduce disulfides of ribonucleotide reductase, peroxiredoxin and ...
CDD:239251	104	PRK	Bacteria:45,nodiv:1	cd02953, DsbDgamma, DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha).  DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing ...
CDD:239252	114	EUK	Invertebrates:9,Plants:8,Primates:1,Vertebrates:3	cd02954, DIM1, Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein. It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a ...
CDD:239253	124	EUKprk	Bacteria:18,Invertebrates:3,Plants:5,Vertebrates:1	cd02955, SSP411, TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein, called SSP411, is specifically expressed in the testis in an age-dependent manner. The SSP411 mRNA is increased during spermiogenesis and is localized in ...
CDD:239254	96	PRK	Bacteria:21	cd02956, ybbN, ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
CDD:239255	113	EUK	Invertebrates:14,Mammals:1,Plants:17,Primates:1,Rodents:1,Vertebrates:4	cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G ...
CDD:239256	114	EUK	Invertebrates:7,Plants:11,Vertebrates:2	cd02958, UAS, UAS family; UAS is a domain of unknown function. Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting ...
CDD:239259	101	EUK	Invertebrates:30,Plants:29,Primates:1,Vertebrates:5	cd02961, PDI_a_family, Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all ...
CDD:239260	152	EUK	Invertebrates:5,Plants:2,Vertebrates:3	cd02962, TMX2, TMX2 family; composed of proteins similar to human TMX2, a 372-amino acid TRX-related transmembrane protein, identified and characterized through the cloning of its cDNA from a human fetal library. It contains a TRX domain but the redox active CXXC motif is replaced with SXXC. Sequence analysis predicts that TMX2 may be a Type I membrane protein, with its C-terminal half protruding on the luminal side of the endoplasmic ...
CDD:239261	111	EUK	Invertebrates:5,Mammals:1,Vertebrates:3	cd02963, TRX_DnaJ, TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of ...
CDD:239262	132	EUK	Invertebrates:6,Plants:4,Primates:1,Vertebrates:4	cd02964, TryX_like_family, Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
CDD:239263	111	PRK	Bacteria:15,nodiv:1	cd02965, HyaE, HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit ...
CDD:239264	116	EUKprk	Bacteria:142,Invertebrates:2,Primates:1,Vertebrates:2,nodiv:2	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which ...
CDD:239266	142	EUKprk	Bacteria:85,Invertebrates:7,Plants:5,Primates:1,Vertebrates:1,nodiv:1	cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the ...
CDD:239267	171	EUKprk	Bacteria:25,Plants:1,nodiv:1	cd02969, PRX_like1, Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic ...
CDD:239268	149	EUKprk	Bacteria:25,Invertebrates:3,Plants:7,Primates:1,Vertebrates:6	cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their ...
CDD:239269	140	EUKprk	Bacteria:144,Invertebrates:25,Plants:28,Primates:1,Rodents:1,Vertebrates:3,nodiv:3	cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. ...
CDD:239270	98	EUKprk	Bacteria:186,Invertebrates:3,Plants:12,Primates:1,Rodents:1,Vertebrates:3,nodiv:3	cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK ...
CDD:239271	67	PRK	Bacteria:23,nodiv:1	cd02973, TRX_GRX_like, Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some ...
CDD:239272	94	PRK	Bacteria:6	cd02974, AhpF_NTD_N, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also ...
CDD:239273	113	PRK	Bacteria:1	cd02975, PfPDO_like_N, Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active ...
CDD:239274	73	PRK	Bacteria:46,nodiv:1	cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at ...
CDD:239275	105	EUKprk	Bacteria:99,Plants:2,nodiv:1	cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate ...
CDD:239276	72	PRK	Bacteria:12	cd02978, KaiB_like, KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as ...
CDD:239277	167	EUKprk	Bacteria:6,Plants:11	cd02979, PHOX_C, FAD-dependent Phenol hydoxylase (PHOX) family, C-terminal TRX-fold domain; composed of proteins similar to PHOX from the aerobic topsoil yeast Trichosporon cutaneum. PHOX is a flavoprotein monooxygenase that catalyzes the hydroxylation of phenol and simple phenol derivatives in the ortho position with the consumption of NADPH and oxygen. This is the first step in the biodegradation and detoxification of phenolic compounds. PHOX contains ...
CDD:239278	77	EUKprk	Bacteria:109,Invertebrates:12,Plants:18,Vertebrates:3,nodiv:2	cd02980, TRX_Fd_family, Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact ...
CDD:239279	97	EUK	Invertebrates:9,Mammals:1,Plants:11,Primates:1,Vertebrates:4	cd02981, PDI_b_family, Protein Disulfide Isomerase (PDIb) family, redox inactive TRX-like domain b; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57, ERp44 and PDIR. PDI, ERp57 (or ERp60), ERp72 and PDIR are all ...
CDD:239280	103	EUK	Invertebrates:5,Plants:9,Primates:1,Vertebrates:2	cd02982, PDI_b'_family, Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all ...
CDD:239281	130	EUK	Invertebrates:1	cd02983, P5_C, P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are ...
CDD:239282	97	miss	miss	cd02984, TRX_PICOT, TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the ...
CDD:239285	175	miss	miss	cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can ...
CDD:239286	192	miss	miss	cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of ...
CDD:239287	113	miss	miss	cd02989, Phd_like_TxnDC9, Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif. The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that ...
CDD:239290	114	miss	miss	cd02992, PDI_a_QSOX, PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein containing an N-terminal redox active TRX domain, similar to that of PDI, and a small C-terminal flavin adenine dinucleotide (FAD)-binding domain homologous to the yeast ERV1p protein. QSOX oxidizes thiol groups to disulfides like PDI, however, unlike PDI, this oxidation is accompanied by the reduction of oxygen to hydrogen peroxide. QSOX is localized in high ...
CDD:239293	104	miss	miss	cd02995, PDI_a_PDI_a'_C, PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any ...
CDD:239295	104	miss	miss	cd02997, PDI_a_PDIR, PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset ...
CDD:239296	105	miss	miss	cd02998, PDI_a_ERp38, PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5. The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase ...
CDD:239297	100	miss	miss	cd02999, PDI_a_ERp44_like, PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by ...
CDD:239299	103	miss	miss	cd03001, PDI_a_P5, PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first ...
CDD:239300	109	miss	miss	cd03002, PDI_a_MPD1_like, PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the ...
CDD:239302	104	miss	miss	cd03004, PDI_a_ERdj5_C, PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as  JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with ...
CDD:239303	102	miss	miss	cd03005, PDI_a_ERp46, PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named ...
CDD:239307	131	miss	miss	cd03009, TryX_like_TryX_NRX, Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic ...
CDD:239308	127	miss	miss	cd03010, TlpA_like_DsbE, TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. ...
CDD:239309	123	miss	miss	cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, ...
CDD:239310	126	miss	miss	cd03012, TlpA_like_DipZ_like, TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
CDD:239311	155	miss	miss	cd03013, PRX5_like, Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5 suggests that it may have an important antioxidant role in organelles that are major sources of reactive oxygen species (ROS), as well as a role in the control of signal transduction. PRX5 has been shown ...
CDD:239312	143	miss	miss	cd03014, PRX_Atyp2cys, Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic ...
CDD:239313	173	miss	miss	cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is ...
CDD:239314	203	miss	miss	cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its ...
CDD:239315	140	miss	miss	cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of  thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than ...
CDD:239316	149	miss	miss	cd03018, PRX_AhpE_like, Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, ...
CDD:239317	178	miss	miss	cd03019, DsbA_DsbA, DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins ...
CDD:239318	197	miss	miss	cd03020, DsbA_DsbC_DsbG, DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase ...
CDD:239319	209	miss	miss	cd03021, DsbA_GSTK, DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when ...
CDD:239320	192	miss	miss	cd03022, DsbA_HCCA_Iso, DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is ...
CDD:239321	154	miss	miss	cd03023, DsbA_Com1_like, DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
CDD:239322	201	miss	miss	cd03024, DsbA_FrnE, DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
CDD:239323	193	miss	miss	cd03025, DsbA_FrnE_like, DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
CDD:239324	89	miss	miss	cd03026, AhpF_NTD_C, TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also ...
CDD:239326	90	miss	miss	cd03028, GRX_PICOT_like, Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while ...
CDD:239328	92	miss	miss	cd03030, GRX_SH3BGR, Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several ...
CDD:239329	147	miss	miss	cd03031, GRX_GRX_like, Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a ...
CDD:239330	115	miss	miss	cd03032, ArsC_Spx, Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts ...
CDD:239331	113	miss	miss	cd03033, ArsC_15kD, Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], ...
CDD:239332	112	miss	miss	cd03034, ArsC_ArsC, Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent ...
CDD:239333	105	miss	miss	cd03035, ArsC_Yffb, Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via ...
CDD:239334	111	miss	miss	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to ...
CDD:239336	84	miss	miss	cd03038, GST_N_etherase_LigE, GST_N family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase ...
CDD:239337	72	miss	miss	cd03039, GST_N_Sigma_like, GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains ...
CDD:239340	73	miss	miss	cd03042, GST_N_Zeta, GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft ...
CDD:239341	73	miss	miss	cd03043, GST_N_1, GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and ...
CDD:239342	75	miss	miss	cd03044, GST_N_EF1Bgamma, GST_N family, Gamma subunit of Elongation Factor 1B (EFB1gamma) subfamily; EF1Bgamma is part of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists of two functionally distinct units, EF1A and EF1B. EF1A catalyzes the GTP-dependent binding of aminoacyl-tRNA to the ribosomal A site concomitant with the hydrolysis of GTP. The resulting inactive ...
CDD:239343	74	miss	miss	cd03045, GST_N_Delta_Epsilon, GST_N family, Class Delta and Epsilon subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. ...
CDD:239344	76	miss	miss	cd03046, GST_N_GTT1_like, GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, ...
CDD:239345	73	miss	miss	cd03047, GST_N_2, GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the ...
CDD:239346	81	miss	miss	cd03048, GST_N_Ure2p_like, GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources when rich sources are available. A transmissible conformational change of Ure2p results in a prion called [Ure3], an inactive, self-propagating and infectious amyloid. Ure2p displays a GST fold ...
CDD:239347	73	miss	miss	cd03049, GST_N_3, GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the ...
CDD:239348	76	miss	miss	cd03050, GST_N_Theta, GST_N family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal ...
CDD:239349	74	miss	miss	cd03051, GST_N_GTT2_like, GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative ...
CDD:239351	76	miss	miss	cd03053, GST_N_Phi, GST_N family, Class Phi subfamily; composed of plant-specific class Phi GSTs and related fungal and bacterial proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold ...
CDD:239352	72	miss	miss	cd03054, GST_N_Metaxin, GST_N family, Metaxin subfamily; composed of metaxins and related proteins. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the metaxin gene may be associated with Gaucher disease. Metaxin 2 binds to metaxin 1 and may also ...
CDD:239354	73	miss	miss	cd03056, GST_N_4, GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the ...
CDD:239355	77	miss	miss	cd03057, GST_N_Beta, GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft ...
CDD:239356	74	miss	miss	cd03058, GST_N_Tau, GST_N family, Class Tau subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft ...
CDD:239359	91	miss	miss	cd03061, GST_N_CLIC, GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division and apoptosis. They can exist in both water-soluble and membrane-bound states, and are found in various vesicles and membranes. Biochemical studies of the C. elegans homolog, ...
CDD:239360	97	miss	miss	cd03062, TRX_Fd_Sucrase, TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
CDD:239361	92	miss	miss	cd03063, TRX_Fd_FDH_beta, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains ...
CDD:239362	80	miss	miss	cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton ...
CDD:239367	104	miss	miss	cd03069, PDI_b_ERp57, PDIb family, ERp57 subfamily, first redox inactive TRX-like domain b; ERp57 (or ERp60) exhibits both disulfide oxidase and reductase functions like PDI, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER and acting as isomerases to correct any non-native disulfide bonds. It also displays chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp57 contains ...
CDD:239368	91	miss	miss	cd03070, PDI_b_ERp44, PDIb family, ERp44 subfamily, first redox inactive TRX-like domain b; ERp44 is an endoplasmic reticulum (ER)-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. Through the formation of reversible mixed disulfides, ERp44 mediates the ER localization of Ero1alpha, a protein ...
CDD:239371	111	miss	miss	cd03073, PDI_b'_ERp72_ERp57, PDIb' family, ERp72 and ERp57 subfamily, second redox inactive TRX-like domain b'; ERp72 and ER57 are involved in oxidative protein folding in the ER, like PDI. They exhibit both disulfide oxidase and reductase functions, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides and acting as isomerases to correct any non-native disulfide bonds. They also display chaperone activity to prevent protein aggregation and ...
CDD:239374	73	miss	miss	cd03076, GST_N_Pi, GST_N family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between ...
CDD:239376	73	miss	miss	cd03078, GST_N_Metaxin1_like, GST_N family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins including Tom37 from fungi. Mammalian metaxin (or metaxin 1) and the fungal protein Tom37 are components of preprotein import complexes of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. ...
CDD:239378	75	miss	miss	cd03080, GST_N_Metaxin_like, GST_N family, Metaxin subfamily, Metaxin-like proteins; a heterogenous group of proteins, predominantly uncharacterized, with similarity to metaxins and GSTs. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the ...
CDD:239379	80	miss	miss	cd03081, TRX_Fd_NuoE_FDH_gamma, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical ...
CDD:239380	72	miss	miss	cd03082, TRX_Fd_NuoE_W_FDH_beta, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal ...
CDD:100086	355	EUKprk	Bacteria:5,Invertebrates:2,Plants:1,Primates:1	cd03084, phosphohexomutase, The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the ...
CDD:100087	548	EUKprk	Bacteria:5,Invertebrates:11,Mammals:1,Plants:6,Vertebrates:3	cd03085, PGM1, Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction, G-1-P produced from sucrose catabolism is converted to G-6-P, the first intermediate in glycolysis. In the other direction, conversion of G-6-P to ...
CDD:100088	513	EUK	Invertebrates:9,Plants:13,Primates:1,Vertebrates:3	cd03086, PGM3, PGM3 (phosphoglucomutase 3), also known as PAGM (phosphoacetylglucosamine mutase) and AGM1 (N-acetylglucosamine-phosphate mutase), is an essential enzyme found in eukaryotes that reversibly catalyzes the conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate as part of the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway. UDP-GlcNAc is an essential metabolite that serves as the biosynthetic precursor ...
CDD:100089	439	PRK	Bacteria:10	cd03087, PGM_like1, This archaeal PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the ...
CDD:100090	459	EUKprk	Bacteria:27,Plants:1	cd03088, ManB, ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In Mycobacterium tuberculosis, the causative agent of tuberculosis, PMM is involved in the biosynthesis of mannosylated lipoglycans that participate in the association of mycobacteria with host ...
CDD:100091	443	EUKprk	Bacteria:71,Environmental:5,Plants:1	cd03089, PMM_PGM, The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during ...
CDD:239382	363	miss	miss	cd03108, AdSS, Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Because of its critical role in purine biosynthesis, ...
CDD:239384	179	miss	miss	cd03110, Fer4_NifH_child, This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
CDD:239385	106	miss	miss	cd03111, CpaE_like, This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
CDD:239386	158	miss	miss	cd03112, CobW_like, The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
CDD:239387	255	miss	miss	cd03113, CTGs, CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. Glutaminase domains have evolved from the same ancestor, whereas the synthetase domains are evolutionarily unrelated ...
CDD:239388	148	miss	miss	cd03114, ArgK-like, The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
CDD:239389	173	miss	miss	cd03115, SRP, The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a ...
CDD:239390	159	miss	miss	cd03116, MobB, Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
CDD:239391	234	miss	miss	cd03117, alpha_CA_IV_XV_like, Carbonic anhydrase alpha, CA_IV, CA_XV, like isozymes. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in ...
CDD:239396	253	miss	miss	cd03122, alpha_CARP_receptor_like, Carbonic anhydrase alpha related protein, receptor_like subfamily. Carbonic anhydrase related proteins (CARPs) are sequence similar to carbonic anhydrases. Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism. CARPs have lost conserved histidines involved in zinc binding and consequently their catalytic activity. This sub-family of carbonic anhydrase-related ...
CDD:239397	248	miss	miss	cd03123, alpha_CA_VI_IX_XII_XIV, Carbonic anhydrase alpha, isozymes VI, IX, XII and XIV. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved ...
CDD:239398	216	miss	miss	cd03124, alpha_CA_prokaryotic_like, Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved ...
CDD:239401	90	EUK	Invertebrates:17,Mammals:1,Primates:1,Vertebrates:3	cd03127, tetraspanin_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst ...
CDD:153222	92	EUKprk	Bacteria:47,Invertebrates:5,Plants:1,Vertebrates:1,nodiv:1	cd03128, GAT_1, Type 1 glutamine amidotransferase (GATase1)-like domain.  Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The ...
CDD:153223	210	miss	miss	cd03129, GAT1_Peptidase_E_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins.  Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E and, extracellular cyanophycinases from Pseudomonas anguilliseptica BI (CphE) and Synechocystis sp. PCC 6803 CphB. In bacteria ...
CDD:153224	198	miss	miss	cd03130, GATase1_CobB, Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase.  Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide.  CobB belongs to the triad family of amidotransferases.  Two of the three residues of the catalytic triad that are involved in glutamine ...
CDD:153225	175	miss	miss	cd03131, GATase1_HTS, Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS).  Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). HTS, the first enzyme in methionine biosynthesis in Escherichia coli, transfers a succinyl group from succinyl-CoA to homoserine forming succinyl homoserine.  It has been suggested that the succinyl group of succinyl-CoA is initially transferred to ...
CDD:153226	142	miss	miss	cd03132, GATase1_catalase, Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases.  Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II.  This GATase1-like domain ...
CDD:153227	213	miss	miss	cd03133, GATase1_ES1, Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1.  Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1.  The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a ...
CDD:153228	165	miss	miss	cd03134, GATase1_PfpI_like, A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus.  A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus.   This group includes proteins similar to PfpI from P.  furiosus. and PH1704 from Pyrococcus horikoshii. These enzymes are ATP-independent intracellular proteases and may hydrolyze small peptides to provide a nutritional source.  Only Cys of the ...
CDD:153229	163	miss	miss	cd03135, GATase1_DJ-1, Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1.  Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. DJ-1 is involved in multiple physiological processes including cancer, Parkinson's disease and male fertility. It is unclear how DJ-1 functions in these. DJ-1 has been shown to possess chaperone activity. DJ-1 is preferentially expressed in the testis and moderately in other tissues; it is ...
CDD:153230	185	miss	miss	cd03136, GATase1_AraC_ArgR_like, AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain.  A subgroup of AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain.  This group contains proteins similar to the Pseudomonas aeruginosa ArgR regulator.  ArgR functions in the control of expression of certain genes of arginine biosynthesis and catabolism. AraC regulators are ...
CDD:153231	187	miss	miss	cd03137, GATase1_AraC_1, AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain.  A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain.  AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal.  AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological ...
CDD:153232	195	miss	miss	cd03138, GATase1_AraC_2, AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain.  A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain.  AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal.  AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological ...
CDD:153233	183	miss	miss	cd03139, GATase1_PfpI_2, Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.  Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.   PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source.  Only Cys of the catalytic triad typical of GATase1 domains is ...
CDD:153234	170	miss	miss	cd03140, GATase1_PfpI_3, Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.  Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.   PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source.  Only Cys of the catalytic triad typical of GATase1 domains is ...
CDD:153235	221	miss	miss	cd03141, GATase1_Hsp31_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein.  Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein (EcHsp31).  This group includes EcHsp31 and Saccharomyces cerevisiae Ydr533c protein.  EcHsp31 has chaperone activity.  Ydr533c is upregulated in response to various stress conditions along with the heat shock ...
CDD:153237	154	miss	miss	cd03143, A4_beta-galactosidase_middle_domain, A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain.  A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to beta-galactosidase from Thermus thermophilus. Beta-Galactosidase hydrolyzes the beta-1,4-D-galactosidic linkage of lactose, as well as those of related chromogens, ...
CDD:153238	114	miss	miss	cd03144, GATase1_ScBLP_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP).  Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Biotin-apoprotein ligase modifies proteins by covalently attaching biotin.  ScBLP is known to biotinylate acety-CoA carboxylase and pyruvate carboxylase.  ...
CDD:153239	217	miss	miss	cd03145, GAT1_cyanophycinase, Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase.  Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase. This group contains proteins similar to the extracellular cyanophycinases from Pseudomonas anguilliseptica BI (CphE) and Synechocystis sp. PCC 6803 CphB.  Cyanophycinases are intracellular exopeptidases which hydrolyze the polymer cyanophycin (multi L-arginyl-poly-L-aspartic acid) ...
CDD:153240	212	miss	miss	cd03146, GAT1_Peptidase_E, Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E.  Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E. In bacteria peptidase E is believed to play a role in degrading peptides generated by intracellular protein breakdown or imported into the cell as nutrient ...
CDD:153241	231	miss	miss	cd03147, GATase1_Ydr533c_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein.  Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein.  This group includes proteins similar to S. cerevisiae Ydr533c.  Ydr533c is upregulated in response to various stress conditions along with the heat shock family.  The catalytic triad typical of GATase1domains is not conserved in ...
CDD:239404	84	EUK	Primates:1,Vertebrates:5	cd03151, CD81_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), CD81_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ...
CDD:239405	84	EUK	Mammals:1,Primates:1,Vertebrates:5	cd03152, CD9_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), CD9 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability ...
CDD:239407	100	EUK	Invertebrates:1,Mammals:1,Rodents:1,Vertebrates:5	cd03154, TM4SF3_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF3_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various ...
CDD:239408	110	EUK	Invertebrates:8,Mammals:1,Primates:1,Vertebrates:4	cd03155, CD151_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), CD151_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various ...
CDD:239409	114	EUK	Invertebrates:7,Primates:2,Vertebrates:5	cd03156, uroplakin_I_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various ...
CDD:239411	119	EUK	Invertebrates:5,Primates:2,Vertebrates:4	cd03158, penumbra_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), penumbra_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions ...
CDD:239412	121	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:4	cd03159, TM4SF9_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF9_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various ...
CDD:239413	117	EUK	Invertebrates:1,Mammals:2,Primates:1,Rodents:1,Vertebrates:5	cd03160, CD37_CD82_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), CD37_CD82_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and ...
CDD:239414	104	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	cd03161, TM4SF2_6_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF2_6_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and ...
CDD:239415	143	EUK	Invertebrates:1,Primates:1,Vertebrates:5	cd03162, peripherin_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), peripherin_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various ...
CDD:239416	105	EUK	Primates:1,Vertebrates:3	cd03163, TM4SF8_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF8_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to ...
CDD:239418	98	EUK	Invertebrates:4,Primates:1,Vertebrates:4	cd03165, NET-5_like_LEL, Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may ...
CDD:153243	180	miss	miss	cd03169, GATase1_PfpI_1, Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.  Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus.   PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source.  Only Cys of the catalytic triad typical of GATase1 domains is ...
CDD:239421	78	miss	miss	cd03171, SORL_Dfx_classI, Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin.  Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. Desulfoferrodoxin (class I) is a homodimeric ...
CDD:239422	104	miss	miss	cd03172, SORL_classII, Superoxide reductase-like (SORL) domain, class II; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin.  Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, ...
CDD:163674	265	EUKprk	Bacteria:432,Environmental:10,Invertebrates:25,Mammals:2,Plants:36,Primates:1,Vertebrates:3,nodiv:2	cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.  The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and ...
CDD:198287	117	EUK	Invertebrates:21	cd03177, GST_C_Delta_Epsilon, C-terminal, alpha helical domain of Class Delta and Epsilon Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Delta and Epsilon subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins ...
CDD:198288	110	EUKprk	Bacteria:11,Invertebrates:3,Plants:1	cd03178, GST_C_Ure2p_like, C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins.  Glutathione S-transferase (GST) C-terminal domain family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p, YfcG and YghU from Escherichia coli, and related GST-like proteins. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in ...
CDD:198289	110	PRK	Bacteria:14	cd03180, GST_C_2, C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 2; composed of uncharacterized bacterial proteins, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including ...
CDD:198290	123	EUK	Invertebrates:28,Plants:27,Vertebrates:1,nodiv:1	cd03181, GST_C_EF1Bgamma_like, Glutathione S-transferase C-terminal-like, alpha helical domain of the Gamma subunit of Elongation Factor 1B and similar proteins.  Glutathione S-transferase (GST) C-terminal domain family, Gamma subunit of Elongation Factor 1B (EF1Bgamma) subfamily; EF1Bgamma is part of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein ...
CDD:198291	116	PRK	Bacteria:7	cd03182, GST_C_GTT2_like, C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the Saccharomyces cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of ...
CDD:198292	126	EUK	Invertebrates:3,Mammals:1,Plants:3,Primates:1,Vertebrates:2	cd03183, GST_C_Theta, C-terminal, alpha helical domain of Class Theta Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of ...
CDD:198293	124	EUK	Invertebrates:5,Primates:1,Rodents:1,Vertebrates:2	cd03184, GST_C_Omega, C-terminal, alpha helical domain of Class Omega Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Omega subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental ...
CDD:198294	127	EUK	Plants:19	cd03185, GST_C_Tau, C-terminal, alpha helical domain of Class Tau Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Tau subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST ...
CDD:198295	108	PRK	Bacteria:12	cd03186, GST_C_SspA, C-terminal, alpha helical domain of Stringent starvation protein A.  Glutathione S-transferase (GST) C-terminal domain family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival during nutrient starvation. SspA adopts the GST fold with an N-terminal ...
CDD:198296	118	EUK	Plants:14	cd03187, GST_C_Phi, C-terminal, alpha helical domain of Class Phi Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Phi subfamily; composed of plant-specific class Phi GSTs and related fungal and bacterial proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, ...
CDD:198297	113	EUKprk	Bacteria:31,Invertebrates:1,Plants:1,nodiv:1	cd03188, GST_C_Beta, C-terminal, alpha helical domain of Class Beta Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and ...
CDD:198298	123	EUKprk	Bacteria:15,Plants:5	cd03189, GST_C_GTT1_like, C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation ...
CDD:198299	142	EUKprk	Bacteria:15,Invertebrates:2,Plants:9	cd03190, GST_C_Omega_like, C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae Omega-like subfamily; composed of three Saccharomyces cerevisiae GST omega-like (Gto) proteins, Gto1p, Gto2p (also known as Extracellular mutant protein 4 or ECM4p), and Gto3p, as well as similar uncharacterized proteins from fungi and bacteria. The ...
CDD:198300	121	EUKprk	Bacteria:23,Invertebrates:5,Plants:7,Vertebrates:3	cd03191, GST_C_Zeta, C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental ...
CDD:198301	104	EUKprk	Bacteria:3,Invertebrates:25,Plants:1,Primates:1,Rodents:1	cd03192, GST_C_Sigma_like, C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi, and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) ...
CDD:198302	88	EUKprk	Bacteria:4,Invertebrates:4,Plants:3,Vertebrates:1	cd03193, GST_C_Metaxin, C-terminal, alpha helical domain of Metaxin and related proteins.  Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily; composed of metaxins and related proteins. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is ...
CDD:198303	115	EUKprk	Bacteria:59,Plants:4	cd03194, GST_C_3, C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 3; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including ...
CDD:198304	114	PRK	Bacteria:2	cd03195, GST_C_4, C-terminal, alpha helical domain of an unknown subfamily 4 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including ...
CDD:198305	115	PRK	Bacteria:70	cd03196, GST_C_5, C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 5; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including ...
CDD:198306	149	EUKprk	Bacteria:1,Invertebrates:14,Plants:6,Primates:1,Vertebrates:2,nodiv:1	cd03197, GST_C_mPGES2, C-terminal, alpha helical domain of microsomal Prostaglandin E synthase Type 2.  Glutathione S-transferase (GST) C-terminal domain family, microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type ...
CDD:198307	119	EUK	Invertebrates:11,Primates:1,Vertebrates:1,nodiv:1	cd03198, GST_C_CLIC, C-terminal, alpha helical domain of Chloride Intracellular Channels.  Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLICs (CLIC1-6 in vertebrates), p64, parchorin, and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell ...
CDD:198308	128	EUKprk	Bacteria:21,Plants:5	cd03199, GST_C_GRX2, C-terminal, alpha helical domain of Glutaredoxin 2.  Glutathione S-transferase (GST) C-terminal domain family, Glutaredoxin 2 (GRX2) subfamily; composed of Escherichia coli GRX2 and similar proteins. Escherichia coli GRX2 is an atypical GRX with a molecular mass of about 24kD (most GRXs range from 9-12kD). It adopts a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. It contains a redox ...
CDD:198311	124	PRK	Bacteria:17	cd03202, GST_C_etherase_LigE, C-terminal, alpha helical domain of Beta etherase LigE.  Glutathione S-transferase (GST) C-terminal domain family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of ...
CDD:198314	109	EUKprk	Bacteria:49,Plants:1	cd03205, GST_C_6, C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 6; composed of uncharacterized bacterial proteins with similarity to GSTs, including Pseudomonas fluorescens GST with a known three-dimensional structure. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione ...
CDD:198315	100	PRK	Bacteria:21	cd03206, GST_C_7, C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 7; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, ...
CDD:198316	101	PRK	Bacteria:9	cd03207, GST_C_8, C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 8; composed of Agrobacterium tumefaciens GST and other uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic ...
CDD:198317	135	EUK	Invertebrates:1,Mammals:2,Primates:1,Vertebrates:3	cd03208, GST_C_Alpha, C-terminal, alpha helical domain of Class Alpha Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Alpha subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental ...
CDD:198318	121	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:2	cd03209, GST_C_Mu, C-terminal, alpha helical domain of Class Mu Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and ...
CDD:198319	126	EUK	Invertebrates:1,Vertebrates:4	cd03210, GST_C_Pi, C-terminal, alpha helical domain of Class Pi Glutathione S-transferases.  Glutathione S-transferase (GST) C-terminal domain family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative ...
CDD:198320	126	EUK	Invertebrates:11	cd03211, GST_C_Metaxin2, C-terminal, alpha helical domain of Metaxin 2.  Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its ...
CDD:198321	137	EUK	Invertebrates:12,Primates:1,Vertebrates:3,nodiv:1	cd03212, GST_C_Metaxin1_3, C-terminal, alpha helical domain of Metaxin 1, Metaxin 3, and similar proteins.  Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins. Mammalian metaxin (or metaxin 1) is a component of the preprotein import complex of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to ...
CDD:213180	194	EUKprk	Bacteria:4,Invertebrates:5,Plants:5,Primates:2,Vertebrates:2	cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette superfamily.  ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared ...
CDD:213181	180	PRK	Bacteria:53	cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins.  ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) ...
CDD:213182	182	PRK	Bacteria:44,nodiv:2	cd03215, ABC_Carb_Monos_II, Second domain of the ATP-binding cassette component of monosaccharide transport system.  This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by ...
CDD:213183	163	PRK	Bacteria:20,nodiv:1	cd03216, ABC_Carb_Monos_I, First domain of the ATP-binding cassette component of monosaccharide transport system.  This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by ...
CDD:213184	200	EUKprk	Bacteria:14,Invertebrates:2,Plants:3	cd03217, ABC_FeS_Assembly, ABC-type transport system involved in Fe-S cluster assembly, ATPase component.  Biosynthesis of iron-sulfur clusters (Fe-S) depends on multi-protein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the ...
CDD:213185	232	EUKprk	Bacteria:21,Plants:3,nodiv:1	cd03218, ABC_YhbG, ATP-binding cassette component of YhbG transport system.  The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative ...
CDD:213186	236	PRK	Bacteria:35,Environmental:2,nodiv:1	cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component of branched chain amino acids transport system.  The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from ...
CDD:213187	224	PRK	Bacteria:31,nodiv:1	cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of polysaccharide transport system.  The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ...
CDD:213188	144	EUKprk	Bacteria:37,Invertebrates:7,Plants:8,Primates:1,Vertebrates:3	cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation factor 3, subfamily F.  Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. ...
CDD:213190	166	EUKprk	Bacteria:8,Invertebrates:6,Plants:5,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of peroxisomal transporter, subfamily D.  Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate ...
CDD:213191	222	PRK	Bacteria:31,nodiv:2	cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of branched-chain amino acid transporter.  LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic ...
CDD:213192	211	EUKprk	Bacteria:51,Plants:2,nodiv:1	cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding cassette component of cobalt transport system.  Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in ...
CDD:213193	205	PRK	Bacteria:2	cd03226, ABC_cobalt_CbiO_domain2, Second domain of the ATP-binding cassette component of cobalt transport system.  Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin ...
CDD:213194	162	miss	miss	cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter proteins.  ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.
CDD:213195	171	EUKprk	Bacteria:107,Environmental:1,Invertebrates:9,Plants:12,Vertebrates:2	cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug resistance protein-like transporters.  The MRP (Multidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion ...
CDD:213196	178	PRK	Bacteria:11	cd03229, ABC_Class3, ATP-binding cassette domain of the binding protein-dependent transport systems.  This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic ...
CDD:213197	173	EUKprk	Bacteria:89,Environmental:1,Invertebrates:3	cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A.  This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. ...
CDD:213199	192	EUK	Invertebrates:1,Plants:7	cd03232, ABCG_PDR_domain2, Second domain of the pleiotropic drug resistance-like (PDR) subfamily G of ATP-binding cassette transporters.  The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a ...
CDD:213200	202	EUK	Plants:1	cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug resistance-like subfamily G of ATP-binding cassette transporters.  The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of ...
CDD:213201	226	EUK	Invertebrates:1,Plants:1,Rodents:1,Vertebrates:2	cd03234, ABCG_White, White pigment protein homolog of ABCG transporter subfamily.  The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from ...
CDD:213202	213	EUKprk	Bacteria:28,Plants:1	cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the metal-type transporters.  This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the ...
CDD:213205	176	PRK	Bacteria:3	cd03238, ABC_UvrA, ATP-binding cassette domain of the excision repair protein UvrA.  Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic ...
CDD:213206	178	EUK	Plants:1	cd03239, ABC_SMC_head, The SMC head domain belongs to the ATP-binding cassette superfamily.  The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct ...
CDD:213207	204	EUKprk	Bacteria:3,Invertebrates:5,Plants:6	cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50.  The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved ...
CDD:213208	276	PRK	Bacteria:34	cd03241, ABC_RecN, ATP-binding cassette domain of RecN.  RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are ...
CDD:213209	270	miss	miss	cd03242, ABC_RecF, ATP-binding cassette domain of RecF.  RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters ...
CDD:213210	202	EUKprk	Bacteria:5,Invertebrates:2,Plants:3	cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS homologs.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic ...
CDD:213211	221	EUKprk	Bacteria:1,Invertebrates:12,Plants:12,Primates:1,Vertebrates:2	cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of multidrug resistance-associated protein.  The ABC subfamily C is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell ...
CDD:213212	220	EUKprk	Bacteria:11,Invertebrates:1	cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain of bacteriocin exporters, subfamily C.  Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic ...
CDD:213213	173	PRK	Bacteria:7	cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of PrtD, subfamily C.  This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion ...
CDD:213216	238	EUKprk	Bacteria:2,Invertebrates:9,Plants:6,Vertebrates:4	cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins.  MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 ...
CDD:213217	204	EUKprk	Bacteria:1,Invertebrates:6,Plants:12,Primates:2,Rodents:1,Vertebrates:2	cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C.  This subfamily is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting ...
CDD:213218	234	PRK	Bacteria:13	cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C.  MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the ...
CDD:213220	236	EUKprk	Bacteria:2,Invertebrates:6,Plants:7,Primates:1,Vertebrates:1	cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C.  ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme ...
CDD:213221	229	EUKprk	Bacteria:12,Plants:1	cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of glucan transporter and related proteins, subfamily C.  Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virulence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common ...
CDD:213222	218	EUKprk	Bacteria:37,Invertebrates:3	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein.  This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter ...
CDD:213223	241	PRK	Bacteria:13,nodiv:1	cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the binding protein-dependent phosphonate transport system.  Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use ...
CDD:213224	228	PRK	Bacteria:35	cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain of nickel/oligopeptides specific transporters.  The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under ...
CDD:213225	233	PRK	Bacteria:29	cd03258, ABC_MetN_methionine_transporter, ATP-binding cassette domain of methionine transporter.  MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in ...
CDD:213226	213	PRK	Bacteria:26	cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of the carbohydrate and solute transporters-like.  This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The ...
CDD:213227	227	EUKprk	Bacteria:36,Plants:3,nodiv:1	cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette domain of the phosphate transport system.  Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. PstA and PstC are ...
CDD:213228	235	EUKprk	Bacteria:30,Plants:1	cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette transport system involved in resistant to organic solvents.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that ...
CDD:213229	213	EUKprk	Bacteria:30,Invertebrates:1	cd03262, ABC_HisP_GlnQ, ATP-binding cassette domain of the histidine and glutamine transporters.  HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, respectively. Histidine permease is a multi-subunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is ...
CDD:213230	220	EUK	Invertebrates:13,Plants:7,Primates:1,Vertebrates:3	cd03263, ABC_subfamily_A, ATP-binding cassette domain of the lipid transporters, subfamily A.  The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 ...
CDD:213231	211	PRK	Bacteria:14	cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component.  The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between ...
CDD:213235	208	PRK	Bacteria:11	cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of the bacitracin-resistance transporter.  The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of ...
CDD:213236	210	PRK	Bacteria:11	cd03269, ABC_putative_ATPase, ATP-binding cassette domain of an uncharacterized transporter.  This subgroup is related to the subfamily A transporters involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two integral membranes. ABC transporters are a large family of proteins involved in the transport of a wide variety of different ...
CDD:213237	226	PRK	Bacteria:10	cd03270, ABC_UvrA_I, ATP-binding cassette domain I of the excision repair protein UvrA.  Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic ...
CDD:213238	261	miss	miss	cd03271, ABC_UvrA_II, ATP-binding cassette domain II of the excision repair protein UvrA.  Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic ...
CDD:213239	243	EUK	Invertebrates:9,Mammals:1,Plants:18,Primates:1,Rodents:1,Vertebrates:4	cd03272, ABC_SMC3_euk, ATP-binding cassette domain of eukaryotic SMC3 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a ...
CDD:213240	251	EUK	Invertebrates:11,Mammals:1,Plants:19,Primates:1,Rodents:2,Vertebrates:4	cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic SMC2 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a ...
CDD:213241	212	EUK	Invertebrates:12,Mammals:1,Plants:18,Primates:1,Rodents:2,Vertebrates:3	cd03274, ABC_SMC4_euk, ATP-binding cassette domain of eukaryotic SMC4 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a ...
CDD:213242	247	EUK	Invertebrates:11,Mammals:1,Plants:17,Primates:2,Rodents:2,Vertebrates:6	cd03275, ABC_SMC1_euk, ATP-binding cassette domain of eukaryotic SMC1 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a ...
CDD:213243	198	EUK	Invertebrates:7,Mammals:1,Plants:18,Primates:1,Vertebrates:4	cd03276, ABC_SMC6_euk, ATP-binding cassette domain of eukaryotic SM6 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' ...
CDD:213244	213	EUK	Invertebrates:8,Mammals:1,Plants:16,Primates:1,Rodents:1,Vertebrates:3	cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic SMC5 proteins.  The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a ...
CDD:213245	197	EUKprk	Bacteria:146,Rodents:1,nodiv:2	cd03278, ABC_SMC_barmotin, ATP-binding cassette domain of barmotin, a member of the SMC protein family.  Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid ...
CDD:213246	213	PRK	Bacteria:9	cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD.  SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.
CDD:213247	200	EUKprk	Bacteria:9,Plants:2	cd03280, ABC_MutS2, ATP-binding cassette domain of MutS2.  MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most ...
CDD:213248	213	EUK	Invertebrates:3,Plants:8,Primates:1	cd03281, ABC_MSH5_euk, ATP-binding cassette domain of eukaryotic MutS5 homolog.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified ...
CDD:213250	199	PRK	Bacteria:7	cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like homolog.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all ...
CDD:213251	216	PRK	Bacteria:11	cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic ...
CDD:213260	220	PRK	Bacteria:41,nodiv:2	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters.  NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest ...
CDD:213261	269	EUKprk	Bacteria:15,Invertebrates:1,nodiv:1	cd03294, ABC_Pro_Gly_Betaine, ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system.  This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate ...
CDD:213262	242	PRK	Bacteria:10	cd03295, ABC_OpuCA_Osmoprotection, ATP-binding cassette domain of the osmoprotectant transporter.  OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more ...
CDD:213264	214	PRK	Bacteria:6	cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette domain of the molybdenum transport system.  ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The ...
CDD:213267	232	PRK	Bacteria:15	cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine transporter.  PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the ...
CDD:213268	213	PRK	Bacteria:10	cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose transporter, MalK.  ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic ...
CDD:176471	436	miss	miss	cd03302, Adenylsuccinate_lyase_2, Adenylsuccinate lyase (ASL)_subgroup 2.  This subgroup contains mainly eukaryotic proteins similar to ASL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues ...
CDD:239423	326	PRK	Bacteria:8	cd03307, Mta_CmuA_like, MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M isozymes, are methylcobamide:Coenzyme M methyltransferases, which play a role in metabolic pathways of methane formation from various substrates, such as methylated amines and methanol. Coenzyme M, 2-mercaptoethylsulfonate or CoM, is methylated during methanogenesis in a reaction catalyzed by three proteins. A methyltransferase methylates the corrinoid ...
CDD:239424	378	PRK	Bacteria:4	cd03308, CmuA_CmuC_like, CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC.
CDD:239425	321	PRK	Bacteria:4	cd03309, CmuC_like, CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism.
CDD:239426	321	PRK	Bacteria:15,Environmental:1	cd03310, CIMS_like, CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a ...
CDD:239427	332	EUKprk	Bacteria:57,Invertebrates:3,Plants:12	cd03311, CIMS_C_terminal_like, CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an ...
CDD:239428	360	EUKprk	Bacteria:25,Plants:3,Rodents:1	cd03312, CIMS_N_terminal_like, CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate ...
CDD:239429	408	EUKprk	Bacteria:27,Environmental:1,Invertebrates:13,Plants:11,Primates:1,Vertebrates:3,nodiv:1	cd03313, enolase, Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions.
CDD:239431	265	PRK	Bacteria:8	cd03315, MLE_like, Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, ...
CDD:239432	357	PRK	Bacteria:39,nodiv:2	cd03316, MR_like, Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues,  a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD),  D-altronate/D-mannonate ...
CDD:239433	354	PRK	Bacteria:19	cd03317, NAAAR, N-acylamino acid racemase (NAAAR), an octameric enzyme that catalyzes the racemization of N-acylamino acids. NAAARs act on a broad range of N-acylamino acids rather than amino acids. Enantiopure amino acids are of industrial interest as chiral building blocks for antibiotics, herbicides, and drugs. NAAAR is a member of the enolase superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the ...
CDD:239434	365	PRK	Bacteria:14	cd03318, MLE, Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate ...
CDD:239435	316	EUKprk	Bacteria:35,Environmental:1,Plants:2,nodiv:1	cd03319, L-Ala-DL-Glu_epimerase, L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which ...
CDD:239436	263	PRK	Bacteria:30	cd03320, OSBS, o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway. Menaquinone is an essential cofactor for anaerobic growth in eubacteria and some archaea. OSBS belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which ...
CDD:239439	395	EUKprk	Bacteria:10,Plants:1,nodiv:1	cd03323, D-glucarate_dehydratase, D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active ...
CDD:239441	352	EUKprk	Bacteria:5,Plants:2	cd03325, D-galactonate_dehydratase, D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active ...
CDD:239443	341	EUKprk	Bacteria:5,Plants:3,nodiv:1	cd03327, MR_like_2, Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues,  a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown.
CDD:239448	383	EUKprk	Bacteria:9,Plants:5	cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases.  It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer.
CDD:239449	209	EUK	Invertebrates:7,Plants:9,Primates:1,Vertebrates:1	cd03333, chaperonin_like, chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or ...
CDD:239450	261	miss	miss	cd03334, Fab1_TCP, TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1.  Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this domain leads to loss of catalytic activity. However no exact function this domain has been defined. In general, chaperonins are involved in productive folding of proteins.
CDD:239451	527	miss	miss	cd03335, TCP1_alpha, TCP-1 (CTT or eukaryotic type II) chaperonin family, alpha subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity ...
CDD:239452	517	miss	miss	cd03336, TCP1_beta, TCP-1 (CTT or eukaryotic type II) chaperonin family, beta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and ...
CDD:239453	480	miss	miss	cd03337, TCP1_gamma, TCP-1 (CTT or eukaryotic type II) chaperonin family, gamma subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity ...
CDD:239454	515	miss	miss	cd03338, TCP1_delta, TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity ...
CDD:239455	526	miss	miss	cd03339, TCP1_epsilon, TCP-1 (CTT or eukaryotic type II) chaperonin family, epsilon subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central ...
CDD:239456	522	miss	miss	cd03340, TCP1_eta, TCP-1 (CTT or eukaryotic type II) chaperonin family, eta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and ...
CDD:239457	472	miss	miss	cd03341, TCP1_theta, TCP-1 (CTT or eukaryotic type II) chaperonin family, theta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity ...
CDD:239458	484	miss	miss	cd03342, TCP1_zeta, TCP-1 (CTT or eukaryotic type II) chaperonin family, zeta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and ...
CDD:239459	517	miss	miss	cd03343, cpn60, cpn60 chaperonin family. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. Archaeal cpn60 (thermosome), together with TF55 from thermophilic bacteria and the eukaryotic cytosol chaperonin (CTT), belong to the type II group of chaperonins. Cpn60 consists of two stacked octameric rings, which are composed of one or two different subunits.  Their common function is to ...
CDD:239460	520	miss	miss	cd03344, GroEL, GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). With the aid of cochaperonin GroES, GroEL encapsulates non-native substrate proteins inside the cavity of the GroEL-ES complex ...
CDD:239464	228	miss	miss	cd03348, pro_PheOH, Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH), tyrosine hydroxylase (TyrOH) and tryptophan hydroxylase (TrpOH). PheOH catalyzes the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the ...
CDD:100040	145	PRK	Bacteria:73,Environmental:2,nodiv:1	cd03349, LbH_XAT, Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and streptogramin, among others. Members of this class of enzymes include Enterococcus faecium streptogramin A acetyltransferase and Pseudomonas aeruginosa chloramphenicol ...
CDD:100041	139	EUKprk	Bacteria:9,Plants:1	cd03350, LbH_THP_succinylT, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA. It is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The enzyme is homotrimeric and ...
CDD:100042	254	EUKprk	Bacteria:72,Environmental:1,Invertebrates:1,Plants:3	cd03351, LbH_UDP-GlcNAc_AT, UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic pathway and is also referred to as LpxA. Lipid A is essential for the growth of Escherichia coli and related bacteria. It is also essential for ...
CDD:100043	205	EUKprk	Bacteria:104,Environmental:2,Plants:1	cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-diacyl-GlcNAc. This constitutes the third step in the lipid A biosynthetic pathway in Gram-negative bacteria. LpxD is a homotrimer, with each subunit consisting of a novel ...
CDD:100044	193	PRK	Bacteria:77	cd03353, LbH_GlmU_C, N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two consecutive steps in the formation of UDP-N-acetylglucosamine (UDP-GlcNAc), an important precursor in bacterial cell wall formation. The two enzymatic activities, uridyltransferase and ...
CDD:100045	101	EUKprk	Bacteria:76,Invertebrates:3,Plants:5	cd03354, LbH_SAT, Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-cysteine. This reaction represents a key metabolic point of regulation for the cysteine biosynthetic pathway due to its feedback inhibition by cysteine. The enzyme is a 175 ...
CDD:100046	79	EUKprk	Bacteria:7,Invertebrates:4,Primates:1	cd03356, LbH_G1P_AT_C_like, Left-handed parallel beta-Helix (LbH) domain of a group of proteins with similarity to glucose-1-phosphate adenylyltransferase: Included in this family are glucose-1-phosphate adenylyltransferase, mannose-1-phosphate guanylyltransferase, and the eukaryotic translation initiation factor eIF-2B subunits, epsilon and gamma. Most members of this family contains an N-terminal catalytic domain that resembles a ...
CDD:100047	169	EUKprk	Bacteria:65,Invertebrates:3,Plants:16	cd03357, LbH_MAT_GAT, Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6 position of the nonreducing end glucosyl moiety. GAT specifically acetylates galactopyranosides. Furthermore, MAT shows higher affinity toward artificial substrates ...
CDD:100048	119	PRK	Bacteria:53	cd03358, LbH_WxcM_N_like, WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization and transacetylation reactions of keto-hexoses. It contains an N-terminal LbH domain responsible for the transacetylation function and a C-terminal isomerase domain. The LbH domain contains ...
CDD:100049	161	EUK	Invertebrates:11,Plants:10,Primates:1,Rodents:1,Vertebrates:3	cd03359, LbH_Dynactin_5, Dynactin 5 (or subunit p25); Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through ...
CDD:100050	197	PRK	Bacteria:122,Environmental:1	cd03360, LbH_AT_putative, Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase ...
CDD:173781	170	miss	miss	cd03361, TOPRIM_TopoIA_RevGyr, TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to ...
CDD:173782	151	miss	miss	cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two ...
CDD:173783	123	miss	miss	cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM ...
CDD:173784	79	miss	miss	cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other ...
CDD:173785	120	miss	miss	cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass ...
CDD:173786	114	miss	miss	cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass ...
CDD:239465	115	EUKprk	Bacteria:4,Invertebrates:14,Plants:7,Primates:1,Vertebrates:3	cd03367, Ribosomal_S23, S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) ...
CDD:239466	108	EUKprk	Bacteria:12,Invertebrates:16,Plants:18,Primates:1,Vertebrates:2	cd03368, Ribosomal_S12, S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and ...
CDD:239468	188	EUKprk	Bacteria:8,Invertebrates:2	cd03371, TPP_PpyrDC, Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors.
CDD:239469	179	PRK	Bacteria:7	cd03372, TPP_ComE, Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.
CDD:239470	193	PRK	Bacteria:26	cd03375, TPP_OGFOR, Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. In the reductive tricarboxylic acid cycle found in the anaerobic autotroph Hydrogenobacter thermophilus, OGFOR catalyzes ...
CDD:239471	235	PRK	Bacteria:21	cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria ...
CDD:239472	365	EUKprk	Bacteria:15,Invertebrates:6,Plants:1	cd03377, TPP_PFOR_PNO, Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. ...
CDD:239473	154	PRK	Bacteria:1	cd03378, beta_CA_cladeC, Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, ...
CDD:239474	142	miss	miss	cd03379, beta_CA_cladeD, Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, ...
CDD:239475	209	miss	miss	cd03380, PAP2_like_1, PAP2_like_1 proteins, a sub-family of PAP2, containing bacterial acid phosphatase, vanadium chloroperoxidases and vanadium bromoperoxidases.
CDD:239476	235	miss	miss	cd03381, PAP2_glucose_6_phosphatase, PAP2_like proteins, glucose-6-phosphatase subfamily. Glucose-6-phosphatase converts glucose-6-phosphate into free glucose and is active in the lumen of the endoplasmic reticulum, where it is bound to the membrane. The generation of free glucose is an important control point in metabolism, and stands at the end of gluconeogenesis and the release of glucose from glycogen. Deficiency of glucose-6-phosphatase leads to von Gierke's disease.
CDD:239477	159	miss	miss	cd03382, PAP2_dolichyldiphosphatase, PAP2_like proteins, dolichyldiphosphatase subfamily. Dolichyldiphosphatase is a membrane-associated protein located in the endoplasmic reticulum and hydrolyzes dolichyl pyrophosphate, as well as dolichylmonophosphate at a low rate. The enzyme is necessary for maintaining proper levels of dolichol-linked oligosaccharides and protein N-glycosylation, and might play a role in re-utilization of the glycosyl carrier lipid for additional ...
CDD:239479	150	miss	miss	cd03384, PAP2_wunen, PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.
CDD:239480	144	miss	miss	cd03385, PAP2_BcrC_like, PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from Bacillus subtilis posesses undecaprenyl pyrophosphate (UPP) phospatase activity, and it is hypothesized that it competes with bacitracin for UPP, increasing the cell's resistance to bacitracin.
CDD:239481	186	miss	miss	cd03386, PAP2_Aur1_like, PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin.
CDD:239482	151	miss	miss	cd03388, PAP2_SPPase1, PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second messenger in the cell, and extracellularly by binding to G-protein coupled receptors of the endothelial differentiation gene family.
CDD:239483	186	miss	miss	cd03389, PAP2_lipid_A_1_phosphatase, PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major constituents of the outer membrane in many gram-negative bacteria.
CDD:239484	193	miss	miss	cd03390, PAP2_containing_1_like, PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity, they may have a more generic housekeeping role in lipid metabolism.
CDD:239485	159	miss	miss	cd03391, PAP2_containing_2_like, PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_2. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to eukaryota, lacks functional characterization and may act as a membrane-associated phosphatidic acid phosphatase.
CDD:239486	182	miss	miss	cd03392, PAP2_like_2, PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase.
CDD:239488	106	miss	miss	cd03394, PAP2_like_5, PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase.
CDD:239489	177	miss	miss	cd03395, PAP2_like_4, PAP2_like_4 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase.
CDD:239490	197	miss	miss	cd03396, PAP2_like_6, PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase.
CDD:239491	232	miss	miss	cd03397, PAP2_acid_phosphatase, PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains to be determined.
CDD:239492	232	miss	miss	cd03398, PAP2_haloperoxidase, PAP2, haloperoxidase_like subfamily. Haloperoxidases catalyze the oxidation of halides such as bromide or chloride by hydrogen peroxide, which results in subsequent halogenation of organic substrates, or halide-assisted disproportionation of hydrogen peroxide forming dioxygen. They are likely to participate in the biosynthesis of halogenated natural products, such as volatile halogenated hydrocarbons, chiral halogenated terpenes, acetogenins ...
CDD:259798	145	EUKprk	Bacteria:83,Invertebrates:16,Plants:11,Primates:1,Vertebrates:3,nodiv:1	cd03399, SPFH_flotillin, Flotillin or reggie family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  The flotillin (reggie) like proteins are lipid raft-associated. Individual proteins of this SPFH family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. In addition, microdomains formed from flotillin proteins may be dynamic units with their own ...
CDD:259799	195	EUKprk	Bacteria:158,Environmental:4,Invertebrates:27,Plants:25,Primates:1,Vertebrates:3	cd03401, SPFH_prohibitin, Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model characterizes proteins similar to prohibitin (a lipid raft-associated integral membrane protein). Individual proteins of the SPFH (band 7) domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains, in ...
CDD:259800	231	EUKprk	Bacteria:41,Invertebrates:2,Plants:3	cd03402, SPFH_like_u2, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH ...
CDD:259802	266	PRK	Bacteria:181,Environmental:4	cd03404, SPFH_HflK, High frequency of lysogenization K (HflK) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model characterizes proteins similar to prokaryotic HflK (High frequency of lysogenization K). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain ...
CDD:259803	249	EUKprk	Bacteria:174,Environmental:2,Invertebrates:1,Plants:1	cd03405, SPFH_HflC, High frequency of lysogenization C (HflC) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model characterizes proteins similar to prokaryotic HflC (High frequency of lysogenization C). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual ...
CDD:259804	293	EUK	Invertebrates:9,Plants:8,Vertebrates:3	cd03406, SPFH_like_u3, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH ...
CDD:259805	269	EUKprk	Bacteria:16,Invertebrates:3,Plants:13	cd03407, SPFH_like_u4, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH ...
CDD:259806	217	PRK	Bacteria:146,Environmental:1	cd03408, SPFH_like_u1, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may ...
CDD:239503	101	PRK	Bacteria:4	cd03409, Chelatase_Class_II, Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. ...
CDD:239504	159	EUKprk	Bacteria:12,Invertebrates:1,Plants:1	cd03411, Ferrochelatase_N, Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes ...
CDD:239505	127	PRK	Bacteria:19	cd03412, CbiK_N, Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
CDD:239506	103	PRK	Bacteria:5	cd03413, CbiK_C, Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases, and is a homomeric enzyme that does not require ATP for its enzymatic activity.
CDD:239507	117	PRK	Bacteria:35	cd03414, CbiX_SirB_C, Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be ...
CDD:239509	101	EUKprk	Bacteria:65,Plants:2,nodiv:1	cd03416, CbiX_SirB_N, Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich ...
CDD:239510	75	miss	miss	cd03418, GRX_GRXb_1_3_like, Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular ...
CDD:239511	82	miss	miss	cd03419, GRX_GRXh_1_2_like, Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for ...
CDD:239513	67	miss	miss	cd03421, SirA_like_N, SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain.  The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA  (also known as UvrY,  and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA.  A variety of microorganisms have similar ...
CDD:239516	137	EUKprk	Bacteria:177,Invertebrates:14,Plants:12,Primates:1,Vertebrates:3,nodiv:1	cd03424, ADPRase_NUDT5, ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which ...
CDD:239517	124	EUKprk	Bacteria:102,Invertebrates:1,nodiv:1	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi). This enzyme requires two divalent cations for activity; one coordinates the phosphoryl groups of the NTP/dNTP substrate, and the ...
CDD:239518	157	EUKprk	Bacteria:91,Environmental:2,Invertebrates:12,Plants:12,Primates:1,Vertebrates:3,nodiv:1	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative stress. CoAse has a conserved Nudix fold and requires a single divalent cation for catalysis. In addition to a signature ...
CDD:239519	137	EUKprk	Bacteria:32,Invertebrates:5,Plants:4,Vertebrates:2	cd03427, MTH1, MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA.  Like other members of the ...
CDD:239520	130	EUKprk	Bacteria:15,Invertebrates:6,Vertebrates:3	cd03428, Ap4A_hydrolase_human_like, Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both ...
CDD:239521	131	EUKprk	Bacteria:59,Invertebrates:4,Plants:9,Primates:1,Vertebrates:3	cd03429, NADH_pyrophosphatase, NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity. Members of this family are also recognized by the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where ...
CDD:239522	144	PRK	Bacteria:9	cd03430, GDPMH, GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix signature sequence. The slight changes to the conserved sequence motif, GX5EX7REUXEEXGU, where U = I, L or V), are believed to contribute to the removal of all magnesium binding sites but one, retaining only ...
CDD:239523	118	EUKprk	Bacteria:69,Invertebrates:4,Plants:7,Vertebrates:2	cd03431, DNA_Glycosylase_C, DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread  A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their ...
CDD:239524	100	EUKprk	Bacteria:225,Environmental:5,Invertebrates:11,Plants:29,Primates:2,Rodents:1,Vertebrates:5,nodiv:2	cd03440, hot_dog, The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that ...
CDD:239525	127	miss	miss	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase].  Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway.  The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold.  The active site lies within a substrate-binding tunnel formed by the homodimer.  Other enzymes with this fold ...
CDD:239526	123	miss	miss	cd03442, BFIT_BACH, Brown fat-inducible thioesterase (BFIT).  Brain acyl-CoA hydrolase (BACH).  These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy.
CDD:239527	113	miss	miss	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria.  Although orthologs of PaaI exist in archaea and eukaryotes, their function has not been determined. Sequence similarity between PaaI, E. coli medium chain acyl-CoA thioesterase II, and human thioesterase III suggests they all belong to the same thioesterase superfamily. The ...
CDD:239528	104	miss	miss	cd03444, Thioesterase_II_repeat1, Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and ...
CDD:239529	94	miss	miss	cd03445, Thioesterase_II_repeat2, Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and ...
CDD:239530	140	miss	miss	cd03446, MaoC_like, MoaC_like    Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
CDD:239531	126	miss	miss	cd03447, FAS_MaoC, FAS_MaoC, the MaoC-like hot dog fold of the fatty acid synthase, beta subunit.  Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and 17-beta-hydroxysteriod dehydrogenase (HSD).
CDD:239532	122	miss	miss	cd03448, HDE_HSD, HDE_HSD  The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins.  Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit.
CDD:239533	128	miss	miss	cd03449, R_hydratase, (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway.  (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.  The active site lies within a ...
CDD:239534	149	miss	miss	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.  Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division.  The nodulation gene products, including ...
CDD:239535	146	miss	miss	cd03451, FkbR2, FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2  has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.  The function of FkbR2 is unknown.
CDD:239537	127	miss	miss	cd03453, SAV4209_like, SAV4209_like.  Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
CDD:239538	140	miss	miss	cd03454, YdeM, YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function.  YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase.   Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
CDD:239539	123	miss	miss	cd03455, SAV4209, SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.  The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
CDD:239540	188	miss	miss	cd03457, intradiol_dioxygenase_like, Intradiol dioxygenase supgroup. Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. They break the catechol C1-C2 bond and utilize Fe3+, as opposed to  the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. The family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases. The specific ...
CDD:239541	256	miss	miss	cd03458, Catechol_intradiol_dioxygenases, Catechol intradiol dioxygenases can be divided into several subgroups according to their substrate specificity for catechol, chlorocatechols and hydroxyquinols. Almost all members of this family are homodimers containing one ferric ion (Fe3+) per monomer. They belong to the intradiol dioxygenase family, a family of mononuclear non-heme iron intradiol-cleaving enzymes that catalyze the oxygenation of catecholates to aliphatic ...
CDD:239542	158	miss	miss	cd03459, 3,4-PCD, Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes that break the C1-C2 bond and utilize Fe3+.
CDD:239544	277	miss	miss	cd03461, 1,2-HQD, Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a intermediate in the degradation of a large variety of aromatic compounds including some polychloro- and nitroaromatic pollutants, to form 3-hydroxy-cis,cis-muconates. 1,2-HQD blongs to the aromatic dioxygenase family, a family of mononuclear non-heme intradiol-cleaving enzymes.
CDD:239545	247	miss	miss	cd03462, 1,2-CCD, chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type II enzymes) are homodimeric intradiol dioxygenases that degrade chlorocatechols via the addition of molecular oxygen and the subsequent cleavage between two adjacent hydroxyl groups. This reaction is part of the modified ortho-cleavage pathway which is a central oxidative bacterial pathway that channels chlorocatechols, derived from the degradation of chlorinated benzoic acids, phenoxyacetic acids, ...
CDD:239546	185	miss	miss	cd03463, 3,4-PCD_alpha, Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-subunit-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes ...
CDD:239547	220	miss	miss	cd03464, 3,4-PCD_beta, Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-subunit-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes ...
CDD:239548	330	PRK	Bacteria:19	cd03465, URO-D_like, The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented ...
CDD:239550	98	EUKprk	Bacteria:91,Invertebrates:3,Plants:6,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd03467, Rieske, Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and ...
CDD:176458	335	EUKprk	Bacteria:33,Invertebrates:6	cd03468, PolY_like, DNA Polymerase Y-family.  Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions.  Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS ...
CDD:239551	118	EUKprk	Bacteria:119,Invertebrates:2,Plants:4,Vertebrates:1,nodiv:2	cd03469, Rieske_RO_Alpha_N, Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, ...
CDD:239552	126	EUKprk	Bacteria:42,Invertebrates:6,Mammals:1,Plants:6,Primates:1,Vertebrates:3	cd03470, Rieske_cytochrome_bc1, Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes ...
CDD:239553	126	EUKprk	Bacteria:8,Invertebrates:1,Plants:5	cd03471, Rieske_cytochrome_b6f, Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, ...
CDD:239556	108	PRK	Bacteria:11,nodiv:1	cd03474, Rieske_T4moC, Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). ...
CDD:239559	91	EUKprk	Bacteria:13,Plants:3	cd03477, Rieske_YhfW_C, YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f ...
CDD:239560	95	EUKprk	Bacteria:8,Invertebrates:7,Plants:6,Vertebrates:3	cd03478, Rieske_AIFL_N, AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), ...
CDD:239561	144	EUKprk	Bacteria:14,Plants:1,nodiv:1	cd03479, Rieske_RO_Alpha_PhDO_like, Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating ...
CDD:239562	138	EUKprk	Bacteria:9,Plants:5	cd03480, Rieske_RO_Alpha_PaO, Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ...
CDD:239563	153	miss	miss	cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA.  S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes.  All type ...
CDD:239564	123	miss	miss	cd03482, MutL_Trans_MutL, MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL.  EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family.  This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of ...
CDD:239565	127	miss	miss	cd03483, MutL_Trans_MLH1, MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 ...
CDD:239566	142	miss	miss	cd03484, MutL_Trans_hPMS_2_like, MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family.  This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion ...
CDD:239567	132	miss	miss	cd03485, MutL_Trans_hPMS_1_like, MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family.  This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to ...
CDD:239568	141	miss	miss	cd03486, MutL_Trans_MLH3, MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion ...
CDD:239569	214	PRK	Bacteria:50	cd03487, RT_Bac_retron_II, RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
CDD:239570	215	miss	miss	cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I.  Topo I enzymes are divided into:  topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick ...
CDD:239573	98	EUKprk	Bacteria:136,Invertebrates:12,Mammals:1,Plants:26,Primates:1,Vertebrates:4,nodiv:1	cd03493, SQR_QFR_TM, Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, ...
CDD:239574	99	miss	miss	cd03494, SQR_TypeC_SdhD, Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the high potential quinine, ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain.  SQR is composed of a ...
CDD:239575	100	miss	miss	cd03495, SQR_TypeC_SdhD_like, Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also ...
CDD:239576	104	miss	miss	cd03496, SQR_TypeC_CybS, SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain.  SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits.  Members of this ...
CDD:239577	207	miss	miss	cd03497, SQR_TypeB_1_TM, Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR ...
CDD:239578	209	miss	miss	cd03498, SQR_TypeB_2_TM, Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. C. glutamicum SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the ...
CDD:239579	117	miss	miss	cd03499, SQR_TypeC_SdhC, Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid ...
CDD:239580	106	miss	miss	cd03500, SQR_TypeA_SdhD_like, Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase D (SdhD)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is ...
CDD:239581	101	miss	miss	cd03501, SQR_TypeA_SdhC_like, Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone.  SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is ...
CDD:239582	178	miss	miss	cd03505, Delta9-FADS-like, The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide range of bacteria. These enzymes play essential roles in fatty acid metabolism and the regulation of cell membrane fluidity. Acyl-CoA desaturases are the enzymes involved in the CoA-bound ...
CDD:239583	204	miss	miss	cd03506, Delta6-FADS-like, The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be ...
CDD:239584	222	miss	miss	cd03507, Delta12-FADS-like, The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of organisms including higher plants, green algae, diatoms, nematodes, fungi, and bacteria. The expression of these proteins appears to be temperature dependent: decreases in temperature result in ...
CDD:239585	289	miss	miss	cd03508, Delta4-sphingolipid-FADS-like, The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, ...
CDD:239586	288	miss	miss	cd03509, DesA_FADS-like, Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane ...
CDD:239587	175	miss	miss	cd03510, Rhizobitoxine-FADS-like, This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that ...
CDD:239588	285	miss	miss	cd03511, Rhizopine-oxygenase-like, This CD includes the putative hydrocarbon oxygenase, MocD, a bacterial rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and other related proteins. It has been proposed that MocD, MocE (Rieske-like ferredoxin), and MocF (ferredoxin reductase) under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine.  This domain family appears to be structurally ...
CDD:239589	314	miss	miss	cd03512, Alkane-hydroxylase, Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a ...
CDD:239590	225	miss	miss	cd03513, CrtW_beta-carotene-ketolase, Beta-carotene ketolase/oxygenase (CrtW, also known as CrtO), the carotenoid astaxanthin biosynthetic enzyme, initially catalyzes the addition of two keto groups to carbons C4 and C4' of beta-carotene. Carotenoids are important natural pigments produced by many microorganisms and plants. Astaxanthin is reported to be an antioxidant, an anti-cancer agent, and an immune system stimulant. A number of bacteria and green algae can convert ...
CDD:239591	207	miss	miss	cd03514, CrtR_beta-carotene-hydroxylase, Beta-carotene hydroxylase (CrtR), the carotenoid zeaxanthin biosynthetic enzyme catalyzes the addition of hydroxyl groups to the beta-ionone rings of beta-carotene to form zeaxanthin and is found in bacteria and red algae. Carotenoids are important natural pigments; zeaxanthin and lutein are the only dietary carotenoids that accumulate in the macular region of the retina and lens. It is proposed that these carotenoids protect ...
CDD:239597	96	EUK	Primates:1,Rodents:1,Vertebrates:3	cd03520, Link_domain_CSPGs_modules_2_4, Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link ...
CDD:239599	312	PRK	Bacteria:42,Environmental:1	cd03522, MoeA_like, MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is unknown.
CDD:239600	105	EUK	Mammals:1,Primates:1,Vertebrates:1	cd03523, NTR_like, NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of ...
CDD:239601	75	EUKprk	Bacteria:10,Invertebrates:5,Plants:14,Primates:1,Rodents:2,nodiv:1	cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and ...
CDD:239603	99	EUKprk	Bacteria:9,Invertebrates:1,Plants:13	cd03527, RuBisCO_small, Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of ...
CDD:239604	98	PRK	Bacteria:59	cd03528, Rieske_RO_ferredoxin, Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic ...
CDD:239605	103	EUKprk	Bacteria:35,Plants:7	cd03529, Rieske_NirD, Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface ...
CDD:239606	98	EUKprk	Bacteria:23,Invertebrates:1	cd03530, Rieske_NirD_small_Bacillus, Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
CDD:239619	484	miss	miss	cd03557, L-arabinose_isomerase, L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a ...
CDD:239620	133	EUK	Invertebrates:3,Plants:14	cd03561, VHS, VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on ...
CDD:239621	114	EUK	Invertebrates:11,Plants:13,Primates:1,Vertebrates:3	cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) ...
CDD:239622	117	EUK	Invertebrates:10,Plants:18,Primates:1,Vertebrates:3	cd03564, ANTH_AP180_CALM, ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a ...
CDD:239624	139	EUK	Invertebrates:6,Primates:1,Vertebrates:3	cd03567, VHS_GGA, VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain ...
CDD:239625	144	EUK	Invertebrates:6,Plants:10,Vertebrates:3	cd03568, VHS_STAM, VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM ...
CDD:239626	142	EUK	Invertebrates:7,Plants:9,Primates:1,Vertebrates:3	cd03569, VHS_Hrs_Vps27p, VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and ...
CDD:239627	123	EUK	Invertebrates:14,Plants:14,Primates:1,Vertebrates:4	cd03571, ENTH_epsin, ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH ...
CDD:239628	122	EUK	Invertebrates:6,Plants:1,Primates:1,Vertebrates:2	cd03572, ENTH_epsin_related, ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to ...
CDD:239629	147	EUK	Invertebrates:2,Primates:1	cd03574, NTR_complement_C345C, NTR/C345C domain; The NTR domains that are found in the C-termini of complement C3, C4 and C5, are also called C345C domains. In C5, the domain interacts with various partners during the formation of the membrane attack complex, a fundamental process in the mammalian defense against infection. It's role in component C3 and C4 is not well understood.
CDD:239631	124	EUK	Primates:1,Vertebrates:4	cd03576, NTR_PCOLCE, NTR domain, PCOLCE subfamily; Procollagen C-endopeptidase enhancers (PCOLCEs) are extracellular matrix proteins that enhance the activity of procollagen C-proteases, by binding to the procollagen I C-peptide. They contain a C-terminal NTR domain, which have been suggested to possess inhibitory functions towards specific serine proteases but not towards metzincins, which are inhibited by the related TIMPs.
CDD:239632	116	EUKprk	Bacteria:4,Invertebrates:8,Mammals:1,Vertebrates:1	cd03577, NTR_TIMP_like, NTR domain, TIMP-like subfamily; TIMPs, or tissue inibitors of metalloproteases, are essential regulators of extracellular matrix turnover and remodeling. They form complexes with matrix metalloproteases (MMPs) and inactivate them irreversibly by non-covalently binding their active zinc-binding sites. This group contains domains similar to the TIMP NTR domain, which binds MMPs. Members of this group ...
CDD:239634	115	EUK	Invertebrates:9,Primates:1,Vertebrates:5	cd03579, NTR_netrin-1_like, NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration during neural development. These proteins may be chemoattractive to some neurons and chemorepellant for others. In the case of netrin-1, attraction and repulsion ...
CDD:239635	126	EUK	Invertebrates:3,Primates:1,Vertebrates:4	cd03580, NTR_Sfrp1_like, NTR domain, Secreted frizzled-related protein (Sfrp) 1-like subfamily; composed of proteins similar to human Sfrp1, Sfrp2 and Sfrp5. Sfrps are soluble proteins containing an NTR domain C-terminal to a cysteine-rich Frizzled domain. They show diverse functions and are thought to work in Wnt signaling indirectly, as modulators or antagonists by binding Wnt ligands, and directly, via the Wnt receptor, Frizzled. ...
CDD:239638	149	EUK	Mammals:1,Primates:1,Vertebrates:5	cd03583, NTR_complement_C3, NTR/C345C domain, complement C3 subfamily; The NTR domain found in complement C3 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C3 plays a pivotal role in the activation of the complement systems, as all pathways (classical, alternative, and lectin) result in the processing of C3 by C3 convertase. The larger fragment, activated C3b, contains the ...
CDD:239639	153	EUK	Vertebrates:3	cd03584, NTR_complement_C4, NTR/C345C domain, complement C4 subfamily; The NTR domain found in complement C4 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C4 is a key player in the activation of the component classical pathway. C4 is cleaved by activated C1 to yield C4a anaphylatoxin, and the larger fragment C4b, an essential component of the C3- and C5-convertase enzymes. C4b binds covalently to the ...
CDD:239640	183	EUK	Primates:1,Vertebrates:5	cd03585, NTR_TIMP, NTR domain, TIMP subfamily; TIMPs, or tissue inibitors of metalloproteases, are essential regulators of extracellular matrix turnover and remodeling. They form complexes with matrix metalloproteases (MMPs) and inactivate them irreversibly by non-covalently binding their active zinc-binding sites. The levels of activated membrane-type MMPs, MMPs, and free TIMPs determine the balance between matrix degradation and matrix formation or ...
CDD:176459	334	EUKprk	Bacteria:93,Environmental:1,Invertebrates:5,Plants:4,Primates:1,Vertebrates:2	cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa.  Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase.  Translesion synthesis is a process that allows the bypass of a variety of DNA lesions.  TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the ...
CDD:239641	41	EUK	Invertebrates:10,Mammals:2,Primates:2,Rodents:2,Vertebrates:6	cd03587, SOCS, SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is ...
CDD:153059	137	miss	miss	cd03589, CLECT_CEL-1_like, C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina.  CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina.  CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  The CEL-1 CTLD binds three calcium ions and has a high ...
CDD:153060	126	miss	miss	cd03590, CLECT_DC-SIGN_like, C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR).  CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR).  This ...
CDD:153061	114	miss	miss	cd03591, CLECT_collectin_like, C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1).  CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1).  CTLD refers to a domain homologous to the ...
CDD:153062	115	miss	miss	cd03592, CLECT_selectins_like, C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins:  P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels).  CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins:  P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels).  CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  P- ...
CDD:153063	116	miss	miss	cd03593, CLECT_NK_receptors_like, C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs).  CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1),  human myeloid ...
CDD:153064	129	miss	miss	cd03594, CLECT_REG-1_like, C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2).  CLECT_REG-1_like: C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2).  CTLD refers to a domain homologous to the carbohydrate-recognition ...
CDD:153070	141	miss	miss	cd03600, CLECT_thrombomodulin_like, C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR.  CLECT_thrombomodulin_like: C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR.  CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  In these thrombomodulin-like proteins the residues involved in coordinating Ca2+ ...
CDD:153072	108	miss	miss	cd03602, CLECT_1, C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  CLECT_1: C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ...
CDD:153073	118	miss	miss	cd03603, CLECT_VCBS, A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  CLECT_VCBS: A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs ...
CDD:239643	147	EUKprk	Bacteria:25,Invertebrates:4,Plants:3	cd03671, Ap4A_hydrolase_plant_like, Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both ...
CDD:239644	145	EUK	Invertebrates:8,Plants:10,Primates:1,Vertebrates:2	cd03672, Dcp2p, mRNA decapping enzyme 2 (Dcp2p), the catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'->3' mRNA-decay pathways. Dcp2p contains an all-alpha helical N-terminal domain and a C-terminal domain which has the Nudix fold. While decapping is not dependent on the N-terminus of Dcp2p, it does affect its efficiency. Dcp1p ...
CDD:239645	131	PRK	Bacteria:30	cd03673, Ap6A_hydrolase, Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most preferred substrate, hydrolyzes to produce two ATP molecules, which is a novel hydrolysis mode for Ap6A. These results indicate that Ap6A  hydrolase is a diadenosine polyphosphate hydrolase. It ...
CDD:239646	138	PRK	Bacteria:24	cd03674, Nudix_Hydrolase_1, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases ...
CDD:239647	134	EUKprk	Bacteria:29,Invertebrates:1,nodiv:1	cd03675, Nudix_Hydrolase_2, Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif ...
CDD:239648	180	EUKprk	Bacteria:5,Invertebrates:2,Plants:9	cd03676, Nudix_hydrolase_3, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include ...
CDD:239649	424	PRK	Bacteria:42	cd03677, MM_CoA_mutase_beta, Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta heterodimers. For P. shermanni MCM, it is known that only the alpha subunit binds coenzyme B12 and substrates. The role of the beta subunit is unclear. MCM catalyzes the isomerization of ...
CDD:239651	536	EUKprk	Bacteria:10,Invertebrates:3,Primates:1,Vertebrates:1,nodiv:1	cd03679, MM_CoA_mutase_alpha_like, Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain an N-terminal MCM domain and a C-terminal coenzyme B12 binding domain. MCM catalyzes the isomerization of methylmalonyl-CoA to ...
CDD:239652	538	PRK	Bacteria:20,nodiv:1	cd03680, MM_CoA_mutase_ICM_like, Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The ...
CDD:239654	378	PRK	Bacteria:17	cd03682, ClC_sycA_like, ClC sycA-like chloride channel proteins. This ClC family presents in bacteria, where it facilitates acid resistance in acidic soil. Mutation of this gene (sycA) in Rhizobium tropici CIAT899 causes serious deficiencies in nodule development, nodulation competitiveness, and N2 fixation on Phaseolus vulgaris plants, due to its reduced ability for acid resistance.  This family is part of the ClC chloride channel superfamiy. These proteins ...
CDD:239655	426	EUK	Invertebrates:5,Primates:1,Vertebrates:3	cd03683, ClC_1_like, ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is exclusively expressed in kidney. Similarly, mutation of ClC-K leads to nephrogenic diabetes insipidus in mice and Bartter's syndrome in human. These proteins belong to ...
CDD:239656	445	EUK	Invertebrates:5,Mammals:1,Plants:9,Primates:1,Vertebrates:3	cd03684, ClC_3_like, ClC-3-like chloride channel proteins.  This CD  includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has been suggested that ClC-3 may be a ubiquitous swelling-activated Cl channel that has very similar characteristics to those of native ...
CDD:239657	466	EUK	Invertebrates:3,Plants:4,Primates:1,Vertebrates:2	cd03685, ClC_6_like, ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes.  This family belongs to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating ...
CDD:239659	113	miss	miss	cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it ...
CDD:239660	85	miss	miss	cd03689, RF3_II, RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of ...
CDD:239661	85	miss	miss	cd03690, Tet_II, Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance.  Tcs are broad-spectrum antibiotics.  Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the ...
CDD:239662	86	miss	miss	cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli.  BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the ...
CDD:239663	84	miss	miss	cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2.  IF2 C2 ...
CDD:239664	91	miss	miss	cd03693, EF1_alpha_II, EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More ...
CDD:239665	87	miss	miss	cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in ...
CDD:239666	81	miss	miss	cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS ...
CDD:239667	83	miss	miss	cd03696, selB_II, selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation ...
CDD:239668	87	miss	miss	cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II ...
CDD:239669	83	miss	miss	cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination ...
CDD:239670	86	miss	miss	cd03699, lepA_II, lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of ...
CDD:239671	93	miss	miss	cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This ...
CDD:239672	95	miss	miss	cd03701, IF2_IF5B_II, IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function ...
CDD:239673	95	miss	miss	cd03702, IF2_mtIF2_II, This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2.  Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
CDD:239674	110	miss	miss	cd03703, aeIF5B_II, aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2).  Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits.  The eIF5B consists of three N-terminal domains  (I, II, II) connected by a ...
CDD:239675	108	EUK	Invertebrates:2,Plants:1,Vertebrates:1	cd03704, eRF3c_III, This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided ...
CDD:239676	104	EUK	Invertebrates:9,Plants:3,Primates:1	cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the ...
CDD:239677	93	EUK	Invertebrates:1,Primates:1	cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU). mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed ...
CDD:239678	90	EUKprk	Bacteria:8,Invertebrates:3,Plants:3	cd03707, EFTU_III, Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu.  EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their ...
CDD:239679	87	EUK	Invertebrates:3,Plants:1,Vertebrates:1	cd03708, GTPBP_III, Domain III of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 ...
CDD:239680	80	miss	miss	cd03709, lepA_C, lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane.   LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in ...
CDD:239681	79	miss	miss	cd03710, BipA_TypA_C, BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. ...
CDD:239682	78	miss	miss	cd03711, Tet_C, Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance.  Tcs are broad-spectrum antibiotics.  Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the  occupation of ...
CDD:239683	78	miss	miss	cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G.  Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the ...
CDD:239684	119	EUK	Invertebrates:6,Vertebrates:2	cd03714, RT_DIRS1, RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by ...
CDD:239685	210	EUKprk	Mammals:1,Primates:1,Rodents:1,Vertebrates:3,Viruses:2	cd03715, RT_ZFREV_like, RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT.  An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, ...
CDD:239686	42	miss	miss	cd03716, SOCS_ASB_like, SOCS (suppressors of cytokine signaling) box of ASB (ankyrin repeat and SOCS box) and SSB (SPRY domain-containing SOCS box proteins) protein families. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence of a variable number of repeats. SSB proteins contain a central SPRY domain and a C-terminal SOCS. Recently, it has been shown that all four SSB proteins interact with the MET, the receptor protein-tyrosine ...
CDD:239687	39	miss	miss	cd03717, SOCS_SOCS_like, SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to cytokines. Identified as negative regulators of the cytokine-JAK-STAT pathway, they seem to play a role in many immunological and pathological processes. The function of the SOCS box is the ...
CDD:239716	312	miss	miss	cd03747, Ntn_PGA_like, Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively.  While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and ...
CDD:239718	211	miss	miss	cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239719	227	miss	miss	cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239720	212	miss	miss	cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239723	215	miss	miss	cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239725	211	miss	miss	cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239726	212	miss	miss	cd03757, proteasome_beta_type_1, proteasome beta type-1 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239727	193	miss	miss	cd03758, proteasome_beta_type_2, proteasome beta type-2 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239728	195	miss	miss	cd03759, proteasome_beta_type_3, proteasome beta type-3 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239729	197	miss	miss	cd03760, proteasome_beta_type_4, proteasome beta type-4 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239730	188	miss	miss	cd03761, proteasome_beta_type_5, proteasome beta type-5 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239731	188	miss	miss	cd03762, proteasome_beta_type_6, proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239732	189	miss	miss	cd03763, proteasome_beta_type_7, proteasome beta type-7 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239733	188	miss	miss	cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal ...
CDD:239734	236	miss	miss	cd03765, proteasome_beta_bacterial, Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile ...
CDD:239735	181	miss	miss	cd03766, Gn_AT_II_novel, Gn_AT_II_novel.  This asparagine synthase-related domain is present in eukaryotes but its function has not yet been determined.  The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as ...
CDD:239736	146	PRK	Bacteria:10	cd03767, SR_Res_par, Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subgroup is composed of proteins similar to ...
CDD:239737	126	EUKprk	Bacteria:128,Phages:1,Plants:1	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, ...
CDD:239738	134	PRK	Bacteria:10	cd03769, SR_IS607_transposase_like, Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally ...
CDD:239740	167	miss	miss	cd03771, MATH_Meprin, Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces. They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related ...
CDD:239744	134	miss	miss	cd03775, MATH_Ubp21p, Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a ...
CDD:239745	147	miss	miss	cd03776, MATH_TRAF6, Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most ...
CDD:99960	401	EUKprk	Bacteria:81,Invertebrates:2,Plants:18,Vertebrates:1	cd03784, GT1_Gtf_like, This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the oxidatively cross-linked heptapeptide core of vancomycin group antibiotics. The core structure is important for the bioactivity of the antibiotics.
CDD:99961	350	EUKprk	Bacteria:132,Plants:2	cd03785, GT1_MurG, MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural ...
CDD:99962	363	EUKprk	Bacteria:162,Environmental:1,Invertebrates:1,Plants:1,Primates:1,Vertebrates:3	cd03786, GT1_UDP-GlcNAc_2-Epimerase, Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase  family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues (UDP-ManNAc) for use in the biosynthesis of a variety of cell surface polysaccharides; The mammalian enzyme is ...
CDD:99963	460	EUKprk	Bacteria:71,Environmental:1,Invertebrates:6,Plants:22	cd03788, GT1_TPS, Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a nonreducing disaccharide present in a wide variety of organisms and may serve as a source of energy and carbon. It is characterized most notably in ...
CDD:99964	279	PRK	Bacteria:114,Environmental:1	cd03789, GT1_LPS_heptosyltransferase, Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family belongs to the GT-B structural superfamily of ...
CDD:99965	476	EUKprk	Bacteria:131,Invertebrates:3,Plants:14	cd03791, GT1_Glycogen_synthase_DULL1_like, This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family includes starch synthases of plants, such as DULL1 in Zea mays and glycogen synthases of various organisms.
CDD:99966	372	EUKprk	Bacteria:15,Environmental:1,Plants:5	cd03792, GT1_Trehalose_phosphorylase, Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose, and the subsequent synthesis of trehalose. This family is most closely related to the GT1 family of glycosyltransferases.
CDD:99968	394	PRK	Bacteria:153,nodiv:1	cd03794, GT1_wbuB_like, This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen.  It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase.
CDD:99969	357	PRK	Bacteria:36	cd03795, GT1_like_4, This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 ...
CDD:99970	398	EUK	Invertebrates:13,Plants:7,Vertebrates:2	cd03796, GT1_PIG-A_like, This family is most closely related to the GT1 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate in glycosyl phosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is an important cellular structure that facilitates the attachment of many proteins to ...
CDD:99971	377	PRK	Bacteria:108,Environmental:1	cd03798, GT1_wlbH_like, This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS.
CDD:99972	355	PRK	Bacteria:64,Environmental:1,nodiv:1	cd03799, GT1_amsK_like, This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor.
CDD:99973	398	EUKprk	Bacteria:53,Environmental:1,Plants:3,nodiv:1	cd03800, GT1_Sucrose_synthase, This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose 6-phosphate and uridine 5'-diphosphate-glucose, a key regulatory step of sucrose metabolism. The activity of this enzyme is regulated by ...
CDD:99974	374	EUKprk	Bacteria:231,Environmental:2,Invertebrates:3,Plants:1	cd03801, GT1_YqgM_like, This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...
CDD:99975	335	PRK	Bacteria:49	cd03802, GT1_AviGT4_like, This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant that accumulated a novel avilamycin derivative lacking the terminal eurekanate residue.
CDD:99976	351	PRK	Bacteria:50,nodiv:1	cd03804, GT1_wbaZ_like, This family is most closely related to the GT1 family of glycosyltransferases.  wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea.
CDD:99977	392	EUK	Invertebrates:12,Plants:16,Primates:1,Vertebrates:2	cd03805, GT1_ALG2_like, This family is most closely related to the GT1 family of glycosyltransferases.  ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is ...
CDD:99978	419	EUK	Invertebrates:17,Plants:17,Primates:1,Vertebrates:3	cd03806, GT1_ALG11_like, This family is most closely related to the GT1 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked ...
CDD:99979	365	PRK	Bacteria:45	cd03807, GT1_WbnK_like, This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis.
CDD:99980	359	PRK	Bacteria:149,Environmental:1	cd03808, GT1_cap1E_like, This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides.
CDD:99981	365	PRK	Bacteria:175,Environmental:1,nodiv:1	cd03809, GT1_mtfB_like, This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the previously synthesized polysaccharide.
CDD:99982	353	PRK	Bacteria:175,Environmental:1	cd03811, GT1_WabH_like, This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core.
CDD:99983	358	PRK	Bacteria:38	cd03812, GT1_CapH_like, This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1).
CDD:99984	475	PRK	Bacteria:26	cd03813, GT1_like_3, This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 ...
CDD:99985	364	EUKprk	Bacteria:81,Plants:4,nodiv:1	cd03814, GT1_like_2, This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined ...
CDD:99986	415	EUK	Invertebrates:6,Plants:12,Vertebrates:3	cd03816, GT1_ALG1_like, This family is most closely related to the GT1 family of glycosyltransferases. The yeast gene ALG1 has been shown to function as a mannosyltransferase that catalyzes the formation of dolichol pyrophosphate (Dol-PP)-GlcNAc2Man from GDP-Man and Dol-PP-Glc-NAc2, and participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. In humans ALG1 has been associated with the congenital ...
CDD:99987	374	PRK	Bacteria:56,Environmental:1	cd03817, GT1_UGDG_like, This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol.
CDD:99988	396	PRK	Bacteria:37	cd03818, GT1_ExpC_like, This family is most closely related to the GT1 family of glycosyltransferases. ExpC in Rhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucan (exopolysaccharide II).
CDD:99989	355	PRK	Bacteria:34	cd03819, GT1_WavL_like, This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
CDD:99990	348	PRK	Bacteria:78,Environmental:1	cd03820, GT1_amsD_like, This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be responsible for the formation of  galactose alpha-1,6 linkages in amylovoran.
CDD:99991	375	PRK	Bacteria:33	cd03821, GT1_Bme6_like, This family is most closely related to the GT1 family of glycosyltransferases. Bme6 in Brucella melitensis has been shown to be involved in the biosynthesis of a polysaccharide.
CDD:99992	366	EUKprk	Bacteria:46,Environmental:1,Plants:1	cd03822, GT1_ecORF704_like, This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides.
CDD:99993	359	PRK	Bacteria:39,nodiv:1	cd03823, GT1_ExpE7_like, This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II).
CDD:99994	365	PRK	Bacteria:33	cd03825, GT1_wcfI_like, This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis.
CDD:199840	321	PRK	Bacteria:18	cd03855, M14_ASTE, Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily.  Peptidase M14 Succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) belongs to the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily of the M14 family of metallocarboxypeptidases. This group includes succinylglutamate desuccinylase that catalyzes the fifth and last ...
CDD:133069	226	EUKprk	Bacteria:3,Plants:1	cd03857, M14-like_1, Peptidase M14-like domain; uncharacterized subfamily.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major ...
CDD:199842	293	EUKprk	Bacteria:1,Invertebrates:10,Plants:2,Primates:1,Vertebrates:1	cd03858, M14_CP_N-E_like, Peptidase M14 carboxypeptidase subfamily N/E-like.  Carboxypeptidase (CP) N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily ...
CDD:199843	297	EUKprk	Bacteria:10,Invertebrates:4	cd03859, M14_CPT, Peptidase M14 Carboxypeptidase T subfamily.  Peptidase M14-like domain of carboxypeptidase (CP) T (CPT), CPT belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPT has moderate similarity to CPA and ...
CDD:199844	293	EUK	Invertebrates:29,Primates:1,Vertebrates:1	cd03860, M14_CP_A-B_like, Peptidase M14 carboxypeptidase subfamily A/B-like.  The Peptidase M14 Carboxypeptidase (CP) A/B subfamily is one of two main M14 CP subfamilies defined by sequence and structural homology, the other being the N/E subfamily. CPs hydrolyze single, C-terminal amino acids from polypeptide chains. They have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Enzymes ...
CDD:133073	273	PRK	Bacteria:15	cd03862, M14-like_7, Peptidase M14-like domain; uncharacterized subfamily.  A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on ...
CDD:199850	293	EUK	Invertebrates:5,Vertebrates:3	cd03868, M14_CPD_I, Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase D, domain I subgroup.  The first carboxypeptidase (CP)-like domain of  Carboxypeptidase D (CPD; EC 3.4.17.22), domain I. CPD differs from all other metallocarboxypeptidases in that it contains multiple CP-like domains. CPD belongs to the N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze ...
CDD:193495	237	EUKprk	Bacteria:18,Plants:3,Primates:1,Vertebrates:1	cd03873, Zinc_peptidase_like, Zinc peptidases M18, M20, M28, and M42.  Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the ...
CDD:193496	279	EUK	Plants:16,Primates:1	cd03874, M28_PMSA_TfR_like, M28 Zn-peptidase Transferrin Receptor-like family.  Peptidase M28 family; Transferrin Receptor (TfR) and prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase or GCP-II) subfamily. TfR and PSMA are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion ...
CDD:193497	307	EUKprk	Bacteria:6,Invertebrates:5,Plants:19,Vertebrates:3	cd03875, M28_Fxna_like, M28 Zn-peptidase Endoplasmic reticulum metallopeptidase 1.  Peptidase family M28; Endoplasmic reticulum metallopeptidase 1 (ERMP1; Felix-ina, FXNA or Fxna peptidase; KIAA1815) subfamily. ERMP1 is a multi-pass membrane protein located in the endoplasmic reticulum membrane. In humans, Fxna may play a crucial role in processing proteins required for the organization of somatic cells and oocytes into ...
CDD:193498	288	EUKprk	Bacteria:15,Plants:10	cd03876, M28_SGAP_like, M28 Zn-peptidase Streptomyces griseus Aminopeptidase and similar proteins.  Peptidase family M28; Streptomyces griseus Aminopeptidase (SGAP, Leucine aminopeptidase (LAP), aminopeptidase S, Mername-AA022 peptidase) subfamily. SGAP is a di-zinc exopeptidase with high preference towards large hydrophobic amino-terminal residues, with Leu being the most efficiently cleaved. It can accommodate all except Pro and Glu residues in the ...
CDD:193499	254	PRK	Bacteria:21	cd03877, M28_like_PA, M28 Zn-Peptidases containing a PA domain insert.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins, many of ...
CDD:193500	285	EUKprk	Bacteria:14,Environmental:1,Plants:17	cd03879, M28_AAP, M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase.  Peptidase family M28; Aeromonas (Vibrio) proteolytica aminopeptidase (AAP; leucine aminopeptidase from Vibrio proteolyticus; Bacterial leucyl aminopeptidase; E.C. 3.4.11.10) subfamily. AAP is a small (32kDa), heat stable leucine aminopeptidase and is active as a monomer. Similar forms of the enzyme have been isolated from Escherichia coli and ...
CDD:193501	304	EUK	Invertebrates:12,Plants:16,Primates:1,Vertebrates:4	cd03880, M28_QC_like, M28 Zn-Peptidase Glutaminyl Cyclase.  Peptidase M28 family; Glutaminyl Cyclase (QC; EC 2.3.2.5) subfamily. QC is involved in N-terminal glutamine cyclization of many endocrine peptides and is typically abundant in brain tissue. N-terminal glutamine residue cyclization is an important post-translational event in the processing of numerous bioactive proteins, including neuropeptides, hormones, and ...
CDD:193502	308	EUK	Invertebrates:8,Plants:2,Vertebrates:3	cd03881, M28_Nicastrin, M28 Zn-Peptidase Nicastrin, a main component of gamma-secretase complex.  Peptidase M28 family, Nicastrin subfamily. Nicastrin is a main component of gamma-secretase complex.  Its extracellular domain sequence resembles aminopeptidases, but certain catalytic residues are not conserved.  It is mainly localized to the endoplasmic reticulum and Golgi. It is highly glycosylated (Mr 120 kDa) and is essential for ...
CDD:193503	290	EUK	Invertebrates:9,Plants:2,Vertebrates:3	cd03882, M28_nicalin_like, M28 Zn-Peptidase Nicalin, Nicastrin-like protein.  Peptidase M28 family, Nicalin (nicastrin-like protein) subfamily. Nicalin is distantly related to Nicastrin, a component of the Alzheimer's disease-associated gamma-secretase, and forms a complex with Nomo (nodal modulator) pM5. Similar to Nicastrin, Nicalin lacks the amino-acid conservation required for catalytically active aminopeptidases. Functional studies ...
CDD:193504	276	EUKprk	Bacteria:27,Invertebrates:9,Plants:1,Primates:1,Vertebrates:2	cd03883, M28_Pgcp_like, M28 Zn-Peptidase Plasma glutamate carboxypeptidase.  Peptidase M28 family; Plasma glutamate carboxypeptidase (PGCP; blood plasma glutamate carboxypeptidase; EC 3.4.17.21) subfamily. PGCP is a 56kDa glutamate carboxypeptidase that is mainly produced in mammalian placenta and kidney, the majority of which is thought to be secreted into the bloodstream. Similar proteins are also found in ...
CDD:193505	399	EUKprk	Bacteria:113,Environmental:1,Plants:12	cd03884, M20_bAS, M20 Peptidase beta-alanine synthase, an amidohydrolase.  Peptidase M20 family, beta-alanine synthase (bAS; N-carbamoyl-beta-alanine amidohydrolase and beta-ureidopropionase; EC 3.5.1.6) subfamily. bAS is an amidohydrolase and is the final enzyme in the pyrimidine catabolic pathway, which is involved in the regulation of the cellular pyrimidine pool. The bAS catalyzes the irreversible hydrolysis of the N-carbamylated ...
CDD:193506	363	PRK	Bacteria:102,Environmental:1	cd03885, M20_CPDG2, M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme.  Peptidase M20 family, Glutamate carboxypeptidase (carboxypeptidase G; carboxypeptidase G1; carboxypeptidase G2; CPDG2; CPG2; Folate hydrolase G2; Pteroylmonoglutamic acid hydrolase G2; Glucarpidase; E.C. 3.4.17.11) subfamily. CPDG2 is a periplasmic enzyme that is synthesized with a signal peptide. It is a dimeric zinc-dependent exopeptidase, with two domains, a ...
CDD:193507	372	EUKprk	Bacteria:166,Invertebrates:4,Plants:1	cd03886, M20_Acy1, M20 Peptidase Aminoacylase 1 family.  Peptidase M20 family, Aminoacylase 1 (ACY1; hippuricase; acylase I; amido acid deacylase; IAA-amino acid hydrolase; dehydropeptidase II; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) subfamily. ACY1 is the most abundant of the aminoacylases, a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. It is encoded by the aminoacylase 1 gene ...
CDD:193508	358	EUKprk	Bacteria:115,Environmental:1,Invertebrates:2,Plants:14,Primates:1,Vertebrates:3,nodiv:1	cd03887, M20_Acy1L2, M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family.  Peptidase M20 family, Aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase) subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia ...
CDD:193509	453	PRK	Bacteria:83	cd03888, M20_PepV, M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides.  Peptidase M20 family, Peptidase V (Xaa-His dipeptidase; PepV g.p. (Lactobacillus lactis); X-His dipeptidase; beta-Ala-His dipeptidase; carnosinase) subfamily. The PepV group of proteins is widely distributed in lactic acid bacteria. PepV, along with PepT, functions at the end of the proteolytic processing system. PepV is a monomeric metalloenzyme that preferentially ...
CDD:193510	474	EUKprk	Bacteria:99,Invertebrates:3,Plants:2	cd03890, M20_pepD, M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide.  Peptidase M20 family, Peptidase D (PepD, Xaa-His dipeptidase; X-His dipeptidase; aminoacylhistidine dipeptidase; dipeptidase D; Beta-alanyl-histidine dipeptidase; pepD g.p. (Escherichia coli); EC 3.4.13.3) subfamily. PepD is a cytoplasmic enzyme family characterized by its unusual specificity for the dipeptides beta-alanyl-L-histidine (L-carnosine ...
CDD:193511	366	PRK	Bacteria:53,Environmental:1	cd03891, M20_DapE_proteobac, M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.  Peptidase M20 family, proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE; aspartyl dipeptidase; succinyl-diaminopimelate desuccinylase) subfamily. DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. It has been shown that DapE is ...
CDD:193512	401	EUKprk	Bacteria:66,Invertebrates:2	cd03892, M20_peptT, M20 Peptidase T specifically cleaves tripeptides.  Peptidase M20 family, Peptidase T (peptT; tripeptide aminopeptidase; tripeptidase) subfamily. PepT acts only on tripeptide substrates, and is thus called a tripeptidase. It catalyzes the release of N-terminal amino acids with hydrophobic side chains from tripeptides with high specificity; dipeptides, tetrapeptides or tripeptides with the N-terminus blocked are not cleaved. ...
CDD:193513	428	EUKprk	Bacteria:22,Rodents:1	cd03893, M20_Dipept_like, M20 Dipeptidases.  Peptidase M20 family, dipeptidase-like subfamily. This group contains a large variety of enzymes, including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase), canosinase, DUG2 type proteins, as well as many proteins inferred by homology to be dipeptidases. These enzymes have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase ...
CDD:193514	372	EUKprk	Bacteria:51,Invertebrates:4	cd03894, M20_ArgE, M20 Peptidase acetylornithine deacetylase.  Peptidase M20 family, acetylornithine deacetylase (ArgE, Acetylornithinase, AO, N2-acetyl-L-ornithine amidohydrolase, EC 3.5.1.16) subfamily. ArgE catalyzes the conversion of N-acetylornithine to ornithine, which can then be incorporated into the urea cycle for the final stage of arginine synthesis. The substrate specificity of ArgE is quite broad; several alpha-N-acyl-L-amino acids ...
CDD:193515	399	EUKprk	Bacteria:40,Invertebrates:1	cd03895, M20_ArgE_DapE_like2, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of ...
CDD:193516	359	PRK	Bacteria:33	cd03896, M20_PAAh_like, M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins.  Peptidase M20 family, Poly(aspartic acid) hydrolase (PAA hydrolase)-like subfamily. PAA hydrolase enzymes are involved in alpha,beta-poly(D,L-aspartic acid) (tPAA) biodegradation. PAA is being extensively studied as a replacement for commercial polycarboxylate components since it can be degraded by enzymes from isolated tPAA degrading bacteria. Thus far, two types of PAA degrading ...
CDD:175976	133	EUK	Invertebrates:13,Primates:1,Vertebrates:4,nodiv:1	cd04009, C2B_Munc13-like, C2 domain second repeat in Munc13 (mammalian uncoordinated)-like proteins.  C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner.  ...
CDD:175977	148	EUK	Invertebrates:7,Vertebrates:2	cd04010, C2B_RasA3, C2 domain second repeat present in RAS p21 protein activator 3 (RasA3).  RasA3 are members of GTPase activating protein 1 (GAP1), a Ras-specific GAP, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras.  In this way it can control cellular proliferation and differentiation.  RasA3 contains an N-terminal C2 domain,  a Ras-GAP domain, a plextrin homology ...
CDD:175978	111	EUK	Invertebrates:9,Plants:1,Primates:1,Rodents:1,Vertebrates:5,nodiv:1	cd04011, C2B_Ferlin, C2 domain second repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide ...
CDD:175979	171	EUK	Invertebrates:11,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd04012, C2A_PI3K_class_II, C2 domain first repeat present in class II phosphatidylinositol 3-kinases (PI3Ks).  There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a N-terminal C2 domain, a PIK domain, and a kinase catalytic domain. Unlike class I and class III, class II PI3Ks have additionally a PX domain and a C-terminal C2 domain containing a nuclear localization signal ...
CDD:175980	146	EUK	Invertebrates:8,Vertebrates:4,nodiv:1	cd04013, C2_SynGAP_like, C2 domain present in Ras GTPase activating protein (GAP) family.  SynGAP, GAP1, RasGAP, and neurofibromin are all members of the Ras-specific GAP (GTPase-activating protein) family.  SynGAP regulates the MAP kinase signaling pathway and is critical for cognition and synapse function.  Mutations in this gene causes mental retardation in humans.   SynGAP contains a PH-like domain, a C2 domain, and a  Ras-GAP domain.  ...
CDD:175981	132	EUK	Invertebrates:15,Vertebrates:4,nodiv:1	cd04014, C2_PKC_epsilon, C2 domain in Protein Kinase C (PKC) epsilon.  A single C2 domain is found in PKC epsilon. The PKC family of serine/threonine kinases regulates apoptosis, proliferation, migration, motility, chemo-resistance, and differentiation.  There are 3 groups: group 1 (alpha, betaI, beta II, gamma) which require phospholipids and calcium, group 2 (delta, epsilon, theta, eta) which do not require calcium for activation, and ...
CDD:175982	158	EUK	Plants:8	cd04015, C2_plant_PLD, C2 domain present in plant phospholipase D (PLD).  PLD hydrolyzes terminal phosphodiester bonds in diester glycerophospholipids resulting in the degradation of phospholipids.  In vitro PLD transfers phosphatidic acid to primary alcohols.  In plants PLD plays a role in germination, seedling growth, phosphatidylinositol metabolism, and changes in phospholipid composition.  There is a single Ca(2+)/phospholipid-binding C2 domain in PLD. C2 domains ...
CDD:175984	135	EUK	Invertebrates:16,Mammals:1,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd04017, C2D_Ferlin, C2 domain fourth repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide ...
CDD:175985	151	EUK	Invertebrates:3	cd04018, C2C_Ferlin, C2 domain third repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide range of diseases including muscular dystrophy ...
CDD:175986	150	EUK	Plants:8	cd04019, C2C_MCTP_PRT_plant, C2 domain third repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset.  MCTPs are involved in Ca2+ signaling at the membrane.  Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended ...
CDD:175987	162	EUK	Invertebrates:5,Primates:1,Rodents:1,Vertebrates:5,nodiv:1	cd04020, C2B_SLP_1-2-3-4, C2 domain second repeat present in Synaptotagmin-like proteins 1-4.  All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length.  Slp1/JFC1 and Slp2/exophilin 4 promote granule docking to the plasma membrane.  Additionally, ...
CDD:175988	125	EUK	Invertebrates:10,Primates:1,Vertebrates:4,nodiv:1	cd04021, C2_E3_ubiquitin_ligase, C2 domain present in E3 ubiquitin ligase.  E3 ubiquitin ligase is part of the ubiquitylation mechanism responsible for controlling surface expression of membrane proteins.  The sequential action of several enzymes are involved: ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, and ubiquitin-protein ligase E3 which is responsible for substrate recognition and promoting the transfer ...
CDD:175989	127	EUK	Plants:3	cd04022, C2A_MCTP_PRT_plant, C2 domain first repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset.  MCTPs are involved in Ca2+ signaling at the membrane.  Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended ...
CDD:175990	128	EUK	Invertebrates:5,Plants:4	cd04024, C2A_Synaptotagmin-like, C2 domain first repeat present in Synaptotagmin-like proteins.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium.  Of the 17 identified ...
CDD:175992	131	EUK	Invertebrates:14,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd04026, C2_PKC_alpha_gamma, C2 domain in Protein Kinase C (PKC) alpha and gamma.  A single C2 domain is found in PKC alpha and gamma. The PKC family of serine/threonine kinases regulates apoptosis, proliferation, migration, motility, chemo-resistance, and differentiation.  There are 3 groups: group 1(alpha, betaI, beta II, gamma) which require phospholipids and calcium, group 2 (delta, epsilon, theta, eta) which do ...
CDD:175996	127	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:6	cd04030, C2C_KIAA1228, C2 domain third repeat present in uncharacterized human KIAA1228-like proteins.  KIAA proteins are uncharacterized human proteins. They were compiled by the Kazusa mammalian cDNA project which identified more than 2000 human genes. They are identified by 4 digit codes that precede the KIAA designation.  Many KIAA genes are still functionally uncharacterized including KIAA1228. C2 domains fold into an ...
CDD:175997	125	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd04031, C2A_RIM1alpha, C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins.  RIMs are believed to organize specialized sites of the plasma membrane called active zones.  They also play a role in controlling neurotransmitter release, plasticity processes, as well as memory and learning.  RIM contains an N-terminal zinc finger domain, a PDZ domain, and two C-terminal C2 domains (C2A, C2B).  C2 domains fold into ...
CDD:175998	127	EUK	Mammals:2,Vertebrates:5	cd04032, C2_Perforin, C2 domain of Perforin.  Perforin contains a single copy of a C2 domain in its C-terminus and plays a role in lymphocyte-mediated cytotoxicity.  Mutations in perforin leads to familial hemophagocytic lymphohistiocytosis type 2.  The function of perforin is calcium dependent and the C2 domain is thought to confer this binding to target cell membranes.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural ...
CDD:175999	133	EUK	Invertebrates:6,Primates:1,Vertebrates:4,nodiv:1	cd04033, C2_NEDD4_NEDD4L, C2 domain present in the Human neural precursor cell-expressed, developmentally down-regulated 4 (NEDD4) and NEDD4-like (NEDD4L/NEDD42).  Nedd4 and Nedd4-2 are two of the nine members of the Human Nedd4 family.  All vertebrates appear to have both Nedd4 and Nedd4-2 genes. They are thought to participate in the regulation of epithelial Na+ channel (ENaC) activity. They also have identical specificity for ...
CDD:176000	123	EUK	Invertebrates:11,Rodents:1,Vertebrates:3,nodiv:1	cd04035, C2A_Rabphilin_Doc2, C2 domain first repeat present in Rabphilin and Double C2 domain.  Rabphilin is found neurons and in neuroendrocrine cells, while Doc2 is found not only in the brain but in tissues, including mast cells, chromaffin cells, and osteoblasts.  Rabphilin and Doc2s share highly homologous tandem C2 domains, although their N-terminal structures are completely different: rabphilin contains an N-terminal ...
CDD:176001	119	EUK	Invertebrates:1,Primates:1,Rodents:1,Vertebrates:4	cd04036, C2_cPLA2, C2 domain present in cytosolic PhosphoLipase A2 (cPLA2).  A single copy of the C2 domain is present in cPLA2 which releases arachidonic acid from membranes initiating the biosynthesis of potent inflammatory mediators such as prostaglandins, leukotrienes, and platelet-activating factor.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished ...
CDD:176002	124	EUK	Invertebrates:11,Plants:2,Vertebrates:1,nodiv:1	cd04037, C2E_Ferlin, C2 domain fifth repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide range of diseases ...
CDD:176003	145	EUK	Plants:6	cd04038, C2_ArfGAP, C2 domain present in Arf GTPase Activating Proteins (GAP).  ArfGAP is a GTPase activating protein which regulates the ADP ribosylation factor Arf, a member of the Ras superfamily of GTP-binding proteins.  The GTP-bound form of Arf is involved in Golgi morphology and is involved in recruiting coat proteins.  ArfGAP is responsible for the GDP-bound form of Arf which is necessary for uncoating the membrane and allowing the Golgi to fuse with an ...
CDD:176004	108	EUK	Plants:12	cd04039, C2_PSD, C2 domain present in Phosphatidylserine decarboxylase (PSD).  PSD is involved in the biosynthesis of aminophospholipid by converting phosphatidylserine (PtdSer) to phosphatidylethanolamine (PtdEtn). There is a single C2 domain present and it is thought to confer PtdSer binding motif that is common to PKC and synaptotagmin. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a ...
CDD:176005	115	EUK	Plants:22	cd04040, C2D_Tricalbin-like, C2 domain fourth repeat present in Tricalbin-like proteins.  5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent ...
CDD:176006	111	EUK	Plants:12	cd04041, C2A_fungal, C2 domain first repeat; fungal group.  C2 domains were first identified in Protein Kinase C (PKC). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol ...
CDD:176007	121	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd04042, C2A_MCTP_PRT, C2 domain first repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP).  MCTPs are involved in Ca2+ signaling at the membrane.  MCTP is composed of a variable N-terminal sequence, three C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, ...
CDD:176008	126	EUK	Plants:16	cd04043, C2_Munc13_fungal, C2 domain in Munc13 (mammalian uncoordinated) proteins; fungal group.  C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner.  Mutations in Unc13 results in abnormal ...
CDD:176009	124	EUK	Plants:9	cd04044, C2A_Tricalbin-like, C2 domain first repeat present in Tricalbin-like proteins.  5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent ...
CDD:176010	120	EUK	Plants:7	cd04045, C2C_Tricalbin-like, C2 domain third repeat present in Tricalbin-like proteins.  5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent ...
CDD:176011	126	EUK	Invertebrates:8,Mammals:1,Primates:1,Vertebrates:5,nodiv:1	cd04046, C2_Calpain, C2 domain present in Calpain proteins.  A single C2 domain is found in calpains (EC 3.4.22.52, EC 3.4.22.53), calcium-dependent, non-lysosomal cysteine proteases.  Caplains are classified as belonging to Clan CA by MEROPS and include six families: C1, C2, C10, C12, C28, and C47.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, ...
CDD:176012	110	EUK	Invertebrates:20,Plants:7,Primates:1,Vertebrates:4,nodiv:2	cd04047, C2B_Copine, C2 domain second repeat in Copine.  There are 2 copies of the C2 domain present in copine, a protein involved in membrane trafficking, protein-protein interactions, and perhaps even cell division and growth.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta ...
CDD:176013	120	EUK	Invertebrates:13,Mammals:1,Plants:3,Primates:2,Rodents:1,Vertebrates:5	cd04048, C2A_Copine, C2 domain first repeat in Copine.  There are 2 copies of the C2 domain present in copine, a protein involved in membrane trafficking, protein-protein interactions, and perhaps even cell division and growth.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and ...
CDD:176014	124	EUK	Plants:7	cd04049, C2_putative_Elicitor-responsive_gene, C2 domain present in the putative elicitor-responsive gene.  In plants elicitor-responsive proteins are triggered in response to specific elicitor molecules such as glycolproteins, peptides, carbohydrates and lipids. A host of defensive responses are also triggered resulting in localized cell death.  Antimicrobial secondary metabolites, such as phytoalexins, or defense-related proteins, including pathogenesis-related (PR) ...
CDD:176015	105	EUK	Invertebrates:6,Primates:2,Rodents:1,Vertebrates:3	cd04050, C2B_Synaptotagmin-like, C2 domain second repeat present in Synaptotagmin-like proteins.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium.  ...
CDD:176016	125	EUK	Plants:15	cd04051, C2_SRC2_like, C2 domain present in Soybean genes Regulated by Cold 2 (SRC2)-like proteins.  SRC2 production is a response to pathogen infiltration.  The initial response of increased Ca2+ concentrations are coupled to downstream signal transduction pathways via calcium binding proteins.  SRC2 contains a single C2 domain which localizes to the plasma membrane and is involved in Ca2+ dependent protein binding. C2 domains fold into an 8-standed beta-sandwich ...
CDD:176017	111	EUK	Plants:9	cd04052, C2B_Tricalbin-like, C2 domain second repeat present in Tricalbin-like proteins.  5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent ...
CDD:173788	361	EUKprk	Bacteria:41,Invertebrates:5,Plants:24,Primates:2,Vertebrates:2	cd04056, Peptidases_S53, Peptidase domain in the S53 family.  Members of the peptidases S53 (sedolisin) family include endopeptidases and exopeptidases sedolisin, kumamolysin, and (PSCP) Pepstatin-insensitive Carboxyl Proteinase.  The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes ...
CDD:173789	297	EUKprk	Bacteria:21,Invertebrates:15,Plants:5,Primates:2,Rodents:1,Vertebrates:4,nodiv:2	cd04059, Peptidases_S8_Protein_convertases_Kexins_Furin-like, Peptidase S8 family domain in Protein convertases.  Protein convertases, whose members include furins and kexins, are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad that is not homologous to trypsin. Kexins are involved in the activation of peptide hormones, growth factors, and ...
CDD:173790	255	EUKprk	Bacteria:17,Invertebrates:3,Plants:40,Primates:1,Vertebrates:3	cd04077, Peptidases_S8_PCSK9_ProteinaseK_like, Peptidase S8 family domain in ProteinaseK-like proteins.  The peptidase S8 or Subtilase clan of proteases have a Asp/His/Ser catalytic triad that is not homologous to trypsin. This CD contains several members of this clan including: PCSK9 (Proprotein convertase subtilisin/kexin type 9), Proteinase_K, Proteinase_T, and other subtilisin-like serine proteases.  PCSK9 ...
CDD:271145	134	PRK	Bacteria:16	cd04079, CBM6_agarase-like, Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases.  This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of ...
CDD:271146	144	EUKprk	Bacteria:110,Environmental:1,Plants:1	cd04080, CBM6_cellulase-like, Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase).  This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that ...
CDD:271147	125	EUKprk	Bacteria:17,Invertebrates:1,Plants:17	cd04081, CBM35_galactosidase-like, Carbohydrate Binding Module family 35 (CBM35); appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH27 and GH43.  This family includes carbohydrate binding module family 35 (CBM35); these are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase ...
CDD:271148	124	PRK	Bacteria:34,Environmental:1	cd04082, CBM35_pectate_lyase-like, Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans.  This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included ...
CDD:271149	125	PRK	Bacteria:18	cd04083, CBM35_Lmo2446-like, Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446.  This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes ...
CDD:271150	123	EUKprk	Bacteria:120,Environmental:1,Plants:5	cd04084, CBM6_xylanase-like, Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains.  This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family domains, including GH3, GH11, and GH43 domains. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic ...
CDD:271151	152	PRK	Bacteria:26	cd04085, delta_endotoxin_C, delta-endotoxin C-terminal domain may be associated with carbohydrate binding functionality.  Delta-endotoxin C-terminal domain (delta endotoxin domain III) is part of the activated region of delta endotoxins, which are insecticidal toxins produced during sporulation by Bacillus species of bacteria. The activated endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is ...
CDD:271152	119	EUKprk	Bacteria:25,Plants:6	cd04086, CBM35_mannanase-like, Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains.  This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes, including periplasmic component of ABC-type sugar transport system involved in carbohydrate transport and metabolism, and several ...
CDD:239754	266	EUK	Invertebrates:14,Plants:18,Primates:1,Vertebrates:2	cd04087, PTPA, Phosphotyrosyl phosphatase activator (PTPA) is also known as protein phosphatase 2A (PP2A) phosphatase activator. PTPA is an essential, well conserved protein that stimulates the tyrosyl phosphatase activity of PP2A. It also reactivates the serine/threonine phosphatase activity of an inactive form of PP2A. Together, PTPA and PP2A constitute an ATPase. It has been suggested that PTPA alters the relative ...
CDD:239755	83	miss	miss	cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is ...
CDD:239756	82	miss	miss	cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the ...
CDD:239757	94	miss	miss	cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p.  This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2.  Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP.  Experiments suggest that GTP ...
CDD:239758	81	miss	miss	cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes.  Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex ...
CDD:239759	83	miss	miss	cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes.  Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex ...
CDD:239760	107	EUK	Invertebrates:2,Plants:2,Vertebrates:1	cd04093, HBS1_C, HBS1_C: this family represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1) which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34.  It has been speculated that yeast Hbs1 and Dom34 proteins may ...
CDD:239761	97	PRK	Bacteria:33	cd04094, selB_III, This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' ...
CDD:239762	103	PRK	Bacteria:55	cd04095, CysN_NoDQ_III, TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an ...
CDD:239763	80	miss	miss	cd04096, eEF2_snRNP_like_C, eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p.  Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP.  Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function ...
CDD:239764	78	miss	miss	cd04097, mtEFG1_C, mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes.  Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than ...
CDD:239765	80	miss	miss	cd04098, eEF2_C_snRNP, eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p.  This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2.  Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP.  Experiments suggest that GTP binding and probably GTP ...
CDD:239766	85	EUKprk	Bacteria:95,Invertebrates:16,Plants:14,Primates:1,Vertebrates:3	cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS).  aaRSs catalyze the specific attachment of amino acids (AAs) to ...
CDD:206690	197	EUK	Mammals:1,Primates:1,Rodents:2,Vertebrates:1	cd04104, p47_IIGP_like, p47 GTPase family includes IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1.  The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type ...
CDD:206691	202	EUK	Invertebrates:8,Plants:10,Rodents:1,Vertebrates:3	cd04105, SR_beta, Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP).  Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are ...
CDD:206692	201	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:3	cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32 (Rab32).  Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and ...
CDD:133319	168	EUK	Invertebrates:6,Plants:2,Primates:1,Rodents:1,Vertebrates:2	cd04119, RJL, Rab GTPase family J-like (RabJ-like).  RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting ...
CDD:133323	162	EUK	Invertebrates:11,Plants:1,Vertebrates:2	cd04123, Rab21, Rab GTPase family 21 (Rab21).  The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound ...
CDD:206704	197	EUK	Invertebrates:1,Plants:7,Primates:1,Vertebrates:1	cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like.  Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may ...
CDD:206709	180	EUK	Invertebrates:4,Plants:7,Primates:1,Vertebrates:2	cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small GTPase.  Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the ...
CDD:206713	166	EUK	Invertebrates:1,Primates:1,Vertebrates:3	cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like families.  RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack ...
CDD:206715	219	EUK	Invertebrates:1,Primates:1,Vertebrates:4	cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases.  RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent ...
CDD:133353	174	EUK	Invertebrates:6,Plants:3,Primates:1,Vertebrates:2	cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.  Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. ...
CDD:206724	159	EUK	Invertebrates:7,Plants:7,Vertebrates:2	cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.  Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.
CDD:206725	168	EUK	Invertebrates:4,Plants:2,Primates:1,Vertebrates:2	cd04160, Arfrp1, Arf-related protein 1 (Arfrp1).  Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also ...
CDD:206726	168	EUKprk	Bacteria:44,Environmental:4,Invertebrates:8,Plants:1,Rodents:1,Vertebrates:2	cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional GTPase.  Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S ...
CDD:206727	159	EUKprk	Bacteria:44,Environmental:1,Invertebrates:5,Plants:10,Primates:1,Vertebrates:2	cd04164, trmE, trmE is a tRNA modification GTPase.  TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and ...
CDD:206728	224	EUK	Invertebrates:2,Plants:1,Rodents:1,Vertebrates:1	cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family includes GTPBP2.  Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human ...
CDD:206729	209	PRK	Bacteria:11	cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex.  CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for ...
CDD:206730	213	EUK	Invertebrates:2,Plants:2	cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.  Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the ...
CDD:206731	237	PRK	Bacteria:9	cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins.  Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are ...
CDD:206732	268	PRK	Bacteria:14	cd04169, RF3, Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria.  Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from ...
CDD:206733	268	PRK	Bacteria:6	cd04170, EF-G_bact, Elongation factor G (EF-G) family.  Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ...
CDD:206734	170	PRK	Bacteria:12	cd04171, SelB, SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It ...
CDD:206753	171	EUK	Invertebrates:20,Plants:13,Primates:1,Vertebrates:3	cd04178, Nucleostemin_like, A circularly permuted subfamily of the Ras GTPases.  Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of ...
CDD:133022	185	EUKprk	Bacteria:211,Invertebrates:14,Plants:10,Primates:1,Vertebrates:3	cd04179, DPM_DPG-synthase_like, DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily.  DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. ...
CDD:133024	217	EUKprk	Bacteria:85,Environmental:4,Vertebrates:1	cd04181, NTP_transferase, NTP_transferases catalyze the transfer of nucleotides onto phosphosugars.  Nucleotidyltransferases transfer nucleotides onto phosphosugars.  The enzyme family includes Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. The products are activated sugars that are precursors for synthesis of lipopolysaccharide, glycolipids and ...
CDD:133025	186	PRK	Bacteria:99	cd04182, GT_2_like_f, GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function.  GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor ...
CDD:133026	231	EUKprk	Bacteria:22,Plants:1	cd04183, GT2_BcE_like, GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule.  GT2_BcbE_like:  The bcbE gene is one of the genes in the capsule biosynthetic locus of Pasteurella multocida. Its deducted product is likely involved in the biosynthesis of the polysaccharide capsule, which is found on surface of a wide range of bacteria. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of ...
CDD:133027	202	PRK	Bacteria:34	cd04184, GT2_RfbC_Mx_like, Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis.  The rfbC gene encodes a predicted protein of 1,276 amino acids, which is required for O-antigen biosynthesis in Myxococcus xanthus. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a ...
CDD:133028	202	PRK	Bacteria:25	cd04185, GT_2_like_b, Subfamily of Glycosyltransferase Family GT2 of unknown function.  GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. ...
CDD:133029	166	PRK	Bacteria:39,Environmental:1	cd04186, GT_2_like_c, Subfamily of Glycosyltransferase Family GT2 of unknown function.  GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming ...
CDD:133030	181	miss	miss	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1.  A family of  bacterial enzymes related to eukaryotic DPM1; Although the mechanism of eukaryotic enzyme is well studied, the mechanism of the  bacterial enzymes is not well understood. The eukaryotic DPM1 is the catalytic subunit of eukaryotic Dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan ...
CDD:133031	211	miss	miss	cd04188, DPG_synthase, DPG_synthase is involved in protein N-linked glycosylation.  UDP-glucose:dolichyl-phosphate glucosyltransferase (DPG_synthase) is a transmembrane-bound enzyme of the endoplasmic reticulum involved in protein N-linked glycosylation. This enzyme catalyzes the transfer of glucose from UDP-glucose to dolichyl phosphate.
CDD:133032	236	PRK	Bacteria:20,Environmental:1	cd04189, G1P_TT_long, G1P_TT_long represents the long form of glucose-1-phosphate thymidylyltransferase.  This family is the long form of Glucose-1-phosphate thymidylyltransferase.  Glucose-1-phosphate thymidylyltransferase catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate. It is the first enzyme in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.There are two forms of   ...
CDD:133033	244	EUKprk	Bacteria:1,Invertebrates:6,Plants:7	cd04190, Chitin_synth_C, C-terminal domain of Chitin Synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin.  Chitin synthase, also called UDP-N-acetyl-D-glucosamine:chitin 4-beta-N-acetylglucosaminyltransferase, catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of GlcNAc residues formed by covalent beta-1,4 linkages. Chitin is an important component of ...
CDD:133034	254	PRK	Bacteria:11	cd04191, Glucan_BSP_ModH, Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan.  Periplasmic Glucan Biosynthesis protein ModH is a glucosyltransferase that catalyzes the elongation of beta-1,2 polyglucose chains of glucan, requiring a beta-glucoside as a primer and UDP-glucose as a substrate. Glucans are composed of 5 to 10 units of glucose forming a highly branched structure, where beta-1,2-linked glucose constitutes a linear backbone ...
CDD:133035	229	PRK	Bacteria:10,Environmental:1	cd04192, GT_2_like_e, Subfamily of Glycosyltransferase Family GT2 of unknown function.  GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming ...
CDD:133036	323	EUKprk	Bacteria:4,Invertebrates:9,Plants:5,Vertebrates:3	cd04193, UDPGlcNAc_PPase, UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc.  UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylase (UAP) (also named GlcNAc1P uridyltransferase), catalyzes the reversible conversion of UTP and GlcNAc1 to PPi and UDPGlcNAc. UDP-N-acetylglucosamine (UDPGlcNAc), the activated form of GlcNAc, is a key precursor of N- and O-linked glycosylations. It is essential for the synthesis ...
CDD:133037	248	PRK	Bacteria:61	cd04194, GT8_A4GalT_like, A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface.  The members of this family of glycosyltransferases catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface. The enzymes exhibit broad substrate specificities. The known functions found ...
CDD:133038	201	PRK	Bacteria:7	cd04195, GT2_AmsE_like, GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis.  AmsE is a glycosyltransferase involved in exopolysaccharide amylovora biosynthesis in Erwinia amylovora. Amylovara is one of the three exopolysaccharide produced by E. amylovora. Amylovara-deficient mutants are non-pathogenic. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural ...
CDD:133039	214	PRK	Bacteria:48	cd04196, GT_2_like_d, Subfamily of Glycosyltransferase Family GT2 of unknown function.  GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. ...
CDD:133040	217	miss	miss	cd04197, eIF-2B_epsilon_N, The N-terminal domain of epsilon subunit of the eIF-2B is a subfamily of glycosyltransferase 2.  N-terminal domain of epsilon subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, ...
CDD:133041	214	miss	miss	cd04198, eIF-2B_gamma_N, The N-terminal domain of gamma subunit of the eIF-2B is a subfamily of glycosyltransferase 2.  N-terminal domain of gamma subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta ...
CDD:259862	177	EUKprk	Bacteria:1,Mammals:1,Primates:1	cd04199, CuRO_1_ceruloplasmin_like, Cupredoxin domains 1, 3, and 5 of ceruloplasmin and similar proteins.  This family includes the first, third, and fifth cupredoxin domains of ceruloplasmin and similar proteins including the first, third and fifth cupredoxin domains of unprocessed coagulation factors V and VIII. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. It functions in copper transport, ...
CDD:259863	141	EUK	Primates:1	cd04200, CuRO_2_ceruloplasmin_like, Cupredoxin domains 2, 4, and 6 of ceruloplasmin and similar proteins.  This family includes the second, fourth and sixth cupredoxin domains of  ceruloplasmin and similar proteins, including the second, fourth, and sixth cupredoxin domains of unprocessed coagulation factors V and VIII. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. Ceruloplasmin also functions in copper transport, amine ...
CDD:259865	138	EUKprk	Bacteria:50,Environmental:2,Plants:1	cd04202, CuRO_D2_2dMcoN_like, The second cupredoxin domain of bacterial two domain multicopper oxidase McoN and similar proteins.  This family includes bacterial two domain multicopper oxidases (2dMCOs) represented by the McoN from Nitrosomonas europaea. McoN is a trimeric type C blue copper oxidase. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The ...
CDD:259868	152	EUKprk	Bacteria:3,Environmental:1,Invertebrates:1,Plants:28,nodiv:1	cd04205, CuRO_2_LCC_like, Cupredoxin domain 2 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins.  Laccase-like multicopper oxidases (MCOs) are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as ...
CDD:259869	120	EUKprk	Bacteria:14,Invertebrates:2,Plants:16,nodiv:1	cd04206, CuRO_1_LCC_like, Cupredoxin domain 1 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins.  Laccase-like multicopper oxidases (MCOs) in this family contain three cupredoxin domains. They are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to ...
CDD:259870	132	EUKprk	Bacteria:12,Environmental:1,Invertebrates:3,Plants:14	cd04207, CuRO_3_LCC_like, Cupredoxin domain 3 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins.  Laccase-like multicopper oxidases (MCOs) in this family contain three cupredoxin domains. They are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from ...
CDD:259871	143	EUKprk	Bacteria:44,Environmental:1,Invertebrates:1,Plants:3	cd04208, CuRO_2_CuNIR, Cupredoxin domain 2 of Copper-containing nitrite reductase.  Copper-containing nitrite reductase (CuNIR), which catalyzes the reduction of NO2- to NO, is the key enzyme in the denitrification process in denitrifying bacteria. CuNIR contains at least one type 1 copper center and a type 2 copper center in the protein. The type 2 copper center of a copper nitrite reductase is the active site of the ...
CDD:259873	110	PRK	Bacteria:14	cd04211, Cupredoxin_like_2, Uncharacterized Cupredoxin-like subfamily.  Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins because they have an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. Some ...
CDD:259874	99	EUKprk	Bacteria:39,Environmental:1,Invertebrates:1	cd04212, CuRO_UO_II, The cupredoxin domain of Ubiquinol oxidase subunit II.  Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits in ubiquinol oxidase varies from two to five.  Although subunit II of ubiquinol oxidase ...
CDD:259875	103	PRK	Bacteria:25,Environmental:1	cd04213, CuRO_CcO_Caa3_II, The cupredoxin domain of Caa3 type Cytochrome c oxidase subunit II.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of most bacteria, is a multi-chain transmembrane protein located in the inner membrane the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Caa3 type of CcO Subunit II contains a copper-copper binuclear site called ...
CDD:259876	108	EUK	Mammals:4,Primates:2,Vertebrates:4	cd04214, PAD_N, N-terminal non-catalytic domain of protein-arginine deiminase.  The N-terminal non-catalytic domain of protein-arginine deiminase has a cupredoxin-like fold, but lacks the Cu binding site. PAD (protein-arginine deiminase) and protein L-arginine iminohydrolase catalyze the conversion of protein arginine residues to citrulline residues post-translationally in a process called citrullination. The modification plays crucial ...
CDD:259878	98	EUK	Plants:17	cd04216, Phytocyanin, Phytocyanins are plant blue or type I copper proteins.  Phytocyanins are plant blue or type I copper proteins. They are involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Phytocyanins are classified into four groups: stellacyanin, plantacyanin, uclacyanin and early nodulin groups. Stellacyanin appears to be associated with the plant cell wall; it may be involved in ...
CDD:259880	117	PRK	Bacteria:17,Environmental:2,nodiv:1	cd04218, Pseudoazurin, Pseudoazurin (Paz) is a type I blue copper electron-transfer protein.  Pseudoazurin (PAz) has been identified as an electron donor to the denitrification pathway. For example, PAz acts as an electron donor to cytochrome c peroxidase and N2OR from Paracoccus pantotrophus (Pp), and to the copper containing nitrite reductase (NiR) that catalyzes the second step of denitrification. It has been shown that pseudoazurin ...
CDD:259881	97	EUKprk	Bacteria:4,Plants:8	cd04219, Plastocyanin, Plastocyanin is a type I copper protein and functions in the electron transfer from PSII to PSI.  Plastocyanin is a small copper-containing protein found in cyanobacteria, higher plants, and some algae, where it plays a role in photosynthesis. The two photosystems that are primarily responsible for photosynthesis are photosystem I (PSI) and photosystem II (PSII). The flow of electrons begins in PSII, which acts as a proton pump. ...
CDD:259882	92	PRK	Bacteria:4	cd04220, Halocyanin, Halocyanin is an archaea blue (type I) copper redox protein.  Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronomonas pharaonis (Natronobacterium pharaonis). Halocyanin may serve as a mobile electron carrier at a peripheral membrane protein. The copper-binding domain is present only once in some halocyanins and is duplicated in others.
CDD:259883	83	PRK	Bacteria:9	cd04221, MauL, Methylamine utilization protein MauL.  MauL is one of the products from the methylamine utilization gene cluster in Methylobacterium extorquens AM1. Mutants generated by insertions in mauL were not able to grow on methylamine or any other primary amine as carbon sources. MauL belongs to the blue or type I copper protein family. They are involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the ...
CDD:259885	95	PRK	Bacteria:25	cd04223, N2OR_C, The C-terminal cupredoxin domain of Nitrous-oxide reductase.  Nitrous-oxide reductase participates in nitrogen metabolism and catalyzes the last step in dissimilatory nitrate reduction, the two-electron reduction of N2O to N2. It contains copper ions as cofactors in the form of a binuclear CuA center at the site of electron entry and a tetranuclear CuZ centre at the active site. The C-terminus of Nitrous-oxide reductase is a cupredoxin domain.
CDD:259891	175	EUKprk	Bacteria:1,Plants:1,nodiv:1	cd04229, CuRO_1_Ceruloplasmin_like_1, cupredoxin domain of ceruloplasmin homologs.  Uncharacterized subfamily of ceruloplasmin homologous proteins. Ceruloplasmin  (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis.  Ceruloplasmin also functions in copper transport, amine oxidase and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains and exhibits internal sequence homology that ...
CDD:259894	120	PRK	Bacteria:29,Environmental:2	cd04232, CuRO_1_CueO_FtsP, The first Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins.  CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP ...
CDD:259895	121	PRK	Bacteria:27,Environmental:1	cd04233, Auracyanin, Auracyanins A and B and similar proteins.  This subfamily includes both auracyanins A and B from the photosynthetic bacterium Chloroflexus aurantiacus and similar proteins. Auracyanins A and B are very  similar blue copper proteins with 38% sequence identity and are homologous to the bacterial redox protein Azurin. However, auracyanin A is expressed only when C. aurantiacus cells are grown in light, whereas auracyanin B is ...
CDD:239767	227	EUKprk	Bacteria:46,Environmental:1,Plants:5	cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK), Aspartokinase (AK); this CD includes the N-terminal catalytic domain of aspartokinase (4-L-aspartate-4-phosphotransferase;). AK is the first enzyme in the biosynthetic pathway of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. It also catalyzes the conversion of aspartate and ATP ...
CDD:239768	308	EUKprk	Bacteria:28,Invertebrates:3	cd04235, AAK_CK, AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase ...
CDD:239770	280	EUKprk	Bacteria:18,Plants:2,nodiv:1	cd04237, AAK_NAGS-ABP, AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal NAG synthase, acetyltransferase (ArgA) domain. Both bacterial and plant sequences in this CD have a conserved ...
CDD:239771	256	EUKprk	Bacteria:50,Environmental:1,Plants:6	cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase (NAGK)-like . Included in this CD are the Escherichia coli and Pseudomonas aeruginosa type NAGKs which catalyze the phosphorylation of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in bacteria and photosynthetic organisms using either the acetylated, noncyclic (NC), or non-acetylated, cyclic (C) route of ornithine biosynthesis. Also ...
CDD:239772	229	EUKprk	Bacteria:44,Plants:2	cd04239, AAK_UMPK-like, AAK_UMPK-like: UMP kinase (UMPK)-like, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis. Regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinases of E. coli (Ec) and Pyrococcus ...
CDD:239773	203	PRK	Bacteria:12	cd04240, AAK_UC, AAK_UC: Uncharacterized (UC) amino acid kinase-like proteins found mainly in archaea and a few bacteria. Sequences in this CD are members of the Amino Acid Kinase (AAK) superfamily.
CDD:239774	252	EUKprk	Bacteria:18,Invertebrates:3,Plants:2	cd04241, AAK_FomA-like, AAK_FomA-like: This CD includes a fosfomycin biosynthetic gene product, FomA, and similar proteins found in a wide range of organisms. Together, the fomA and fomB genes in the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis confer high-level fosfomycin resistance. FomA and FomB proteins converted fosfomycin to fosfomycin monophosphate and fosfomycin diphosphate in the presence of ATP and a ...
CDD:239775	251	EUKprk	Bacteria:59,Invertebrates:6,Plants:8,Vertebrates:3	cd04242, AAK_G5K_ProB, AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine) biosynthesis. G5K is subject to feedback allosteric inhibition by proline or ornithine. In microorganisms and plants, proline plays an important role as ...
CDD:239776	293	miss	miss	cd04243, AAK_AK-HSDH-like, AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such bacteria as E. coli (AKI-HSDHI, ThrA  and  AKII-HSDHII, MetL) and in higher plants (Z. mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of ...
CDD:239778	288	miss	miss	cd04245, AAK_AKiii-YclM-BS, AAK_AKiii-YclM-BS: Amino Acid Kinase Superfamily (AAK), AKiii-YclM-BS; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate ...
CDD:239779	239	miss	miss	cd04246, AAK_AK-DapG-like, AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine ...
CDD:239783	279	miss	miss	cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the non-acetylated, cyclic route of ornithine biosynthesis. In this pathway, glutamate is first N-acetylated and then phosphorylated by NAGK to give phosphoryl NAG, which is converted to NAG-ornithine. ...
CDD:239786	221	miss	miss	cd04253, AAK_UMPK-PyrH-Pf, AAK_UMPK-PyrH-Pf: UMP kinase (UMPK)-Pf, the mostly archaeal uridine monophosphate kinase (uridylate kinase) enzymes that catalyze UMP phosphorylation and play a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of Pyrococcus furiosus (Pf) is known to function as a ...
CDD:239787	231	miss	miss	cd04254, AAK_UMPK-PyrH-Ec, UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of E. coli (Ec) is known to function as a homohexamer, with GTP ...
CDD:239790	294	miss	miss	cd04257, AAK_AK-HSDH, AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli AKI-HSDHI, ThrA  and E. coli AKII-HSDHII, MetL) and higher plants (Z. mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK ...
CDD:239791	292	miss	miss	cd04258, AAK_AKiii-LysC-EC, AAK_AKiii-LysC-EC: Amino Acid Kinase Superfamily (AAK), AKiii-LysC-EC: this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is a monofunctional class enzyme (LysC) found in some bacteria such as E. coli. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. In E. coli, LysC ...
CDD:239794	239	miss	miss	cd04261, AAK_AKii-LysC-BS, AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, ...
CDD:176265	98	EUK	Plants:10	cd04263, DUF619-NAGK-FABP, DUF619 domain of N-acetylglutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway.  DUF619-NAGK-FABP: DUF619 domain of N-acetylglutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (FABP). The nuclear-encoded, mitochondrial polyprotein precursor (ARG5,6) consists of an N-terminal NAGK (ArgB) domain, a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-Acetylglutamate Phosphate Reductase, NAGPR). The ...
CDD:176266	99	EUKprk	Bacteria:3,Invertebrates:4,Plants:2,Vertebrates:2	cd04264, DUF619-NAGS, DUF619 domain of various N-acetylglutamate Synthases of the fungal arginine-biosynthetic pathway and urea cycle found in humans and fish.  DUF619-NAGS: This family includes the DUF619 domain of various N-acetylglutamate synthases (NAGS) of the urea cycle found in humans and fish, the DUF619 domain of the NAGS of the fungal arginine-biosynthetic pathway (FABP), as well as the DUF619 domain present in ...
CDD:176267	99	miss	miss	cd04265, DUF619-NAGS-U, DUF619 domain of various N-acetylglutamate Synthases (NAGS) of the urea (U) cycle of humans and fish.  This family includes the DUF619 domain of various N-acetylglutamate synthases (NAGS) of the urea cycle found in humans and fish, the DUF619 domain of the NAGS of the fungal arginine-biosynthetic pathway (FABP), as well as the DUF619 domain present in C-terminal of a NAG kinase-like domain in a limited number of predicted NAGSs found in bacteria ...
CDD:239795	192	EUK	Invertebrates:2	cd04267, ZnMc_ADAM_like, Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
CDD:239796	165	EUKprk	Bacteria:26,Plants:1,nodiv:1	cd04268, ZnMc_MMP_like, Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
CDD:239797	194	EUK	Invertebrates:5,Mammals:3,Primates:4,Rodents:3,Vertebrates:22	cd04269, ZnMc_adamalysin_II_like, Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
CDD:239798	244	EUK	Invertebrates:3,Primates:1,Vertebrates:3	cd04270, ZnMc_TACE_like,  Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
CDD:239799	228	EUK	Plants:10	cd04271, ZnMc_ADAM_fungal, Zinc-dependent metalloprotease, ADAM_fungal subgroup. The adamalysin_like or ADAM (A Disintegrin And Metalloprotease) family of metalloproteases are integral membrane proteases acting on a variety of extracellular targets. They are involved in shedding soluble peptides or proteins from the cell surface. This subfamily contains fungal ADAMs, whose precise function has yet to be determined.
CDD:239800	220	EUK	Invertebrates:8	cd04272, ZnMc_salivary_gland_MPs, Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
CDD:239801	207	EUK	Invertebrates:8,Primates:1,Vertebrates:5	cd04273, ZnMc_ADAMTS_like, Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases ...
CDD:239802	225	EUKprk	Bacteria:11,Plants:9,Primates:1,Vertebrates:2	cd04275, ZnMc_pappalysin_like, Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal ...
CDD:239803	197	miss	miss	cd04276, ZnMc_MMP_like_2, Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
CDD:239804	186	PRK	Bacteria:24	cd04277, ZnMc_serralysin_like, Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple ...
CDD:239805	157	EUKprk	Bacteria:1,Invertebrates:9,Mammals:1,Plants:4,Primates:1,Vertebrates:4,nodiv:1	cd04278, ZnMc_MMP, Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, ...
CDD:239806	156	EUKprk	Bacteria:21,Plants:2	cd04279, ZnMc_MMP_like_1, Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
CDD:239807	180	EUKprk	Bacteria:6,Invertebrates:23,Vertebrates:1,nodiv:1	cd04280, ZnMc_astacin_like, Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: ...
CDD:239810	182	EUK	Vertebrates:9	cd04283, ZnMc_hatching_enzyme, Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related  metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different  substrate specificities and cooperatively digest the chorion.
CDD:99995	778	PRK	Bacteria:32	cd04299, GT1_Glycogen_Phosphorylase_like, This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The members of this family are found in bacteria and Archaea.
CDD:99996	797	EUKprk	Bacteria:59,Invertebrates:11,Mammals:1,Plants:5,Primates:1,Vertebrates:2	cd04300, GT1_Glycogen_Phosphorylase, This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. ...
CDD:173926	65	EUKprk	Bacteria:388,Environmental:3,Invertebrates:24,Mammals:1,Plants:35,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd04301, NAT_SF, N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate.  NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to ...
CDD:239811	108	PRK	Bacteria:5,Environmental:1	cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS).  This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein ...
CDD:239812	135	EUK	Vertebrates:1	cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS.  These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon ...
CDD:239813	82	EUKprk	Bacteria:37,Environmental:1,Invertebrates:6,Plants:11,Vertebrates:1	cd04318, EcAsnRS_like_N, EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA ...
CDD:239815	102	EUK	Invertebrates:13,Plants:15,Primates:1,Vertebrates:3	cd04320, AspRS_cyto_N, AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to ...
CDD:239816	86	EUK	Plants:14	cd04321, ScAspRS_mt_like_N, ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during ...
CDD:239817	108	EUKprk	Bacteria:96,Invertebrates:4,Plants:15,Primates:1,Vertebrates:1,nodiv:1	cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction ...
CDD:239818	84	EUKprk	Bacteria:4,Invertebrates:6,Plants:7,Primates:1	cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs.  This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA ...
CDD:239819	198	EUKprk	Bacteria:8,Plants:3	cd04327, ZnMc_MMP_like_3, Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
CDD:239820	89	EUK	Invertebrates:8,Plants:13,Primates:1,Vertebrates:4	cd04328, RNAP_I_Rpa43_N, RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and ...
CDD:239821	80	EUK	Invertebrates:9,Plants:10,Vertebrates:1	cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a ...
CDD:239822	80	EUK	Invertebrates:7,Plants:9,Primates:1,Vertebrates:3	cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 ...
CDD:239823	80	PRK	Bacteria:12	cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains ...
CDD:239824	136	EUKprk	Bacteria:226,Environmental:1,Invertebrates:16,Plants:4,Rodents:1,Vertebrates:4,nodiv:1	cd04332, YbaK_like, YbaK-like.  The YbaK family of deacylase domains includes the INS amino acid-editing domain of  the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX.  The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation.  Organisms whose ProRS lacks the INS ...
CDD:239825	148	miss	miss	cd04333, ProX_deacylase, This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens  ProX Ala-tRNA(Pro) deacylase and also the cis-acting prolyl-tRNA synthetase-editing domain (ProRS-INS). While ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro), the E. coli YbaK hydrolyzes misacylated ...
CDD:239826	160	miss	miss	cd04334, ProRS-INS, INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-celled parasites.  ProRS catalyzes the attachment of proline to tRNA(Pro); proline is first activated by ATP, and then transferred to the acceptor end of tRNA(Pro). ProRS can inadvertently process ...
CDD:239827	156	miss	miss	cd04335, PrdX_deacylase, This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the YbaK and ProX proteins, and the prolyl-tRNA synthetase-editing domain (ProRS-INS), specifically hydrolyzes Ala-tRNA(Pro). In this CD, many of the eukaryotic editing domains are N-terminal and ...
CDD:239828	153	miss	miss	cd04336, YeaK, YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function.  The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX.  The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation.  Organisms whose ProRS lacks the INS domain express a ...
CDD:239831	59	miss	miss	cd04365, IlGF_relaxin_like, IlGF_like family, relaxin_like subgroup, specific to vertebrates. Members include a number of active peptides including (pro)relaxin, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), and insulin-like peptides 5 (INSL5) and 6 (INSL6). Members of this subgroup are widely expressed in testes (INSL3, INSL6), decidua, placenta, prostate, corpus luteum, brain (various relaxins), ...
CDD:239832	42	miss	miss	cd04366, IlGF_insulin_bombyxin_like, IlGF_like family, insulin_bombyxin_like subgroup. Members include a number of peptides including insulin, insulin-like growth factors I and II, insect prothoracicotropic hormone (bombyxin), locust insulin-related peptide (LIRP), molluscan insulin-related peptides 1 to 5 (MIP), and C. elegans insulin-like peptides. With the exception of insulin-like growth factors, the active forms of these peptide hormones are composed of two chains (A ...
CDD:239833	79	miss	miss	cd04367, IlGF_insulin_like, IlGF_like family, insulin_like subgroup, specific to vertebrates. Members include a number of peptides including insulin and insulin-like growth factors I and II, which play a variety of roles in controlling processes such as metabolism, growth and differentiation, and reproduction. On a cellular level they affect cell cycle, apoptosis, cell migration, and differentiation. With the exception of the insulin-like growth factors, the active forms ...
CDD:239834	67	EUK	Primates:1	cd04368, IlGF, IlGF, insulin_like growth factors; specific to vertebrates. Members include a number of peptides including insulin-like growth factors I and II, which play a variety of roles in controlling processes such as growth, differentiation, and reproduction. On a cellular level they affect cell cycle, apoptosis, cell migration, proliferation, and differentiation. Typically, the active forms of these peptide hormones are single chains cross-linked by three ...
CDD:99922	99	EUK	Invertebrates:25,Plants:35,Primates:1,Rodents:1,Vertebrates:3	cd04369, Bromodomain, Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
CDD:239835	123	EUK	Invertebrates:3,Plants:10,Primates:1,Vertebrates:4	cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor ...
CDD:239836	81	EUKprk	Bacteria:4,Invertebrates:15,Mammals:2,Plants:24,Primates:1,Rodents:1,Vertebrates:6,nodiv:1	cd04371, DEP, DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
CDD:239845	220	EUK	Invertebrates:8,Plants:8,Primates:1,Vertebrates:2	cd04380, RhoGAP_OCRL1, RhoGAP_OCRL1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in OCRL1-like proteins. OCRL1 (oculocerebrorenal syndrome of Lowe 1)-like proteins contain two conserved domains: a central inositol polyphosphate 5-phosphatase domain and a C-terminal Rho GAP domain, this GAP domain lacks the catalytic residue and therefore maybe inactive. OCRL-like proteins are type II ...
CDD:239847	193	EUK	Invertebrates:7,Vertebrates:3	cd04382, RhoGAP_MgcRacGAP, RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective ...
CDD:239850	184	EUK	Invertebrates:5,Plants:1,Primates:1,Vertebrates:2	cd04385, RhoGAP_ARAP, RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct ...
CDD:239856	216	EUK	Invertebrates:2,Primates:1,Vertebrates:4	cd04391, RhoGAP_ARHGAP18, RhoGAP_ARHGAP18: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP18-like proteins. The function of ArhGAP18 is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including ...
CDD:239864	212	EUK	Plants:3	cd04399, RhoGAP_fRGD2, RhoGAP_fRGD2: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton ...
CDD:239866	198	EUK	Plants:7	cd04401, RhoGAP_fMSB1, RhoGAP_fMSB1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal MSB1-like proteins. Msb1 was originally identified as a multicopy suppressor of temperature sensitive cdc42 mutation. Msb1 is a positive regulator of the Pkc1p-MAPK pathway and 1,3-beta-glucan synthesis, both pathways involve Rho1 regulation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound ...
CDD:239867	192	EUK	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:4	cd04402, RhoGAP_ARHGAP20, RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular ...
CDD:239870	235	EUK	Invertebrates:1,Primates:1,Vertebrates:2	cd04405, RhoGAP_BRCC3-like, RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain and an N-terminal DEP (Disheveled, Egl-10, and Pleckstrin) domain. The function(s) of  BRCC3 and DEPDC7 are unknown. Small GTPases cluster into distinct ...
CDD:239875	134	EUK	Invertebrates:13,Vertebrates:3	cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B (NDPk7B): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, ...
CDD:239876	130	EUKprk	Bacteria:53,Invertebrates:14,Mammals:1,Plants:7,Primates:1,Vertebrates:3,nodiv:1	cd04413, NDPk_I, Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian ...
CDD:239879	132	EUK	Invertebrates:2,Mammals:2,Primates:1,Vertebrates:2	cd04416, NDPk_TX, NDP kinase domain of thioredoxin domain-containing proteins  (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin ...
CDD:213270	338	EUKprk	Bacteria:33,Invertebrates:1,Plants:2,Primates:1,Vertebrates:1	cd04433, AFD_class_I, Adenylate forming domain, Class I.  This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or ...
CDD:271198	351	EUKprk	Bacteria:28,Environmental:6,Plants:1,Primates:1	cd04434, LanC_like, Cyclases involved in the biosynthesis of lantibiotics, and similar proteins.  LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans), in addition to  ...
CDD:239884	125	miss	miss	cd04437, DEP_Epac, DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion.  Epac-like proteins share a common domain architecture, ...
CDD:239885	84	miss	miss	cd04438, DEP_dishevelled, DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins.  Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
CDD:239896	83	miss	miss	cd04449, DEP_DEPDC5-like, DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
CDD:239897	88	miss	miss	cd04450, DEP_RGS7-like, DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha ...
CDD:239898	64	EUKprk	Bacteria:30,Invertebrates:1,Plants:3	cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits,  the presence of three ...
CDD:239899	76	EUKprk	Bacteria:7,Invertebrates:9,Plants:6,Primates:1,Vertebrates:3	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. ...
CDD:239900	88	EUKprk	Bacteria:42,Plants:4	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme)  ...
CDD:239902	67	PRK	Bacteria:49	cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, ...
CDD:239904	60	EUKprk	Bacteria:10,Invertebrates:10,Mammals:1,Plants:7,Primates:2,Vertebrates:3	cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure ...
CDD:239905	65	EUKprk	Bacteria:140,Invertebrates:15,Plants:4,Primates:1,Vertebrates:4	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea.  CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The ...
CDD:239906	68	EUKprk	Bacteria:14,Invertebrates:1	cd04459, Rho_CSD, Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is ...
CDD:239907	99	PRK	Bacteria:2	cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA ...
CDD:239908	83	EUK	Invertebrates:2,Mammals:1,Plants:9,Vertebrates:4	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits.  Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. ...
CDD:239909	88	EUK	Invertebrates:2,Plants:5,Primates:1	cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal ...
CDD:239911	67	EUKprk	Bacteria:41,Invertebrates:1,Plants:5	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP ...
CDD:239912	68	PRK	Bacteria:27	cd04466, S1_YloQ_GTPase, S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains ...
CDD:239913	57	PRK	Bacteria:11	cd04467, S1_aIF5A, S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain ...
CDD:239914	69	EUK	Invertebrates:16,Plants:10,Primates:1,Vertebrates:4	cd04468, S1_eIF5A, S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 ...
CDD:239916	61	EUKprk	Bacteria:110,Plants:3	cd04470, S1_EF-P_repeat_1, S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P ...
CDD:239917	83	PRK	Bacteria:85	cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
CDD:239918	68	EUKprk	Bacteria:18,Plants:3	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase  is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. ...
CDD:239919	77	PRK	Bacteria:15	cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
CDD:239920	104	EUK	Invertebrates:11,Plants:11,Primates:1,Vertebrates:3	cd04474, RPA1_DBD_A, RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various ...
CDD:239921	101	EUK	Invertebrates:11,Plants:7,Primates:2,Vertebrates:1	cd04475, RPA1_DBD_B, RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various ...
CDD:239922	166	EUK	Invertebrates:4,Plants:11,Vertebrates:3	cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear ...
CDD:239923	97	EUK	Invertebrates:1,Plants:6,Primates:1	cd04477, RPA1N, RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, ...
CDD:239924	95	EUK	Invertebrates:12,Plants:21,Primates:1,Vertebrates:3	cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear ...
CDD:239925	101	EUK	Invertebrates:10,Plants:15,Primates:1,Vertebrates:3	cd04479, RPA3, RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer ...
CDD:239926	86	EUK	Plants:5	cd04480, RPA1_DBD_A_like, RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear ...
CDD:239927	106	EUK	Plants:4	cd04481, RPA1_DBD_B_like, RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear ...
CDD:239928	91	PRK	Bacteria:16	cd04482, RPA2_OBF_like, RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear ...
CDD:239929	92	EUK	Plants:4,Rodents:1,Vertebrates:2	cd04483, hOBFC1_like, hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. ...
CDD:239930	82	PRK	Bacteria:27,Environmental:1	cd04484, polC_OBF, polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading ...
CDD:239931	84	PRK	Bacteria:197,nodiv:1	cd04485, DnaE_OBF, DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus ...
CDD:239932	78	EUKprk	Bacteria:73,Plants:6	cd04486, YhcR_OBF_like, YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
CDD:239933	73	PRK	Bacteria:6	cd04487, RecJ_OBF2_like, RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most ...
CDD:239934	75	PRK	Bacteria:160,Environmental:1,nodiv:1	cd04488, RecG_wedge_OBF, RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal ...
CDD:239935	78	PRK	Bacteria:104	cd04489, ExoVII_LU_OBF, ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by ...
CDD:239936	79	PRK	Bacteria:8	cd04490, PolII_SU_OBF, PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this ...
CDD:239937	82	EUKprk	Bacteria:20,Invertebrates:5,Plants:3,Primates:1,Vertebrates:2	cd04491, SoSSB_OBF, SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is ...
CDD:239938	83	PRK	Bacteria:41	cd04492, YhaM_OBF_like, YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the ...
CDD:239939	100	EUK	Invertebrates:7,Plants:7,Vertebrates:2	cd04493, BRCA2DBD_OB1, BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. ...
CDD:239940	251	EUK	Plants:1,Vertebrates:1	cd04494, BRCA2DBD_OB2, BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also ...
CDD:239942	100	EUKprk	Bacteria:153,Environmental:1,Invertebrates:5,Plants:20,Primates:1,Vertebrates:3,nodiv:1	cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a ...
CDD:239943	138	EUK	Invertebrates:1,Plants:16,Vertebrates:3	cd04497, hPOT1_OB1_like, hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the ...
CDD:239944	123	EUK	Invertebrates:4	cd04498, hPOT1_OB2, hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA ...
CDD:239945	183	PRK	Bacteria:13	cd04501, SGNH_hydrolase_like_4, Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
CDD:239946	171	PRK	Bacteria:10,nodiv:2	cd04502, SGNH_hydrolase_like_7, Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
CDD:239947	204	PRK	Bacteria:16	cd04506, SGNH_hydrolase_YpmR_like, Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. This subfamily contains sequences similar to Bacillus YpmR.
CDD:119391	48	EUK	Invertebrates:26,Mammals:3,Plants:15,Primates:2,Rodents:1,Vertebrates:7	cd04508, TUDOR, Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked ...
CDD:107261	299	miss	miss	cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems.  This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems.  The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA ...
CDD:239948	130	EUKprk	Bacteria:13,Plants:1,nodiv:1	cd04511, Nudix_Hydrolase_4, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and ...
CDD:271334	249	EUKprk	Bacteria:33,Environmental:1,Primates:1	cd04512, Ntn_Asparaginase_2_like, L-Asparaginase type 2-like enzymes of the NTN-hydrolase superfamily.  This family includes Glycosylasparaginase, Taspase 1, and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 ...
CDD:271335	294	EUKprk	Bacteria:28,Invertebrates:23,Plants:21,Primates:1,Vertebrates:5	cd04513, Glycosylasparaginase, Glycosylasparaginase and similar proteins.  Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoproteins. This enzyme is an amidase located inside lysosomes. Mutation of this gene in humans causes a genetic disorder known as aspartylglycosaminuria (AGU). The glycosylasparaginase precursor undergoes autoproteolysis through an N-O or N-S ...
CDD:271336	313	EUK	Invertebrates:14,Plants:67,Vertebrates:3,nodiv:1	cd04514, Taspase1_like, Taspase 1 (threonine aspartase 1) and similar proteins.  Taspase1 catalyzes the cleavage of the mix lineage leukemia (MLL) nuclear protein and transcription factor TFIIA. Taspase1 is a threonine aspartase, a member of the Ntn hydrolase superfamily and the type 2 asparaginase family. A threonine residue acts as the active site nucleophile in both endopeptidease and protease activities to cleave polypeptide ...
CDD:239952	174	miss	miss	cd04516, TBP_eukaryotes, eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase ...
CDD:239953	174	miss	miss	cd04517, TLF, TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate ...
CDD:239954	174	miss	miss	cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, ...
CDD:213328	256	EUK	Invertebrates:14,Mammals:1,Plants:10,Primates:2,Rodents:2,Vertebrates:1	cd04519, RasGAP, Ras GTPase Activating Domain.  RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid ...
CDD:239955	106	PRK	Bacteria:8	cd04582, CBS_pair_ABC_OpuCA_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown.  In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function ...
CDD:239956	109	PRK	Bacteria:33	cd04583, CBS_pair_ABC_OpuCA_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown.  In the related ABC transporter, OpuA, the tandem CBS domains have been shown to ...
CDD:239957	121	PRK	Bacteria:15	cd04584, CBS_pair_ACT_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in  the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms.  They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are ...
CDD:239958	122	EUKprk	Bacteria:13,Invertebrates:1	cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in  the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms.  They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these ...
CDD:239959	135	PRK	Bacteria:18	cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection proteins. It is also found in some secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. CBS is a small domain originally identified ...
CDD:239960	113	EUKprk	Bacteria:6,Plants:9	cd04587, CBS_pair_CAP-ED_DUF294_PBI_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain.  Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme ...
CDD:239961	110	PRK	Bacteria:8	cd04588, CBS_pair_CAP-ED_DUF294_assoc_arch, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the archaeal CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain.  Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the ...
CDD:239962	111	PRK	Bacteria:18	cd04589, CBS_pair_CAP-ED_DUF294_assoc_bac, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain.  Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the ...
CDD:239963	111	EUKprk	Bacteria:202,Environmental:2,Invertebrates:1,Plants:3,Primates:1,nodiv:2	cd04590, CBS_pair_CorC_HlyC_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function.  The function of the CorC_HlyC ...
CDD:239964	105	EUK	Invertebrates:8,Plants:14,Primates:1,Vertebrates:4	cd04591, CBS_pair_EriC_assoc_euk_bac, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be ...
CDD:239966	115	PRK	Bacteria:4	cd04593, CBS_pair_EriC_assoc_bac_arch, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the ...
CDD:239968	110	PRK	Bacteria:23	cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called ...
CDD:239969	108	PRK	Bacteria:20	cd04596, CBS_pair_DRTGG_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman ...
CDD:239971	119	PRK	Bacteria:20	cd04598, CBS_pair_GGDEF_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a ...
CDD:239973	124	EUKprk	Bacteria:27,Invertebrates:1,nodiv:2	cd04600, CBS_pair_HPP_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide ...
CDD:239974	110	EUKprk	Bacteria:46,Invertebrates:1	cd04601, CBS_pair_IMPDH, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein.  IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide ...
CDD:239975	114	EUKprk	Bacteria:6,Invertebrates:7,Plants:5,Rodents:1	cd04602, CBS_pair_IMPDH_2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein.  IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. CBS is a small domain originally identified in cystathionine beta-synthase and ...
CDD:239977	114	EUKprk	Bacteria:121,Plants:2,nodiv:1	cd04604, CBS_pair_KpsF_GutQ_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein.  These APIs catalyze the conversion of the pentose pathway intermediate D-ribulose 5-phosphate into A5P, a precursor of 3-deoxy-D-manno-octulosonate, which is an integral carbohydrate component of various glycolipids coating ...
CDD:239978	110	PRK	Bacteria:8	cd04605, CBS_pair_MET2_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine.  It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come ...
CDD:239979	109	PRK	Bacteria:142,nodiv:1	cd04606, CBS_pair_Mg_transporter, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE.  MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide ...
CDD:239980	113	PRK	Bacteria:47,Environmental:1	cd04607, CBS_pair_NTP_transferase_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream.  CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which ...
CDD:239981	124	EUK	Invertebrates:6,Mammals:1,Plants:6,Vertebrates:3	cd04608, CBS_pair_PALP_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream.   The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives.  The members of ...
CDD:239982	110	PRK	Bacteria:27	cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream.   The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives.  The members of the PALP family are principally ...
CDD:239984	111	PRK	Bacteria:16	cd04611, CBS_pair_PAS_GGDEF_DUF1_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be ...
CDD:239985	111	PRK	Bacteria:29	cd04612, CBS_pair_SpoIVFB_EriC_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC.  SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA ...
CDD:239986	114	PRK	Bacteria:20	cd04613, CBS_pair_SpoIVFB_EriC_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC.  SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA ...
CDD:239987	96	PRK	Bacteria:6	cd04614, CBS_pair_1, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:239989	118	PRK	Bacteria:14	cd04617, CBS_pair_4, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:239990	98	EUK	Invertebrates:7,Plants:10,Primates:1,Vertebrates:2	cd04618, CBS_pair_5, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS ...
CDD:239992	115	PRK	Bacteria:4	cd04620, CBS_pair_7, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:239993	135	EUKprk	Bacteria:7,Invertebrates:1	cd04621, CBS_pair_8, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the ...
CDD:239994	113	PRK	Bacteria:54,nodiv:1	cd04622, CBS_pair_9, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical ...
CDD:239995	113	EUKprk	Bacteria:71,Invertebrates:1,Plants:3,nodiv:1	cd04623, CBS_pair_10, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS ...
CDD:239996	112	PRK	Bacteria:12	cd04624, CBS_pair_11, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:239999	123	EUK	Invertebrates:2,Plants:10	cd04627, CBS_pair_14, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the ...
CDD:240000	114	PRK	Bacteria:24	cd04629, CBS_pair_16, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240001	114	PRK	Bacteria:14	cd04630, CBS_pair_17, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240002	125	PRK	Bacteria:12	cd04631, CBS_pair_18, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240004	121	PRK	Bacteria:7	cd04633, CBS_pair_20, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240007	132	PRK	Bacteria:11	cd04636, CBS_pair_23, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240008	122	PRK	Bacteria:8	cd04637, CBS_pair_24, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240010	111	PRK	Bacteria:9	cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240011	126	PRK	Bacteria:11	cd04640, CBS_pair_27, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240012	120	EUK	Invertebrates:2,Plants:2,Vertebrates:1	cd04641, CBS_pair_28, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can ...
CDD:240013	126	EUK	Invertebrates:1,Plants:4	cd04642, CBS_pair_29, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the ...
CDD:240014	116	PRK	Bacteria:19	cd04643, CBS_pair_30, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:100051	153	EUKprk	Bacteria:104,Invertebrates:6,Plants:5	cd04645, LbH_gamma_CA_like, Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active ...
CDD:100052	164	EUK	Invertebrates:10,Plants:1,Vertebrates:3	cd04646, LbH_Dynactin_6, Dynactin 6 (or subunit p27): Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through interaction with microtubules ...
CDD:100053	109	EUKprk	Bacteria:134,Environmental:1,Plants:4	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively while GAT specifically acetylates galactopyranosides. XAT catalyzes ...
CDD:100056	104	EUKprk	Bacteria:62,Plants:5	cd04651, LbH_G1P_AT_C, Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-limiting step in starch biosynthesis in plants and glycogen biosynthesis in bacteria. It is the enzymatic site for regulation of storage polysaccharide accumulation in plants and ...
CDD:100057	81	EUK	Invertebrates:5,Plants:10,Vertebrates:1	cd04652, LbH_eIF2B_gamma_C, eIF-2B gamma subunit, C-terminal Left-handed parallel beta-Helix (LbH) domain: eIF-2B is a eukaryotic translation initiator, a guanine nucleotide exchange factor (GEF) composed of five different subunits (alpha, beta, gamma, delta and epsilon). eIF2B is important for regenerating GTP-bound eIF2 during the initiation process. This event is obligatory for eIF2 to bind initiator methionyl-tRNA, forming the ternary ...
CDD:240015	426	EUK	Invertebrates:8,Plants:11,Vertebrates:2	cd04657, Piwi_ago-like, Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
CDD:240016	448	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd04658, Piwi_piwi-like_Euk, Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes. This domain is found in Piwi and closely related proteins, where it is believed to perform a crucial role in germline cells, via RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The mechanism in Piwi is ...
CDD:240017	404	PRK	Bacteria:28	cd04659, Piwi_piwi-like_ProArk, Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two ...
CDD:240018	73	EUK	Plants:8	cd04660, nsLTP_like, nsLTP_like: Non-specific lipid-transfer protein (nsLTP)-like subfamily; composed of predominantly uncharacterized proteins with similarity to nsLTPs, including Medicago truncatula MtN5, the root-specific Phaseolus vulgaris PVR3, Antirrhinum majus FIL1, and Lilium longiflorum LIM3. Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. The MtN5 gene is induced ...
CDD:240019	132	EUK	Invertebrates:5,Plants:1,Vertebrates:1	cd04661, MRP_L46, Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the Nudix hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the Nudix motif, a highly conserved 23-residue ...
CDD:240022	129	EUKprk	Bacteria:18,Plants:2	cd04664, Nudix_Hydrolase_7, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and ...
CDD:240023	118	PRK	Bacteria:12	cd04665, Nudix_Hydrolase_8, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240024	122	EUKprk	Bacteria:18,Invertebrates:3,Plants:7,Primates:1,Vertebrates:3	cd04666, Nudix_Hydrolase_9, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates ...
CDD:240025	112	PRK	Bacteria:9	cd04667, Nudix_Hydrolase_10, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240027	127	EUKprk	Bacteria:3,Invertebrates:3,Plants:2,Vertebrates:3	cd04670, Nudix_Hydrolase_12, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix ...
CDD:240029	123	EUKprk	Bacteria:23,Invertebrates:1	cd04672, Nudix_Hydrolase_14, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include ...
CDD:240030	122	PRK	Bacteria:24	cd04673, Nudix_Hydrolase_15, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240032	129	PRK	Bacteria:16	cd04676, Nudix_Hydrolase_17, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240033	132	PRK	Bacteria:19	cd04677, Nudix_Hydrolase_18, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240034	129	EUKprk	Bacteria:7,Invertebrates:1,Plants:7,Primates:1,Vertebrates:3	cd04678, Nudix_Hydrolase_19, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates ...
CDD:240036	120	PRK	Bacteria:13	cd04680, Nudix_Hydrolase_21, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240038	122	PRK	Bacteria:23	cd04682, Nudix_Hydrolase_23, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240039	120	PRK	Bacteria:8	cd04683, Nudix_Hydrolase_24, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240040	128	PRK	Bacteria:24	cd04684, Nudix_Hydrolase_25, Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = ...
CDD:240041	133	PRK	Bacteria:8	cd04685, Nudix_Hydrolase_26, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240042	131	PRK	Bacteria:7	cd04686, Nudix_Hydrolase_27, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240044	126	PRK	Bacteria:16,nodiv:1	cd04688, Nudix_Hydrolase_29, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and ...
CDD:240046	118	PRK	Bacteria:19,nodiv:1	cd04690, Nudix_Hydrolase_31, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and ...
CDD:240048	144	EUKprk	Bacteria:12,Plants:2	cd04692, Nudix_Hydrolase_33, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and ...
CDD:240049	127	PRK	Bacteria:11	cd04693, Nudix_Hydrolase_34, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:240054	129	PRK	Bacteria:10	cd04699, Nudix_Hydrolase_39, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively ...
CDD:271337	264	EUKprk	Bacteria:30,Invertebrates:5,Mammals:1,Plants:59,Vertebrates:3	cd04701, Asparaginase_2, Bacterial/fungal L-Asparaginase type 2.  L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta subunit. The threonine residue plays a central role in hydrolase activity. Some asparaginases can also hydrolyze ...
CDD:271338	289	EUKprk	Bacteria:2,Invertebrates:12,Mammals:1,Plants:3,Primates:2,Rodents:5,Vertebrates:12,nodiv:1	cd04702, ASRGL1_like, Metazoan L-Asparaginase type 2.  ASRGL1 and similar proteins constitute a subfamily of the L-Asparaginase type 2-like enzymes. The wider family includes Glycosylasparaginase, Taspase 1, and  L-Asparaginase type 2 enzymes. The proenzymes undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal ...
CDD:271339	243	PRK	Bacteria:17,Environmental:3	cd04703, Asparaginase_2_like_1, Uncharacterized subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family.  The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and  L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription ...
CDD:153093	97	miss	miss	cd04704, PLA2_bee_venom_like, PLA2_bee_venom_like: A sub-family of  Phospholipase A2, similar to bee venom PLA2. PLA2 is a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is ...
CDD:153095	117	miss	miss	cd04706, PLA2_plant, PLA2_plant: Plant-specific sub-family of  Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which ...
CDD:240060	164	EUK	Invertebrates:5,Primates:1,Vertebrates:3	cd04709, BAH_MTA, BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these ...
CDD:240061	135	EUK	Plants:8	cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
CDD:240063	130	EUK	Plants:11	cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X ...
CDD:240065	121	EUK	Invertebrates:2,Plants:3,Primates:1,Vertebrates:2	cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
CDD:240068	121	EUK	Invertebrates:7,Plants:3,Primates:1,Vertebrates:3	cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins ...
CDD:240070	128	EUK	Invertebrates:4,Primates:1,Vertebrates:3	cd04719, BAH_Orc1p_animal, BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1  is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in ...
CDD:240071	179	EUK	Plants:9	cd04720, BAH_Orc1p_Yeast, BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
CDD:240073	200	EUKprk	Bacteria:11,Plants:1	cd04722, TIM_phosphate_binding, TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.
CDD:240074	233	EUKprk	Bacteria:25,Environmental:1,Plants:6,nodiv:1	cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR ...
CDD:240075	242	EUKprk	Bacteria:119,Environmental:1,Plants:12	cd04724, Tryptophan_synthase_alpha, Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and ...
CDD:240076	216	EUKprk	Bacteria:120,Environmental:2,Invertebrates:10,Plants:10,Primates:1,Vertebrates:2	cd04725, OMP_decarboxylase_like, Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two domains:  the orotate phosphoribosyltransferase (OPRTase) domain that catalyzes the transfer of phosphoribosyl ...
CDD:240077	202	PRK	Bacteria:28,Environmental:2	cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for L-ascorbate utilization in some eubacteria. HPS catalyzes the formation of D-arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can ...
CDD:240078	283	EUKprk	Bacteria:19,Invertebrates:2,Plants:4	cd04727, pdxS, PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP,  present in some eubacteria, in archaea, fungi, plants, plasmodia, and some metazoa. Together with PdxT, PdxS forms the PLP synthase, a heteromeric glutamine amidotransferase (GATase), whereby PdxT produces ammonia from glutamine and PdxS combines ...
CDD:240079	248	EUKprk	Bacteria:35,Plants:4,nodiv:1	cd04728, ThiG, Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole ...
CDD:240080	219	PRK	Bacteria:22	cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.
CDD:240081	236	EUKprk	Bacteria:114,Invertebrates:1,Plants:19	cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer ...
CDD:240082	243	EUKprk	Bacteria:62,Environmental:1,Plants:4	cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion ...
CDD:240083	234	PRK	Bacteria:74	cd04732, HisA, HisA.  Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.
CDD:240084	338	EUKprk	Bacteria:21,Invertebrates:1,Plants:8	cd04733, OYE_like_2_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 2.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, ...
CDD:240085	343	PRK	Bacteria:17	cd04734, OYE_like_3_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate ...
CDD:240086	353	PRK	Bacteria:18	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate ...
CDD:240089	327	EUKprk	Bacteria:38,Environmental:1,Invertebrates:7,Plants:7,Primates:1,Vertebrates:3	cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and ...
CDD:240090	325	PRK	Bacteria:10,Environmental:1	cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like proteins.  DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers ...
CDD:240091	296	PRK	Bacteria:32	cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers ...
CDD:240092	294	EUKprk	Bacteria:2,Invertebrates:1,Plants:6	cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are ...
CDD:240093	418	PRK	Bacteria:17	cd04742, NPD_FabD, 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase  FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDPs are members of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative  electron acceptors. Most use FAD/FMN as a cofactor and ...
CDD:240095	361	PRK	Bacteria:11,Environmental:2	cd04747, OYE_like_5_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 5.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol ...
CDD:240096	87	EUK	Invertebrates:3,Primates:1,Vertebrates:4	cd04748, Commd, COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been ...
CDD:240098	166	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd04750, Commd2, COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
CDD:240099	95	EUK	Invertebrates:8,Plants:1,Primates:1,Vertebrates:2	cd04751, Commd3, COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
CDD:240106	186	EUK	Invertebrates:6,Primates:1,Vertebrates:3	cd04758, Commd10, COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
CDD:212498	244	EUK	Invertebrates:7,Mammals:1,Primates:1,Rodents:1,Vertebrates:5,nodiv:2	cd04759, Rib_hydrolase, ADP-ribosyl cyclase, also known as cyclic ADP-ribose hydrolase or CD38.  ADP-ribosyl cyclase (EC:3.2.2.5) synthesizes the second messenger cyclic-ADP ribose (cADPR), which in turn releases calcium from internal stores. Mammals possess two membrane proteins, CD38 and BST-1/CD157, which exhibit ADP-ribosyl cyclase activity, as well as intracellular soluble ADP-ribose cyclases. CD38 is ...
CDD:133389	49	PRK	Bacteria:11	cd04761, HTH_MerR-SF, Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily.  Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and ...
CDD:133390	49	PRK	Bacteria:24	cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins.  Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 ...
CDD:133392	67	PRK	Bacteria:8	cd04764, HTH_MlrA-like_sg1, Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators.  Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription ...
CDD:133393	99	PRK	Bacteria:27,Environmental:1	cd04765, HTH_MlrA-like_sg2, Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators.  Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the ...
CDD:133394	91	PRK	Bacteria:15	cd04766, HTH_HspR, Helix-Turn-Helix DNA binding domain of the HspR transcription regulator.  Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain  with other transcription regulators of the MerR ...
CDD:133396	96	PRK	Bacteria:4	cd04768, HTH_BmrR-like, Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators.  Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains ...
CDD:133397	116	PRK	Bacteria:9	cd04769, HTH_MerR2, Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators.  Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by ...
CDD:133398	123	PRK	Bacteria:32	cd04770, HTH_HMRTR, Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators.  Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper),  CadR (cadmium),  PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription ...
CDD:133399	99	PRK	Bacteria:6	cd04772, HTH_TioE_rpt1, First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE.  Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote ...
CDD:133400	108	PRK	Bacteria:4	cd04773, HTH_TioE_rpt2, Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE.  Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote ...
CDD:133403	118	PRK	Bacteria:26	cd04776, HTH_GnyR, Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR.  Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between ...
CDD:133405	219	PRK	Bacteria:9	cd04778, HTH_MerR-like_sg2, Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily.  Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress ...
CDD:133407	95	PRK	Bacteria:11	cd04780, HTH_MerR-like_sg5, Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily.  Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of ...
CDD:133408	120	PRK	Bacteria:12	cd04781, HTH_MerR-like_sg6, Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily.  Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR ...
CDD:133409	97	PRK	Bacteria:10	cd04782, HTH_BltR, Helix-Turn-Helix DNA binding domain of the BltR transcription regulator.  Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory ...
CDD:133410	126	PRK	Bacteria:20,nodiv:1	cd04783, HTH_MerR1, Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator.  Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH ...
CDD:133411	127	PRK	Bacteria:31	cd04784, HTH_CadR-PbrR, Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators.  Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their ...
CDD:133412	126	PRK	Bacteria:24	cd04785, HTH_CadR-PbrR-like, Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators.  Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted ...
CDD:133414	133	PRK	Bacteria:11	cd04787, HTH_HMRTR_unk, Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators.  Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote ...
CDD:271199	327	PRK	Bacteria:75,Environmental:1	cd04791, LanC_SerThrkinase, Lanthionine synthetase C-like domain associated with serine/threonine kinases.  Some members of this subgroup lack the zinc binding site and the active site residues, and therefore are most likely inactive. The function of this domain is unknown.
CDD:271200	836	PRK	Bacteria:59,Environmental:1	cd04792, LanM-like, Cyclases involved in the biosynthesis of class II lantibiotics, and similar proteins.  LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be ...
CDD:271201	377	PRK	Bacteria:45	cd04793, LanC, Cyclases involved in the biosynthesis of lantibiotics.  LanC is the cyclase enzyme of the lanthionine synthetase. Lanthinoine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as precursor peptides and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans) in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These ...
CDD:271202	349	EUKprk	Bacteria:10,Invertebrates:34,Mammals:1,Plants:45,Primates:1,Vertebrates:4,nodiv:1	cd04794, euk_LANCL, Eukaryotic Lanthionine synthetase C-like protein.  This family contains the lanthionine synthetase C-like proteins 1 and 2 which are related to the bacterial lanthionine synthetase components C (LanC). LANCL1 and LANCL2 (testes-specific adriamycin sensitivity protein) were thought to be peptide-modifying enzyme components in eukaryotic cells. Both proteins are produced in ...
CDD:240112	87	EUKprk	Bacteria:17,Rodents:1	cd04795, SIS, SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
CDD:240113	111	PRK	Bacteria:59,nodiv:1	cd04800, CBS_pair_CAP-ED_DUF294_PBI_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain.  Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme ...
CDD:240114	114	PRK	Bacteria:12	cd04801, CBS_pair_M50_like, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50.  CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface ...
CDD:240116	122	PRK	Bacteria:14	cd04803, CBS_pair_15, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core ...
CDD:240117	117	EUK	Plants:8	cd04813, PA_1, PA_1: Protease-associated (PA) domain subgroup 1. A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the ...
CDD:240119	134	EUKprk	Bacteria:10,Invertebrates:2,Primates:1,Vertebrates:1	cd04815, PA_M28_2, PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted ...
CDD:240120	122	EUKprk	Bacteria:4,Plants:3	cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH).This group contains various PA domain-containing proteins similar SaNapH.  Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to ...
CDD:240122	118	PRK	Bacteria:16	cd04818, PA_subtilisin_1, PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the ...
CDD:240123	127	PRK	Bacteria:4	cd04819, PA_2, PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the ...
CDD:240124	137	PRK	Bacteria:14	cd04820, PA_M28_1_1, PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a ...
CDD:240125	157	PRK	Bacteria:19	cd04821, PA_M28_1_2, PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a ...
CDD:240126	151	PRK	Bacteria:5	cd04822, PA_M28_1_3, PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a ...
CDD:240127	320	EUKprk	Bacteria:11,Environmental:1,Invertebrates:1,Plants:7	cd04823, ALAD_PBGS_aspartate_rich, Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between ...
CDD:173791	293	EUKprk	Bacteria:13,Invertebrates:5,Plants:6	cd04842, Peptidases_S8_Kp43_protease, Peptidase S8 family domain in Kp43 proteases.  Kp43 proteases are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Kp43 is topologically similar to kexin and furin both of which are proprotein convertases, but ...
CDD:173792	277	EUKprk	Bacteria:14,Plants:2	cd04843, Peptidases_S8_11, Peptidase S8 family domain, uncharacterized subfamily 11.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to ...
CDD:173793	291	EUKprk	Bacteria:76,Plants:1,nodiv:1	cd04847, Peptidases_S8_Subtilisin_like_2, Peptidase S8 family domain in Subtilisin-like proteins.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been ...
CDD:173794	267	PRK	Bacteria:38	cd04848, Peptidases_S8_Autotransporter_serine_protease_like, Peptidase S8 family domain in Autotransporter serine proteases.  Autotransporter serine proteases belong to Peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution).  Autotransporters are a superfamily of ...
CDD:173795	307	EUKprk	Bacteria:4,Plants:9	cd04852, Peptidases_S8_3, Peptidase S8 family domain, uncharacterized subfamily 3.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ...
CDD:173796	412	EUKprk	Bacteria:1,Invertebrates:8,Plants:5,Primates:1,Vertebrates:3	cd04857, Peptidases_S8_Tripeptidyl_Aminopeptidase_II, Peptidase S8 family domain in Tripeptidyl aminopeptidases_II.  Tripeptidyl aminopeptidases II are member of the peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent ...
CDD:240129	152	miss	miss	cd04859, Prim_Pol, Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase ...
CDD:240130	232	miss	miss	cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit ...
CDD:240131	227	miss	miss	cd04861, LigD_Pol_like, LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a ...
CDD:240132	227	miss	miss	cd04862, PaeLigD_Pol_like, PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a ...
CDD:240135	228	miss	miss	cd04865, LigD_Pol_like_2, LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to ...
CDD:133440	83	EUKprk	Bacteria:1,Invertebrates:5,Plants:3,Primates:1,Vertebrates:2	cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There ...
CDD:153140	60	miss	miss	cd04868, ACT_AK-like, ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase).  This CD includes each of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). Typically, AK consists of two ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region ...
CDD:153141	81	miss	miss	cd04869, ACT_GcvR_2, ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains.  This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and ...
CDD:153142	75	miss	miss	cd04870, ACT_PSP_1, CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB).  The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine ...
CDD:153143	84	miss	miss	cd04871, ACT_PSP_2, ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB).  The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine ...
CDD:153144	88	miss	miss	cd04872, ACT_1ZPV, ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein.  This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
CDD:153145	70	miss	miss	cd04873, ACT_UUR-ACR-like, ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD.  This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. ...
CDD:153146	72	miss	miss	cd04874, ACT_Af1403, N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains.  This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
CDD:153147	74	miss	miss	cd04875, ACT_F4HF-DF, N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase).  This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase  generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step ...
CDD:153148	71	miss	miss	cd04876, ACT_RelA-SpoT, ACT  domain found C-terminal of the RelA/SpoT domains.  ACT_RelA-SpoT: the ACT  domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and ...
CDD:153149	74	miss	miss	cd04877, ACT_TyrR, N-terminal ACT domain of the TyrR protein.  ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its ...
CDD:153150	72	miss	miss	cd04878, ACT_AHAS, N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS).  ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment ...
CDD:153151	71	miss	miss	cd04879, ACT_3PGDH-like, ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH).  ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and ...
CDD:153152	75	miss	miss	cd04880, ACT_AAAH-PDT-like, ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH).  ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced ...
CDD:153153	79	miss	miss	cd04881, ACT_HSDH-Hom, ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains.  The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from ...
CDD:153154	65	miss	miss	cd04882, ACT_Bt0572_2, C-terminal ACT domain of a novel protein composed of just two ACT domains.  Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
CDD:153155	72	miss	miss	cd04883, ACT_AcuB, C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB.  This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, ...
CDD:153157	68	miss	miss	cd04885, ACT_ThrD-I, Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase).  This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I ...
CDD:153158	73	miss	miss	cd04886, ACT_ThrD-II-like, C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains.  This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and ...
CDD:153159	74	miss	miss	cd04887, ACT_MalLac-Enz, ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains.  The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme  (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to ...
CDD:153160	76	miss	miss	cd04888, ACT_PheB-BS, C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains.  This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase ...
CDD:153161	56	miss	miss	cd04889, ACT_PDH-BS-like, C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate.  Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and ...
CDD:153162	62	miss	miss	cd04890, ACT_AK-like_1, ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase).  This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, ...
CDD:153163	61	miss	miss	cd04891, ACT_AK-LysC-DapG-like_1, ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins.  This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the first and third, of four, ACT domains present in cyanobacteria AK. Also included are the N-terminal of the ...
CDD:153164	65	miss	miss	cd04892, ACT_AK-like_2, ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase).  This CD includes the second of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). The exception in this group, is the inclusion of the first ACT domain of the bifunctional  aspartokinase - homoserine dehydrogenase-like enzyme group (ACT_AKi-HSDH-ThrA-like_1) which includes the  ...
CDD:153165	77	miss	miss	cd04893, ACT_GcvR_1, ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains.  This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and ...
CDD:153171	70	miss	miss	cd04899, ACT_ACR-UUR-like_2, C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains.  This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, ...
CDD:153172	73	miss	miss	cd04900, ACT_UUR-like_1, ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains.  This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric ...
CDD:153173	69	miss	miss	cd04901, ACT_3PGDH, C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria.  The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, ...
CDD:153174	73	miss	miss	cd04902, ACT_3PGDH-xct, C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH).  The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step ...
CDD:153175	71	miss	miss	cd04903, ACT_LSD, C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit.  The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate ...
CDD:153176	74	miss	miss	cd04904, ACT_AAAH, ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH).  ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom ...
CDD:153177	80	miss	miss	cd04905, ACT_CM-PDT, C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme.  The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the ...
CDD:153178	85	miss	miss	cd04906, ACT_ThrD-I_1, First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase).  This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or ...
CDD:153179	81	miss	miss	cd04907, ACT_ThrD-I_2, Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase).  This CD includes the second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate ...
CDD:153180	66	miss	miss	cd04908, ACT_Bt0572_1, N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains.  Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
CDD:153181	69	miss	miss	cd04909, ACT_PDH-BS, C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH).  The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. ...
CDD:153182	71	miss	miss	cd04910, ACT_AK-Ectoine_1, ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway.  This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other ...
CDD:153183	76	miss	miss	cd04911, ACT_AKiii-YclM-BS_1, ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII.  This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic ...
CDD:153184	75	miss	miss	cd04912, ACT_AKiii-LysC-EC-like_1, ACT domains located C-terminal to the catalytic domain of  the lysine-sensitive aspartokinase isoenzyme AKIII.  This CD includes the first of two ACT domains located C-terminal to the catalytic domain of  the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the ...
CDD:153185	75	miss	miss	cd04913, ACT_AKii-LysC-BS-like_1, ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins.  This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate ...
CDD:153186	67	miss	miss	cd04914, ACT_AKi-DapG-BS_1, ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI.  This CD includes the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria, bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by ...
CDD:153187	66	miss	miss	cd04915, ACT_AK-Ectoine_2, ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway.  This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other ...
CDD:153188	66	miss	miss	cd04916, ACT_AKiii-YclM-BS_2, ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII.  This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate ...
CDD:153189	64	miss	miss	cd04917, ACT_AKiii-LysC-EC_2, ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII.  This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate ...
CDD:153193	80	miss	miss	cd04921, ACT_AKi-HSDH-ThrA-like_1, ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH).  This CD includes the first of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first ...
CDD:153195	63	miss	miss	cd04923, ACT_AK-LysC-DapG-like_2, ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains.  This CD includes the C-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the second and fourth, of four, ACT domains present in cyanobacteria AK. ...
CDD:153202	115	miss	miss	cd04930, ACT_TH, ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH).  ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by ...
CDD:153208	63	miss	miss	cd04936, ACT_AKii-LysC-BS-like_2, ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains.  This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the ...
CDD:133441	76	EUK	Invertebrates:1,Plants:4	cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of Obg-like GTPases such as those present in DRG (developmentally regulated GTP-binding protein), and GTP-binding proteins Ygr210 and YchF. The TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its ...
CDD:99997	407	PRK	Bacteria:10	cd04946, GT1_AmsK_like, This family is most closely related to the GT1 family of glycosyltransferases. AmsK is involved in the biosynthesis of amylovoran, which functions as a virulence factor. It functions as a glycosyl transferase which transfers galactose from UDP-galactose to a lipid-linked amylovoran-subunit precursor.  The members of this family are found mainly in bacteria and Archaea.
CDD:99998	372	PRK	Bacteria:27	cd04949, GT1_gtfA_like, This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding.  In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a ...
CDD:99999	373	PRK	Bacteria:46	cd04950, GT1_like_1, Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked ...
CDD:100000	360	PRK	Bacteria:10	cd04951, GT1_WbdM_like, This family is most closely related to the GT1 family of glycosyltransferases and is named after WbdM in Escherichia coli. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely ...
CDD:100001	363	PRK	Bacteria:28	cd04955, GT1_like_6, This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family ...
CDD:100002	371	EUKprk	Bacteria:6,Invertebrates:1	cd04962, GT1_like_5, This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined ...
CDD:143172	81	miss	miss	cd04971, Ig_TrKABC_d5, Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC.  TrkABC_d5: the fifth domain of Trk receptors TrkA, TrkB and TrkC, this is an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share ...
CDD:143173	90	miss	miss	cd04972, Ig_TrkABC_d4, Fourth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC.  TrkABC_d4: the fourth domain of Trk receptors TrkA, TrkB and TrkC, this is an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share ...
CDD:143175	90	miss	miss	cd04974, Ig3_FGFR, Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR).  Ig3_FGFR: third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a ...
CDD:143176	101	miss	miss	cd04975, Ig4_SCFR_like, Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins.  Ig4_SCFR_like; fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). In addition to SCFR this group also includes the fourth Ig domain of platelet-derived growth factor receptors (PDGFR), alpha and beta, the fourth Ig domain of macrophage colony stimulating factor (M-CSF), and the Ig domain of the receptor tyrosine kinase KIT. ...
CDD:143179	76	miss	miss	cd04978, Ig4_L1-NrCAM_like, Fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related).  Ig4_L1-NrCAM_like: fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related). These proteins belong to the L1 subfamily of cell adhesion molecules (CAMs) and are comprised of an extracellular region having six Ig-like domains and five fibronectin type III ...
CDD:143180	89	miss	miss	cd04979, Ig_Semaphorin_C, Immunoglobulin (Ig)-like domain of semaphorin.  Ig_Semaphorin_C; Immunoglobulin (Ig)-like domain in semaphorins. Semaphorins are transmembrane protein that have important roles in a variety of tissues. Functionally, semaphorins were initially characterized for their importance in the development of the nervous system and in axonal guidance. Later they have been found to be important for the formation and functioning of the cardiovascular, ...
CDD:143182	117	miss	miss	cd04981, IgV_H, Immunoglobulin (Ig) heavy chain (H), variable (V) domain.  IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant ...
CDD:143183	116	miss	miss	cd04982, IgV_TCR_gamma, Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain.  IgV_TCR_gamma: immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains.  Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs but a small ...
CDD:143184	109	EUK	Primates:1	cd04983, IgV_TCR_alpha_like, Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins.  IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha ...
CDD:143186	95	miss	miss	cd04985, IgC_CH1, CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin.  IgC_CH1: The first immunoglobulin constant domain (IgC), of immunoglobulin (Ig) heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable ...
CDD:240138	179	EUKprk	Bacteria:36,Plants:2	cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
CDD:240139	177	PRK	Bacteria:110,Environmental:1	cd05006, SIS_GmhA, Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
CDD:240140	257	EUKprk	Bacteria:22,Plants:2	cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
CDD:240141	126	EUKprk	Bacteria:120,Invertebrates:4,Plants:6,Vertebrates:2	cd05008, SIS_GlmS_GlmD_1, SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into ...
CDD:240142	153	EUKprk	Bacteria:29,Invertebrates:3,Plants:1,Vertebrates:1	cd05009, SIS_GlmS_GlmD_2, SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into ...
CDD:240143	151	PRK	Bacteria:9	cd05010, SIS_AgaS_like, AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases (GlmS) which catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source.
CDD:240144	139	PRK	Bacteria:173,nodiv:1	cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
CDD:240145	128	EUKprk	Bacteria:23,Invertebrates:1,Plants:8	cd05014, SIS_Kpsf, KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
CDD:240146	158	EUKprk	Bacteria:61,Invertebrates:13,Mammals:2,Plants:9,Primates:1,Vertebrates:3	cd05015, SIS_PGI_1, Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), ...
CDD:240147	164	EUKprk	Bacteria:13,Invertebrates:1,Mammals:1,Plants:2,Primates:2,Vertebrates:2	cd05016, SIS_PGI_2, Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), ...
CDD:240148	119	PRK	Bacteria:10	cd05017, SIS_PGI_PMI_1, The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
CDD:176853	144	PRK	Bacteria:44	cd05018, CoxG, Carbon monoxide dehydrogenase subunit G (CoxG).  CoxG has been shown, in Oligotropha carboxidovorans, to anchor the carbon monoxide (CO) dehydrogenase to the cytoplasmic membrane. The gene encoding CoxG is part of the Cox cluster (coxBCMSLDEFGHIK) located on a low-copy-number, circular, megaplasmid pHCG3. This cluster includes genes encoding subunits of CO dehydrogenase and several accessory components involved in the utilization of CO. This family ...
CDD:240149	89	miss	miss	cd05022, S-100A13, S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast ...
CDD:240156	88	miss	miss	cd05030, calgranulins, Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as ...
CDD:173625	277	EUK	Invertebrates:7,Primates:1	cd05032, PTKc_InsR_like, Catalytic domain of Insulin Receptor-like Protein Tyrosine Kinases.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The InsR subfamily is composed of InsR, Insulin-like Growth Factor-1 Receptor (IGF-1R), and similar proteins. InsR and IGF-1R are receptor PTKs (RTKs) composed of two alphabeta heterodimers. Binding of the ligand (insulin, IGF-1, or IGF-2) to ...
CDD:270630	248	EUK	Invertebrates:9,Primates:1,Vertebrates:1,nodiv:1	cd05034, PTKc_Src_like, Catalytic domain of Src kinase-like Protein Tyrosine Kinases.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, and Yes. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a ...
CDD:270636	258	EUK	Invertebrates:8,Primates:1,Vertebrates:4	cd05040, PTKc_Ack_like, Catalytic domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily includes Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. They are cytoplasmic (or nonreceptor) PTKs containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB ...
CDD:270644	297	EUK	Invertebrates:11,Vertebrates:2	cd05051, PTKc_DDR, Catalytic domain of the Protein Tyrosine Kinases, Discoidin Domain Receptors.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The DDR subfamily consists of homologs of mammalian DDR1, DDR2, and similar proteins. They are receptor PTKs (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an ...
CDD:270687	258	EUK	Invertebrates:19,Plants:15,Primates:1	cd05117, STKc_CAMK, The catalytic domain of CAMK family Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. There are several types of CaMKs including CaMKI, CaMKII, and CaMKIV. CaMKI proteins are monomeric and they play pivotal roles in the ...
CDD:270688	249	EUK	Invertebrates:2,Plants:4,Primates:1,Rodents:2,Vertebrates:1	cd05118, STKc_CMGC, Catalytic domain of CMGC family Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The CMGC family consists of Cyclin-Dependent protein Kinases (CDKs), Mitogen-activated protein kinases (MAPKs) such as Extracellular signal-regulated kinase (ERKs), c-Jun N-terminal kinases (JNKs), and p38, and other ...
CDD:270690	158	EUKprk	Bacteria:11,Plants:5,Primates:1,nodiv:1	cd05120, APH_ChoK_like, Aminoglycoside 3'-phosphotransferase and Choline Kinase family.  This family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to ...
CDD:270691	247	EUKprk	Bacteria:173,Environmental:2,Invertebrates:4,Plants:22,Primates:1,Viruses:1	cd05121, ABC1_ADCK3-like, Activator of bc1 complex (ABC1) kinases (also called aarF domain containing kinase 3) and similar proteins.  This family is composed of the atypical yeast protein kinase Abc1p, its human homolog ADCK3 (also called CABC1), and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in ...
CDD:270692	254	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:1	cd05122, PKc_STE, Catalytic domain of STE family Protein Kinases.  PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. This family is composed of STKs, and some dual-specificity PKs that phosphorylate both threonine and tyrosine residues of target proteins. Most members are kinases involved in mitogen-activated protein kinase (MAPK) signaling ...
CDD:270693	250	EUK	Invertebrates:15,Mammals:1,Plants:13,Primates:1,Vertebrates:1	cd05123, STKc_AGC, Catalytic domain of AGC family Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. AGC kinases regulate many cellular processes including division, growth, survival, metabolism, motility, and differentiation. Many are implicated in the development of various human diseases. Members of this family include ...
CDD:270694	240	EUK	Invertebrates:10,Plants:3	cd05124, AFK, Catalytic domain of Actin-Fragmin Kinase.  AFK is found in slime molds, ciliates, and flowering plants. It catalyzes the transfer of the gamma-phosphoryl group from ATP specifically to threonine residues in the actin-fragmin complex. The phosphorylation sites are located at a minor contact site for DNase I and at an actin-actin contact site. Fragmin is an actin-binding protein that functions as a regulator of the microfilament system. It ...
CDD:240161	114	EUK	Invertebrates:8,Plants:10,Primates:1,Vertebrates:2	cd05125, Mth938_2P1-like, Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
CDD:240162	117	EUKprk	Bacteria:8,Invertebrates:2,Primates:1,Vertebrates:2	cd05126, Mth938, Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
CDD:213329	331	EUK	Invertebrates:10,Mammals:1,Plants:9,Primates:1	cd05127, RasGAP_IQGAP_like, Ras-GTPase Activating Domain of IQ motif containing GTPase activating proteins.  This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% identity. ...
CDD:213330	269	EUK	Invertebrates:12,Primates:1,Vertebrates:1	cd05128, RasGAP_GAP1_like, Ras-GTPase Activating Domain of GAP1 and similar proteins.  The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP ...
CDD:213331	365	EUK	Invertebrates:10,Rodents:1,Vertebrates:2,nodiv:1	cd05129, RasGAP_RAP6, Ras-GTPase Activating Domain of Rab5-activating protein 6.  Rab5-activating protein 6 (RAP6) is an endosomal protein with a role in the regulation of receptor-mediated endocytosis. RAP6 contains a Vps9 domain, which is involved in the activation of Rab5, and a Ras GAP domain (RGD). Rab5 is a small GTPase required for the control of the endocytic route, and its activity is regulated by guanine nucleotide ...
CDD:213332	332	EUK	Invertebrates:9,Mammals:1,Vertebrates:4,nodiv:1	cd05130, RasGAP_Neurofibromin, Ras-GTPase Activating Domain of neurofibromin.  Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low ...
CDD:213334	352	EUK	Invertebrates:5,Plants:7,nodiv:1	cd05132, RasGAP_GAPA, Ras-GTPase Activating Domain of GAPA.  GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests ...
CDD:213338	324	EUK	Invertebrates:12,Primates:1,Vertebrates:6	cd05136, RasGAP_DAB2IP, Ras-GTPase Activating Domain of DAB2IP and similar proteins.  The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism ...
CDD:213339	356	EUK	Plants:45	cd05137, RasGAP_CLA2_BUD2, Ras-GTPase Activating Domain of CLA2/BUD2.  CLA2/BUD2 functions as a GTPase-activating protein (GAP) for BUD1/RSR1 and is necessary for proper bud-site selection in yeast. BUD2 has sequence similarity to the catalytic domain of RasGAPs, and stimulates the hydrolysis of BUD1-GTP to BUD1-GDP. Elimination of Bud2p activity by mutation causes a random budding pattern with no growth defect. Overproduction of Bud2p also alters the budding pattern.
CDD:240163	86	PRK	Bacteria:6	cd05140, Barstar_AU1054-like, Barstar_AU1054-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor AU1054 found in Burkholderia cenocepacia. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially ...
CDD:240164	81	PRK	Bacteria:21	cd05141, Barstar_evA4336-like, Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal ...
CDD:240165	87	PRK	Bacteria:11	cd05142, Barstar, Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell.  Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
CDD:270695	183	EUKprk	Bacteria:15,Invertebrates:23,Plants:17,Primates:1,Vertebrates:3	cd05144, RIO2_C, C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase.  RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for ...
CDD:270696	189	EUKprk	Bacteria:22,Environmental:1,Invertebrates:2,Primates:1	cd05145, RIO1_like, Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar proteins.  RIO1 is present in archaea, bacteria and eukaryotes. In addition, RIO3 is present in multicellular eukaryotes. Both RIO1 and RIO3 are associated with precursors of 40S ribosomal subunits, just like RIO2. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle ...
CDD:270698	190	EUK	Invertebrates:22,Plants:12,Vertebrates:3	cd05147, RIO1_euk, Catalytic domain of the atypical protein serine kinase, Eukaryotic RIO1 kinase.  RIO1 is present in archaea, bacteria and eukaryotes. This subfamily is composed of RIO1 proteins from eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and chromosome maintenance. It is associated with precursors of 40S ribosomal subunits, just like RIO2. Although depletion ...
CDD:270699	244	EUKprk	Bacteria:65,Environmental:1,Invertebrates:1,Rodents:1,Synthetic:1	cd05150, APH, Aminoglycoside 3'-phosphotransferase.  APH catalyzes the transfer of the gamma-phosphoryl group from ATP to aminoglycoside antibiotics such as kanamycin, streptomycin, neomycin, and gentamicin, among others. The aminoglycoside antibiotics target the 30S ribosome and promote miscoding, leading to the production of defective proteins which insert into the bacterial membrane, resulting in membrane ...
CDD:270700	152	EUKprk	Bacteria:82,Environmental:5,Invertebrates:1	cd05151, ChoK-like, Choline Kinase and similar proteins.  This subfamily is composed of bacterial and eukaryotic choline kinases, as well as eukaryotic ethanolamine kinase. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC), and sphingomyelin (SM). ...
CDD:270701	276	PRK	Bacteria:35,Environmental:1	cd05152, MPH2', Macrolide 2'-Phosphotransferase.  MPH2' catalyzes the transfer of the gamma-phosphoryl group from ATP to the 2'-hydroxyl of macrolide antibiotics such as erythromycin, clarithromycin, and azithromycin, among others. Macrolides penetrate the bacterial cell and bind to ribosomes, where it interrupts protein elongation, leading ultimately to the demise of the bacterium. Phosphorylation of macrolides leads to their inactivation. Based on ...
CDD:270702	300	EUKprk	Bacteria:70,Environmental:1,Invertebrates:1	cd05153, HomoserineK_II, Type II Homoserine Kinase.  This subfamily is composed of unusual homoserine kinases, from a subset of bacteria, which have a Protein Kinase fold. These proteins do not bear any similarity to the GHMP family homoserine kinases present in most bacteria and eukaryotes. Homoserine kinase catalyzes the transfer of the gamma-phosphoryl group from ATP to L-homoserine producing L-homoserine phosphate, an ...
CDD:270703	254	EUKprk	Bacteria:144,Invertebrates:12,Plants:25,Primates:1,Vertebrates:4	cd05154, ACAD10_11_N-like, N-terminal domain of Acyl-CoA dehydrogenase (ACAD) 10 and 11, and similar proteins.  This subfamily is composed of the N-terminal domains of vertebrate ACAD10 and ACAD11, and similar uncharacterized bacterial and eukaryotic proteins. ACADs are a family of flavoproteins that are involved in the beta-oxidation of fatty acyl-CoA derivatives. ACAD deficiency can cause metabolic disorders ...
CDD:270704	234	PRK	Bacteria:48,Environmental:1	cd05155, APH_ChoK_like_1, Uncharacterized bacterial proteins with similarity to Aminoglycoside 3'-phosphotransferase and Choline kinase.  This subfamily is composed of uncharacterized bacterial proteins with similarity to APH and ChoK. Other APH/ChoK-like proteins include ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA ...
CDD:270705	326	EUK	Invertebrates:15,Primates:1,Vertebrates:3	cd05156, ChoK_euk, Euykaryotic Choline Kinase.  ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC) and sphingomyelin (SM). Although choline is the preferred substrate, ChoK also shows substantial activity towards ethanolamine and its N-methylated ...
CDD:270706	307	EUK	Invertebrates:27,Plants:41,Rodents:1,Vertebrates:2	cd05157, ETNK_euk, Euykaryotic Ethanolamine kinase.  ETNK catalyzes the transfer of the gamma-phosphoryl group from CTP to ethanolamine (Etn), the first step in the CDP-Etn pathway for the formation of the major phospholipid, phosphatidylethanolamine (PtdEtn). Unlike ChoK, ETNK shows specific activity for its substrate, and displays negligible activity towards N-methylated derivatives of Etn. The Drosophila ETNK is implicated ...
CDD:176646	199	EUKprk	Bacteria:8,Invertebrates:1,Primates:1,Rodents:1,Vertebrates:1	cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclease domain of family-B DNA polymerases.  The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA ...
CDD:99894	87	EUK	Invertebrates:1,Plants:4,Primates:1,Rodents:1	cd05162, PWWP, The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain ...
CDD:270707	252	EUK	Invertebrates:10,Plants:40,Primates:1,Vertebrates:3	cd05163, PIKK_TRRAP, Pseudokinase domain of TRansformation/tRanscription domain-Associated Protein.  TRRAP belongs to the the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. It contains a FATC (FRAP, ATM and TRRAP, C-terminal) domain and has a large molecular weight. Unlike most PIKK proteins, however, it contains an inactive PI3K-like pseudokinase domain, which lacks the conserved residues necessary for ...
CDD:270708	222	EUK	Invertebrates:6,Primates:1,Rodents:1,Vertebrates:1	cd05164, PIKKc, Catalytic domain of Phosphoinositide 3-kinase-related protein kinases.  PIKK subfamily members include ATM (Ataxia telangiectasia mutated), ATR (Ataxia telangiectasia and Rad3-related), TOR (Target of rapamycin), SMG-1 (Suppressor of morphogenetic effect on genitalia-1), and DNA-PK (DNA-dependent protein kinase). PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their ...
CDD:270709	363	EUK	Invertebrates:12,Primates:1,Rodents:1	cd05165, PI3Kc_I, Catalytic domain of Class I Phosphoinositide 3-kinase.  PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. In vitro, they can also phosphorylate the substrates PtdIns and PtdIns(4)P. Class I ...
CDD:270710	352	EUK	Invertebrates:10,Primates:1,Vertebrates:1	cd05166, PI3Kc_II, Catalytic domain of Class II Phosphoinositide 3-kinase.  PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They ...
CDD:270711	307	EUK	Invertebrates:18,Plants:7,Primates:1,Vertebrates:2	cd05167, PI4Kc_III_alpha, Catalytic domain of Type III Phosphoinositide 4-kinase alpha.  PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two isoforms of type III PI4K, alpha and beta, ...
CDD:270712	292	EUK	Invertebrates:27,Plants:14,Vertebrates:2	cd05168, PI4Kc_III_beta, Catalytic domain of Type III Phosphoinositide 4-kinase beta.  PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two isoforms of type III PI4K, alpha and beta, exist in ...
CDD:270713	279	EUK	Invertebrates:24,Plants:16,Primates:1,Vertebrates:1	cd05169, PIKKc_TOR, Catalytic domain of Target of Rapamycin.  TOR contains a rapamycin binding domain, a catalytic domain, and a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. It is also called FRAP (FK506 binding protein 12-rapamycin associated protein). TOR is a central component of the eukaryotic growth regulatory network. It controls the expression of many genes transcribed by all three RNA polymerases. ...
CDD:270714	304	EUK	Invertebrates:13,Plants:6,Vertebrates:2	cd05170, PIKKc_SMG1, Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1.  SMG-1 plays a critical role in the mRNA surveillance mechanism known as non-sense mediated mRNA decay (NMD). NMD protects the cells from the accumulation of aberrant mRNAs with premature termination codons (PTCs) generated by genome mutations and by errors during transcription and splicing. SMG-1 phosphorylates Upf1, another central component of ...
CDD:270715	282	EUK	Invertebrates:23,Plants:26,Primates:1,Vertebrates:1	cd05171, PIKKc_ATM, Catalytic domain of Ataxia Telangiectasia Mutated.  ATM is critical in the response to DNA double strand breaks (DSBs) caused by radiation. It is activated at the site of a DSB and phosphorylates key substrates that trigger pathways that regulate DNA repair and cell cycle checkpoints at the G1/S, S phase, and G2/M transition. Patients with the human genetic disorder Ataxia telangiectasia (A-T), caused by ...
CDD:270716	235	EUK	Invertebrates:16,Plants:9,Vertebrates:1	cd05172, PIKKc_DNA-PK, Catalytic domain of DNA-dependent protein kinase.  DNA-PK is comprised of a regulatory subunit, containing the Ku70/80 subunit, and a catalytic subunit, which contains a NUC194 domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. It is part of a multi-component system involved in non-homologous end joining (NHEJ), a process of repairing double ...
CDD:176178	271	EUKprk	Bacteria:123,Environmental:2,Invertebrates:3,Mammals:2,Plants:20,Primates:1,Rodents:2,Vertebrates:1	cd05188, MDR, Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I ...
CDD:133449	86	EUKprk	Bacteria:5,Invertebrates:1,Plants:1,Primates:1	cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino acid dehydrogenase-like proteins.  Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate ...
CDD:176179	293	EUKprk	Bacteria:68,Environmental:3,Invertebrates:18,Mammals:1,Plants:42,Primates:1,Vertebrates:5	cd05195, enoyl_red, enoyl reductase of polyketide synthase.  Putative enoyl reductase of polyketide synthase. Polyketide synthases produce polyketides in step by step mechanism that is similar to fatty acid synthesis. Enoyl reductase reduces a double to single bond. Erythromycin is one example of a polyketide generated by 3 complex enzymes (megasynthases). 2-enoyl thioester reductase ...
CDD:240622	302	EUKprk	Bacteria:29,Plants:10,Primates:1,Rodents:1	cd05198, formate_dh_like, Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family.  Formate dehydrogenase, D-specific 2-hydroxy acid dehydrogenase, Phosphoglycerate Dehydrogenase, Lactate dehydrogenase, Thermostable Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate reductase, among others, share a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ ...
CDD:240623	319	EUKprk	Bacteria:19,Plants:2	cd05199, SDH_like, Saccharopine Dehydrogenase like proteins.  Saccharopine Dehydrogenase (SDH) and related proteins, including bifunctional lysine ketoglutarate reductase/SDH enzymes and N(5)-(carboxyethyl)ornithine synthases. SDH catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to alpha-ketoglutarate and lysine, in the alpha-aminoadipate pathway of L-lysine biosynthesis. SDH is structurally related to ...
CDD:133452	311	EUKprk	Bacteria:15,Environmental:1,Plants:1	cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of glutamyl-tRNA reductase.  Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In ...
CDD:187537	176	EUKprk	Bacteria:7,Plants:3,Primates:1	cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs.  Extended or atypical short-chain dehydrogenases/reductases (SDRs, aka tyrosine-dependent oxidoreductases) are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection ...
CDD:187538	301	EUKprk	Bacteria:5,Invertebrates:6,Plants:12	cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs.  This subgroup contains aldehyde reductase of the extended SDR-type and related proteins. Aldehyde reductase I (aka carbonyl reductase) is an NADP-binding SDR; it has an NADP-binding motif consensus that is slightly different from the canonical SDR form and lacks the Asn of the extended SDR active site tetrad. Aldehyde reductase I catalyzes the NADP-dependent  reduction of ethyl ...
CDD:187539	318	EUKprk	Bacteria:16,Plants:1	cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs.  This subgroup contains proteins of unknown function related to aldehyde reductase and flavonoid reductase of the extended SDR-type. Aldehyde reductase I (aka carbonyl reductase) is an NADP-binding SDR; it has an NADP-binding motif consensus that is slightly different from the canonical SDR form and lacks the Asn of ...
CDD:187540	302	PRK	Bacteria:10	cd05229, SDR_a3, atypical (a) SDRs, subgroup 3.  These atypical SDR family members of unknown function have a glycine-rich NAD(P)-binding motif consensus that is very similar to the extended SDRs, GXXGXXG.  Generally, this group has poor conservation of the active site tetrad, However, individual sequences do contain matches to the YXXXK active site motif, and generally Tyr or Asn in place of the upstream Ser found in most SDRs. Atypical SDRs generally lack the ...
CDD:187541	305	EUKprk	Bacteria:10,Invertebrates:4,Plants:3,Vertebrates:3	cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs.  UGD catalyzes the formation of UDP-xylose from UDP-glucuronate; it is an extended-SDR, and has the characteristic glycine-rich NAD-binding pattern, TGXXGXXG, and active site tetrad.  Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core ...
CDD:187542	259	PRK	Bacteria:11	cd05231, NmrA_TMR_like_1_SDR_a, NmrA (a transcriptional regulator) and triphenylmethane reductase (TMR) like proteins, subgroup 1, atypical (a) SDRs.  Atypical SDRs related to NMRa, TMR, and HSCARG (an NADPH sensor). This subgroup resembles the SDRs and has a partially conserved characteristic [ST]GXXGXXG NAD-binding motif, but lacks the conserved active site residues. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational ...
CDD:187543	303	PRK	Bacteria:11	cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs.  UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup is comprised of bacterial proteins, and includes the Staphylococcus aureus capsular polysaccharide Cap5N, which may have a role in the synthesis of ...
CDD:212491	234	EUKprk	Bacteria:75,Invertebrates:5,Mammals:1,Plants:12,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	cd05233, SDR_c, classical (c) SDRs.  SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately ...
CDD:187545	305	PRK	Bacteria:12	cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2, extended (e) SDRs.  UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup is comprised of archaeal and bacterial proteins, and has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are ...
CDD:187546	290	EUKprk	Bacteria:10,Invertebrates:2,Plants:8	cd05235, SDR_e1, extended (e) SDRs, subgroup 1.  This family consists of an SDR module of multidomain proteins identified as putative polyketide sythases fatty acid synthases (FAS), and nonribosomal peptide synthases, among others. However, unlike the usual ketoreductase modules of FAS and polyketide synthase, these domains are related to the extended SDRs, and have canonical NAD(P)-binding motifs and an active site tetrad. Extended SDRs ...
CDD:187547	320	EUKprk	Bacteria:3,Invertebrates:8,Plants:4,Primates:1,Vertebrates:3	cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended (e) SDRs.  SDRs are Rossmann-fold NAD(P)H-binding proteins, many of which may function as fatty acyl CoA reductases (FAR), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis ...
CDD:187548	287	PRK	Bacteria:21	cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs.  UDP-Glcnac inverting 4,6-dehydratase was identified in Helicobacter pylori as the hexameric flaA1 gene product (FlaA1). FlaA1 is hexameric, possesses UDP-GlcNAc-inverting 4,6-dehydratase activity,  and catalyzes the first step in the creation of a pseudaminic acid derivative in protein glycosylation. Although this subgroup has the NADP-binding ...
CDD:187549	305	EUKprk	Bacteria:7,Plants:2,nodiv:1	cd05238, Gne_like_SDR_e, Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs.  Nucleoside-diphosphate-sugar 4-epimerase has the characteristic active site tetrad and NAD-binding motif of the extended SDR, and is related to more specifically defined epimerases such as UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), which catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final ...
CDD:187550	300	EUKprk	Bacteria:15,Invertebrates:5,Plants:2,Primates:1,Vertebrates:3	cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.  GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase) acts in the NADP-dependent synthesis of GDP-fucose from GDP-mannose. Two activities have been proposed for the same active site: epimerization and reduction. Proteins in this subgroup are extended SDRs, which have a characteristic active site tetrad and an NADP-binding motif, [AT]GXXGXXG, that ...
CDD:187551	306	PRK	Bacteria:12	cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup 3, extended (e) SDRs.  Members of this bacterial subgroup are identified as possible sugar epimerases, such as UDP-glucose 4 epimerase. However, while the NAD(P)-binding motif is fairly well conserved, not all members retain the canonical active site tetrad of the extended SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent ...
CDD:187553	296	EUKprk	Bacteria:18,Invertebrates:1,Plants:1,Vertebrates:2	cd05242, SDR_a8, atypical (a) SDRs, subgroup 8.  This subgroup contains atypical SDRs of unknown function. Proteins in this subgroup have a glycine-rich NAD(P)-binding motif consensus that resembles that of the extended SDRs, (GXXGXXG or GGXGXXG), but lacks the characteristic active site residues of the SDRs. A Cys often replaces the usual Lys of the YXXXK active site motif, while the upstream Ser is generally present and ...
CDD:187554	203	EUKprk	Bacteria:27,Plants:7	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5.  This subgroup contains atypical SDRs, some of which are identified as putative NAD(P)-dependent epimerases, one as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is very similar to the extended SDRs, GXXGXXG, and binds NADP. Generally, this subgroup has poor conservation of the active ...
CDD:187555	207	EUKprk	Bacteria:22,Invertebrates:3,Plants:2,Primates:1,Rodents:1,Vertebrates:6	cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs.  Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by ...
CDD:187556	293	PRK	Bacteria:9	cd05245, SDR_a2, atypical (a) SDRs, subgroup 2.  This subgroup contains atypical SDRs, one member is identified as Escherichia coli protein ybjT, function unknown. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif consensus that generally matches the extended SDRs, TGXXGXXG, but lacks the characteristic active site residues of the SDRs. This subgroup has basic residues (HXXXR) in place of the active ...
CDD:187557	315	EUKprk	Bacteria:23,Invertebrates:4,Plants:2,Primates:1,Vertebrates:3	cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs.  This subgroup contains dTDP-D-glucose 4,6-dehydratase and related proteins, members of the extended-SDR family, with the characteristic Rossmann fold core region, active site tetrad and NAD(P)-binding motif. dTDP-D-glucose 4,6-dehydratase is closely related to other sugar epimerases of the SDR family. dTDP-D-dlucose 4,6,-dehydratase ...
CDD:187558	323	EUKprk	Bacteria:22,Invertebrates:7,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs.  UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs ...
CDD:187559	317	EUKprk	Bacteria:10,Plants:1	cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs.  This subgroup contains ADP-L-glycero-D-mannoheptose 6-epimerase, an extended SDR, which catalyzes the NAD-dependent interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose.  This subgroup has the canonical active site tetrad and NAD(P)-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold ...
CDD:187560	214	EUKprk	Bacteria:6,Environmental:1,Invertebrates:3,Plants:3,Rodents:1,Vertebrates:3	cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.  Atypical SDRs in this subgroup include CC3 (also known as TIP30) which is implicated in tumor suppression. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine rich NAD(P)-binding motif that resembles the extended SDRs, and have an active site triad of the SDRs (YXXXK and upstream Ser), although the ...
CDD:187561	242	EUKprk	Bacteria:13,Invertebrates:2,Plants:10,Primates:1,Vertebrates:2	cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and HSCARG (an NADPH sensor) like proteins, atypical (a) SDRs.  NmrA and HSCARG like proteins. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad, ...
CDD:187562	336	PRK	Bacteria:11	cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e) SDRs.  This subgroup contains CDP-D-glucose 4,6-dehydratase, an extended SDR, which catalyzes the conversion of CDP-D-glucose to CDP-4-keto-6-deoxy-D-glucose. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core ...
CDD:187563	332	EUKprk	Bacteria:12,Plants:1	cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e) SDRs.  This subgroup contains UDP-D-glucuronic acid 4-epimerase, an extended SDR, which catalyzes the conversion of UDP-alpha-D-glucuronic acid to UDP-alpha-D-galacturonic acid. This group has the SDR's canonical catalytic tetrad and the TGxxGxxG NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding ...
CDD:187564	280	EUKprk	Bacteria:28,Invertebrates:3,Plants:5,Primates:1,Vertebrates:3	cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs.  dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended SDR, synthesizes dTDP-L-rhamnose from alpha-D-glucose-1-phosphate,  providing the precursor of L-rhamnose, an essential cell wall component of many pathogenic bacteria. This subgroup has the characteristic active site tetrad and NADP-binding motif. ...
CDD:187566	304	PRK	Bacteria:21	cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs.  This subgroup contains UDP-N-acetylglucosamine 4-epimerase of Pseudomonas aeruginosa, WbpP,  an extended SDR, that catalyzes the NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to UDP-Glc and UDP-Gal.  This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold ...
CDD:187567	316	EUKprk	Bacteria:15,Plants:1	cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e) SDRs.  Decarboxylase domain of ArnA. ArnA, is an enzyme involved in the modification of outer membrane protein lipid A of gram-negative bacteria. It is a bifunctional enzyme that catalyzes the NAD-dependent decarboxylation of UDP-glucuronic acid and N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent decaboxylating activity is in the ...
CDD:187568	337	PRK	Bacteria:12	cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.  CDP-tyvelose 2-epimerase is a tetrameric SDR that catalyzes the conversion of CDP-D-paratose to CDP-D-tyvelose, the last step in tyvelose biosynthesis. This subgroup is a member of the extended SDR subfamily, with a characteristic active site tetrad and NAD-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central ...
CDD:187569	282	EUKprk	Bacteria:6,Plants:18	cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase (PCBER) like, atypical (a) SDRs.  PCBER and pinoresinol-lariciresinol reductases are NADPH-dependent aromatic alcohol reductases, and are atypical members of the SDR family. Other proteins in this subgroup are identified as eugenol synthase. These proteins contain an N-terminus characteristic of NAD(P)-binding proteins and a small C-terminal domain presumed to be involved in substrate ...
CDD:187570	316	EUKprk	Bacteria:24,Invertebrates:5,Plants:2,Primates:1,Vertebrates:3	cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e) SDRs.  GDP-mannose 4,6 dehydratase, a homodimeric SDR, catalyzes the NADP(H)-dependent conversion of GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in the fucose biosynthesis pathway. These proteins have the canonical active site triad and NAD-binding pattern, however the active site Asn is often missing and may be substituted with Asp. A Glu ...
CDD:187571	248	PRK	Bacteria:8	cd05261, CAPF_like_SDR_e, capsular polysaccharide assembling protein (CAPF) like, extended (e) SDRs.  This subgroup of extended SDRs, includes some members which have been identified as capsular polysaccharide assembling proteins, such as Staphylococcus aureus Cap5F which is involved in the biosynthesis of N-acetyl-l-fucosamine, a constituent of surface polysaccharide structures of S. aureus. This subgroup has the characteristic active site tetrad and NAD-binding ...
CDD:187572	291	EUKprk	Bacteria:8,Plants:5	cd05262, SDR_a7, atypical (a) SDRs, subgroup 7.  This subgroup contains atypical SDRs of unknown function. Members of this subgroup have a glycine-rich NAD(P)-binding motif consensus that matches the extended SDRs, TGXXGXXG, but lacks the characteristic active site residues of the SDRs. This subgroup has basic residues (HXXXR) in place of the active site motif YXXXK, these may have a catalytic role. Atypical SDRs generally lack the catalytic residues ...
CDD:187573	293	EUKprk	Bacteria:13,Invertebrates:2	cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like, extended (e) SDRs.  This subgroup of extended SDR family domains have the characteristic active site tetrad and a well-conserved NAD(P)-binding motif. This subgroup is not well characterized, its members are annotated as having a variety of putative functions. One characterized member is Pseudomonas fluorescens MupV a protein  involved in the biosynthesis of Mupirocin, a ...
CDD:187574	300	PRK	Bacteria:10	cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup 5, extended (e) SDRs.  This subgroup partially conserves the characteristic active site tetrad and NAD-binding motif of the extended SDRs, and has been identified as possible UDP-glucose 4-epimerase (aka UDP-galactose 4-epimerase), a homodimeric member of the extended SDR family. UDP-glucose 4-epimerase catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir ...
CDD:187575	250	EUKprk	Bacteria:16,Plants:2	cd05265, SDR_a1, atypical (a) SDRs, subgroup 1.  Atypical SDRs in this subgroup are poorly defined and have been identified putatively as isoflavones reductase, sugar dehydratase, mRNA binding protein etc. Atypical SDRs are distinct from classical SDRs. Members of this subgroup retain the canonical active site triad (though not the upstream Asn found in most SDRs) but have an unusual putative glycine-rich NAD(P)-binding motif, GGXXXXG, in the usual ...
CDD:187576	251	EUKprk	Bacteria:29,Plants:2	cd05266, SDR_a4, atypical (a) SDRs, subgroup 4.  Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; ...
CDD:187577	203	PRK	Bacteria:7	cd05267, SDR_a6, atypical (a) SDRs, subgroup 6.  These atypical SDR family members of unknown function have only a partial match to a prototypical glycine-rich NAD(P)-binding motif consensus, GXXG, which conserves part of the motif of extended SDR. Furthermore, they lack the characteristic active site residues of the SDRs. This subgroup is related to phenylcoumaran benzylic ether reductase, an NADPH-dependent aromatic alcohol reductase. One member is identified as a ...
CDD:187578	272	EUKprk	Bacteria:23,Invertebrates:2,Plants:4,nodiv:1	cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs.  TMR is an atypical NADP-binding protein of the SDR family. It lacks the active site residues of the SDRs but has a glycine rich NAD(P)-binding motif that matches the extended SDRs. Proteins in this subgroup however, are more similar in length to the classical SDRs. TMR was identified as a reducer of triphenylmethane dyes, important ...
CDD:187579	273	EUKprk	Bacteria:9,Invertebrates:7,Mammals:1,Plants:6,Vertebrates:3	cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs.  This subgroup of extended SDR-like proteins are atypical SDRs. They have a glycine-rich NAD(P)-binding motif similar to the typical SDRs, GXXGXXG, and have the YXXXK active site motif (though not the other residues of the SDR tetrad). Members identified include NDUFA9 ...
CDD:187580	308	EUKprk	Bacteria:7,Invertebrates:4,Mammals:1,Rodents:1,Vertebrates:3	cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.  This subgroup contains members identified as L-threonine dehydrogenase (TDH). TDH catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. This group is distinct from TDHs that are members of the medium chain dehydrogenase/reductase family. This group has the NAD-binding motif and active site ...
CDD:187582	375	EUKprk	Bacteria:25,Invertebrates:1,Plants:2,Vertebrates:1	cd05274, KR_FAS_SDR_x, ketoreductase (KR) and fatty acid synthase (FAS), complex (x) SDRs.  Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding  to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal ...
CDD:176180	323	EUKprk	Bacteria:103,Environmental:1,Invertebrates:4,Plants:11,Vertebrates:3,nodiv:2	cd05276, p53_inducible_oxidoreductase, PIG3 p53-inducible quinone oxidoreductase.  PIG3 p53-inducible quinone oxidoreductase, a medium chain dehydrogenase/reductase family member, acts in the apoptotic pathway. PIG3 reduces ortho-quinones, but its apoptotic activity has been attributed to oxidative stress generation, since overexpression of PIG3 accumulates reactive oxygen species. PIG3 resembles ...
CDD:176181	347	EUKprk	Bacteria:8,Invertebrates:2	cd05278, FDH_like, Formaldehyde dehydrogenases.  Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family.  Formaldehyde dehydrogenase (aka ADH3) may be the ancestral form of alcohol dehydrogenase, which evolved to detoxify formaldehyde.  This CD contains glutathione dependant FDH, glutathione independent FDH, and related alcohol dehydrogenases. FDH converts formaldehyde and NAD(P) to formate and ...
CDD:176183	325	PRK	Bacteria:33	cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone oxidoreductases.  Yhdh and yhfp-like putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in ...
CDD:176184	341	PRK	Bacteria:36	cd05281, TDH, Threonine dehydrogenase.  L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)- dependent oxidation.  THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs  have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and ...
CDD:176645	323	EUKprk	Bacteria:25,Invertebrates:1,Plants:6	cd05282, ETR_like, 2-enoyl thioester reductase-like.  2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase ...
CDD:176186	337	EUKprk	Bacteria:31,Invertebrates:9,Plants:44	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD).  Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium ...
CDD:176187	340	PRK	Bacteria:26	cd05284, arabinose_DH_like, D-arabinose dehydrogenase.  This group contains arabinose dehydrogenase (AraDH) and related alcohol dehydrogenases. AraDH is a member of the medium chain dehydrogenase/reductase family and catalyzes the NAD(P)-dependent oxidation of D-arabinose and other pentoses, the initial step in the metabolism of d-arabinose into 2-oxoglutarate. Like the alcohol dehydrogenases, AraDH binds a zinc in the catalytic cleft as well as a distal structural ...
CDD:176188	343	EUKprk	Bacteria:23,Invertebrates:10,Plants:32,Primates:1,Vertebrates:3	cd05285, sorbitol_DH, Sorbitol dehydrogenase.  Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. Aldose reductase catalyzes the NADP(H)-dependent conversion of glucose to sorbital, and SDH uses NAD(H) in the conversion of sorbitol to fructose.  ...
CDD:176189	320	EUKprk	Bacteria:86,Environmental:2,Invertebrates:3,Plants:28	cd05286, QOR2, Quinone oxidoreductase (QOR).  Quinone oxidoreductase (QOR) and 2-haloacrylate reductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds.  Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens ...
CDD:176190	329	EUKprk	Bacteria:68,Invertebrates:5,Plants:32,Primates:1,nodiv:1	cd05288, PGDH, Prostaglandin dehydrogenases.  Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it ...
CDD:176191	309	EUKprk	Bacteria:109,Invertebrates:1,Plants:33,nodiv:1	cd05289, MDR_like_2, alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases.  Members identified as zinc-dependent alcohol dehydrogenases and quinone oxidoreductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds.  Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while ...
CDD:133426	307	PRK	Bacteria:7	cd05290, LDH_3, A subgroup of L-lactate dehydrogenases.  L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of some bacterial LDHs from firmicutes, gammaproteobacteria, and actinobacteria. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the ...
CDD:133427	306	PRK	Bacteria:48	cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases.  L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be ...
CDD:133428	308	EUKprk	Bacteria:41,Plants:2	cd05292, LDH_2, A subgroup of L-lactate dehydrogenases.  L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed predominantly of bacterial LDHs and a few fungal LDHs. Bacterial LDHs may be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, ...
CDD:133429	312	EUK	Invertebrates:10,Mammals:1,Plants:2,Primates:1,Rodents:1,Vertebrates:5	cd05293, LDH_1, A subgroup of L-lactate dehydrogenases.  L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are ...
CDD:133432	419	PRK	Bacteria:37	cd05296, GH4_P_beta_glucosidase, Glycoside Hydrolases Family 4; Phospho-beta-glucosidase.  Some bacteria simultaneously translocate and phosphorylate  disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases such as the phospho-beta-glucosidases. Other organisms (such as archaea and Thermotoga maritima ) lack the PEP-PTS system, but ...
CDD:133433	423	PRK	Bacteria:27	cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases.  Glucosidases cleave glycosidic bonds to release glucose from oligosaccharides. Alpha-glucosidases and alpha-galactosidases release alpha-D-glucose and alpha-D-galactose, respectively, via the hydrolysis of alpha-glycopyranoside bonds. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent ...
CDD:133434	437	PRK	Bacteria:19	cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases.  Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the ...
CDD:240624	312	EUKprk	Bacteria:57,Environmental:1,Invertebrates:4,Plants:1,Primates:1,Rodents:1,Vertebrates:3	cd05299, CtBP_dh, C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor.  The transcriptional corepressor CtBP is a dehydrogenase with sequence and structural similarity to the d2-hydroxyacid dehydrogenase family. CtBP was initially identified as a protein that bound the PXDLS sequence at the adenovirus E1A C terminus, causing the loss of ...
CDD:240625	313	EUKprk	Bacteria:120,Invertebrates:4,Plants:5	cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid dehydrogenase.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, ...
CDD:240626	309	EUKprk	Bacteria:119,Environmental:3,Invertebrates:17,Plants:10,Primates:1,Vertebrates:2	cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH).  D-glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase, HPR) catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. In humans, HPR deficiency causes primary hyperoxaluria type 2, characterized by over-excretion of L-glycerate and oxalate in the urine, possibly due to an ...
CDD:240627	348	EUKprk	Bacteria:8,Environmental:1,Invertebrates:1,Plants:10	cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).  NAD-dependent formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of a formate anion to carbon dioxide coupled with the reduction of NAD+ to NADH. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family have 2 highly similar subdomains of the alpha/beta form, with NAD binding occurring in the cleft between ...
CDD:240628	301	PRK	Bacteria:33,Environmental:1	cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains.  Phosphoglycerate dehydrogenase (PGDH) catalyzes the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDH comes in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form ...
CDD:240629	363	EUKprk	Bacteria:127,Environmental:3,Invertebrates:19,Plants:11,Primates:1,Vertebrates:2,nodiv:1	cd05304, Rubrum_tdh, Rubrum transdehydrogenase NAD-binding and catalytic domains.  Transhydrogenases found in bacterial and inner mitochondrial membranes link NAD(P)(H)-dependent redox reactions to proton translocation. The energy of the proton electrochemical gradient (delta-p), generated by the respiratory electron transport chain, is consumed by transhydrogenase in NAD(P)+ reduction. ...
CDD:240630	359	EUKprk	Bacteria:129,Environmental:3,Invertebrates:3	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains.  Alanine dehydrogenase (L-AlaDH) catalyzes the NAD-dependent conversion of pyruvate to L-alanine via reductive amination. Like formate dehydrogenase and related enzymes, L-AlaDH is comprised of 2 domains connected by a long alpha helical stretch, each resembling a Rossmann fold NAD-binding domain. The NAD-binding domain is inserted within the linear ...
CDD:133453	226	EUKprk	Bacteria:10,Invertebrates:1	cd05311, NAD_bind_2_malic_enz, NAD(P) binding domain of malic enzyme (ME), subgroup 2.  Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically  Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+.  ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as ...
CDD:133454	279	EUKprk	Bacteria:4,Invertebrates:5,Plants:8,Primates:1,Vertebrates:3	cd05312, NAD_bind_1_malic_enz, NAD(P) binding domain of malic enzyme (ME), subgroup 1.  Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically  Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+.  ME has been found in all organisms, and plays important roles in ...
CDD:133455	254	EUKprk	Bacteria:3,Invertebrates:5,Plants:8	cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate dehydrogenase, subgroup 2.  Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is ...
CDD:187584	244	EUK	Invertebrates:6,Plants:7,Primates:1,Vertebrates:3	cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase (ADH)-like, classical (c) SDRs.  This subgroup contains insect type ADH, and 15-hydroxyprostaglandin dehydrogenase (15-PGDH) type I; these proteins are classical SDRs. ADH catalyzes the NAD+-dependent oxidation of alcohols to aldehydes/ketones. This subgroup is distinct from the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase/reductase family, ...
CDD:187585	225	EUKprk	Bacteria:6,Invertebrates:5,Plants:6,Primates:1,Vertebrates:3	cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl reductase (PTCR)-like, classical (c) SDRs.  PTCR is a classical SDR which catalyzes the NADPH-dependent reduction of ketones on steroids and prostaglandins. Unlike most SDRs, PTCR functions as a monomer. This subgroup also includes human carbonyl reductase 1 (CBR1) and CBR3. CBR1 is an NADPH-dependent SDR with broad substrate specificity and may be ...
CDD:187586	233	EUKprk	Bacteria:10,Invertebrates:2,Plants:12,Vertebrates:3	cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase sniffer-like, classical (c) SDRs.  Sniffer is an NADPH-dependent carbonyl reductase of the classical SDR family. Studies in Drosophila melanogaster implicate Sniffer in the prevention of neurodegeneration due to aging and oxidative-stress. This subgroup also includes Rhodococcus sp. AD45 IsoH, which is an NAD-dependent 1-hydroxy-2-glutathionyl-2-methyl-3-butene ...
CDD:212492	269	EUKprk	Bacteria:9,Invertebrates:10,Plants:5,Primates:1,Rodents:1	cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs.  Classical SDR subgroup containing retinol-DHs, LPORs, and related proteins. Retinol is processed by a medium chain alcohol dehydrogenase followed by retinol-DHs. Pchlide reductases act in chlorophyll biosynthesis. There are distinct ...
CDD:187593	257	EUKprk	Bacteria:2,Invertebrates:4,Plants:1,Primates:1,Rodents:1,Vertebrates:4	cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs.  Human 11beta_HSD1 catalyzes the NADP(H)-dependent interconversion of cortisone and cortisol. This subgroup also includes human dehydrogenase/reductase SDR family member 7C (DHRS7C) and DHRS7B. These proteins have the GxxxGxG nucleotide binding motif and S-Y-K catalytic triad characteristic ...
CDD:187594	240	EUKprk	Bacteria:23,Invertebrates:2,Plants:1,Primates:1,Vertebrates:2	cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs.  This subgroup includes the Escherichai coli K12 BKR, FabG. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo ...
CDD:187595	221	EUKprk	Bacteria:1,Invertebrates:6,Rodents:1,Vertebrates:3	cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR), classical (c) SDRs.  Dihydropteridine reductase is an NAD-binding protein related to the SDRs. It converts dihydrobiopterin into tetrahydrobiopterin, a cofactor necessary in catecholamines synthesis. Dihydropteridine reductase has the YXXXK of these tyrosine-dependent oxidoreductases, but lacks the typical upstream Asn and Ser catalytic residues. SDRs are a ...
CDD:187597	246	EUKprk	Bacteria:3,Plants:1,Primates:1	cd05338, DHRS1_HSDL2-like_SDR_c, human dehydrogenase/reductase (SDR family) member 1 (DHRS1) and human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs.  This subgroup includes human DHRS1 and human HSDL2 and related proteins. These are members of the classical SDR family, with a canonical Gly-rich  NAD-binding motif and the typical YXXXK active site motif. However, the rest of the catalytic tetrad is not strongly ...
CDD:187598	243	EUKprk	Bacteria:2,Invertebrates:5,Plants:7,Primates:1,Rodents:1,Vertebrates:3	cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs.  17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. 17betaHSD type XI, a classical SDR, preferentially converts 3alpha-adiol to androsterone but not numerous other tested steroids. This subgroup of classical ...
CDD:187602	253	PRK	Bacteria:23,Environmental:1	cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR.  This subgroup resembles the SDR family, but does not have a perfect match to the NAD-binding motif or the catalytic tetrad characteristic of the SDRs. It includes the SDRs, Q9HYA2 from Pseudomonas aeruginosa PAO1 and APE0912 from Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty ...
CDD:187604	249	EUKprk	Bacteria:6,Invertebrates:1,Plants:3	cd05346, SDR_c5, classical (c) SDR, subgroup 5.  These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. ...
CDD:187605	248	PRK	Bacteria:7	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs.  Ga5DH catalyzes the NADP-dependent conversion of carbon source D-gluconate and 5-keto-D-gluconate. This SDR subgroup has a classical Gly-rich NAD(P)-binding motif and a conserved active site tetrad pattern. However, it has been proposed that Arg104 (Streptococcus suis Ga5DH numbering), as well as an active site Ca2+, play a critical role in catalysis. In addition to Ga5DHs this ...
CDD:187608	239	PRK	Bacteria:6	cd05350, SDR_c6, classical (c) SDR, subgroup 6.  These proteins are members of the classical SDR family, with a canonical active site tetrad  and a fairly well conserved typical Gly-rich  NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. ...
CDD:187610	252	EUK	Plants:10	cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like, classical (c) SDRs.  NADP-mannitol dehydrogenase catalyzes the conversion of fructose to mannitol, an acyclic 6-carbon sugar. MDH is a tetrameric member of the SDR family. This subgroup also includes various other tetrameric SDRs, including Pichia stipitis D-arabinitol dehydrogenase (aka polyol dehydrogenase), Candida albicans Sou1p, a sorbose reductase, and Candida parapsilosis (S)-specific carbonyl ...
CDD:187611	250	EUKprk	Bacteria:3,Invertebrates:4,Plants:1,Primates:1,Rodents:1,Vertebrates:2	cd05353, hydroxyacyl-CoA-like_DH_SDR_c-like, (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs.  Beta oxidation of fatty acids in eukaryotes occurs by a four-reaction cycle, that may take place in mitochondria or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is part of rat peroxisomal multifunctional MFE-2, it is a member of the NAD-dependent SDRs, but contains an additional small ...
CDD:187613	270	EUKprk	Bacteria:10,Plants:3	cd05355, SDR_c1, classical (c) SDR, subgroup 1.  These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs ...
CDD:187614	239	EUKprk	Bacteria:1,Invertebrates:8,Plants:9,Primates:1,Vertebrates:3	cd05356, 17beta-HSD1_like_SDR_c, 17-beta-hydroxysteroid dehydrogenases (17beta-HSDs) types -1, -3, and -12, -like, classical (c) SDRs.  This subgroup includes various 17-beta-hydroxysteroid dehydrogenases and 3-ketoacyl-CoA reductase, these are members of the SDR family, and contain the canonical active site tetrad and glycine-rich NAD-binding motif of the classical SDRs. 3-ketoacyl-CoA reductase (KAR, aka ...
CDD:187615	234	EUKprk	Bacteria:7,Invertebrates:4	cd05357, PR_SDR_c, pteridine reductase (PR), classical (c) SDRs.  Pteridine reductases (PRs), members of the SDR family, catalyzes the NAD-dependent reduction of folic acid, dihydrofolate and related compounds. In Leishmania, pteridine reductase (PTR1) acts to circumvent the anti-protozoan drugs that attack dihydrofolate reductase activity. Proteins in this subgroup have an N-terminal NAD-binding motif and a YxxxK active site motif, but have an ...
CDD:187617	242	EUKprk	Bacteria:8,Plants:1	cd05359, ChcA_like_SDR_c, 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs.  This subgroup contains classical SDR proteins, including members identified as 1-cyclohexenylcarbonyl coenzyme A reductase. ChcA of Streptomyces collinus is implicated in the final reduction step of shikimic acid to ansatrienin. ChcA shows sequence similarity to the SDR family of NAD-binding proteins, but it lacks the conserved Tyr of the ...
CDD:187620	243	EUKprk	Bacteria:7,Plants:5	cd05362, THN_reductase-like_SDR_c, tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs.  1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of Magnaporthe grisea and the related 1,3,8-trihydroxynaphthalene reductase (3HNR) are typical members of the SDR family containing the canonical glycine rich NAD(P)-binding site and active site tetrad, and function in fungal melanin biosynthesis. This subgroup also includes an SDR from ...
CDD:187625	241	EUKprk	Bacteria:4,Invertebrates:3,Plants:4,Primates:1,Rodents:1,Vertebrates:4	cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like, classical (c) SDRs.  Human SPR, a member of the SDR family, catalyzes the NADP-dependent reduction of sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to SPRs, this subgroup also contains Bacillus cereus yueD, a benzil reductase, which catalyzes the stereospecific reduction of benzil to (S)-benzoin. SDRs are a functionally diverse family of ...
CDD:187627	249	EUKprk	Bacteria:9,Invertebrates:3,Plants:4,Primates:1,Vertebrates:3	cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.  TTER is a peroxisomal protein with a proposed role in fatty acid elongation. Fatty acid synthesis is known to occur in the both endoplasmic reticulum and mitochondria; peroxisomal TER has been proposed as an additional fatty acid elongation system, it reduces the double bond at C-2 as the last step ...
CDD:187628	228	EUKprk	Bacteria:7,Plants:2	cd05370, SDR_c2, classical (c) SDR, subgroup 2.  Short-chain dehydrogenases/reductases (SDRs, aka Tyrosine-dependent oxidoreductases) are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended ...
CDD:187629	252	EUKprk	Bacteria:3,Invertebrates:7,Plants:1,Primates:1,Rodents:1,Vertebrates:2	cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs.  HSD10, also known as amyloid-peptide-binding alcohol dehydrogenase (ABAD), was previously identified as a L-3-hydroxyacyl-CoA dehydrogenase, HADH2. In fatty acid metabolism, HADH2 catalyzes the third step of beta-oxidation, the conversion of a hydroxyl to a keto group in the NAD-dependent oxidation of ...
CDD:187630	250	EUKprk	Bacteria:24,Environmental:1,Invertebrates:5,Plants:1	cd05372, ENR_SDR, Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR.  This bacterial subgroup of ENRs includes Escherichia coli ENR. ENR catalyzes the NAD(P)H-dependent reduction of enoyl-ACP in the last step of fatty acid biosynthesis. De novo fatty acid biosynthesis is catalyzed by the fatty acid synthetase complex, through the serial addition of 2-carbon subunits. In bacteria and plants,ENR catalyzes one ...
CDD:187632	248	EUKprk	Bacteria:18,Invertebrates:3,Plants:12,Primates:1	cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs.  17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding ...
CDD:240179	122	EUKprk	Bacteria:192,Invertebrates:5,Plants:2	cd05379, SCP_bacterial, SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed that SCP domains may function as endopeptidases. Little is known about the biological roles of the bacterial and archaeal ...
CDD:240180	144	EUKprk	Bacteria:9,Invertebrates:45,Plants:13,Primates:1,Vertebrates:1	cd05380, SCP_euk, SCP_euk: SCP-like extracellular protein domain, as found mainly in eukaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed that SCP domains may function as endopeptidases.
CDD:240181	136	EUK	Plants:9	cd05381, SCP_PR-1_like, SCP_PR-1_like: SCP-like extracellular protein domain, PR-1 like subfamily. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. It also includes CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed that SCP domains may ...
CDD:240182	132	EUK	Invertebrates:15,Plants:2,Vertebrates:3,nodiv:1	cd05382, SCP_GAPR-1_like, SCP_GAPR-1_like: SCP-like extracellular protein domain, golgi-associated plant pathogenesis related protein (GAPR)-like sub-family. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. It has been proposed that SCP ...
CDD:240183	138	EUK	Invertebrates:2,Mammals:2,Primates:1,Vertebrates:9	cd05383, SCP_CRISP, SCP_CRISP: SCP-like extracellular protein domain, CRISP-like sub-family. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Involvement of CRISP in response to pathogens, fertilization, and sperm maturation have been ...
CDD:240184	129	EUK	Plants:14	cd05384, SCP_PRY1_like, SCP_PRY1_like: SCP-like extracellular protein domain, PRY1-like sub-family restricted to fungi. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed that SCP domains may function as endopeptidases. PRY1 is a yeast protein that is up-regulated in core ESCRT mutants. This PRY1-like group also ...
CDD:240185	144	EUK	Mammals:3,Primates:1,Rodents:1,Vertebrates:2	cd05385, SCP_GLIPR-1_like, SCP_GLIPR-1_like: SCP-like extracellular protein domain, glioma pathogenesis-related protein (GLIPR)-like sub-family. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed that SCP domains may function as endopeptidases.
CDD:213341	317	EUK	Invertebrates:6,Plants:14	cd05392, RasGAP_Neurofibromin_like, Ras-GTPase Activating Domain of proteins similar to neurofibromin.  Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In ...
CDD:188647	370	EUKprk	Bacteria:3,Invertebrates:6,Mammals:3,Plants:4	cd05396, An_peroxidase_like, Animal heme peroxidases and related proteins.  A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well.
CDD:143387	49	EUKprk	Bacteria:6,Plants:1	cd05397, NT_Pol-beta-like, Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins.  This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase ...
CDD:143388	139	EUKprk	Bacteria:46,Invertebrates:13,Plants:5,Vertebrates:2	cd05398, NT_ClassII-CCAase, Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes.  CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, ...
CDD:143389	129	EUKprk	Bacteria:54,Invertebrates:1,Plants:8	cd05399, NT_Rel-Spo_like, Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases.  This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp ...
CDD:143390	143	EUKprk	Bacteria:47,Invertebrates:2,Mammals:1,Primates:1,Rodents:1,Vertebrates:1	cd05400, NT_2-5OAS_ClassI-CCAase, Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme.  In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, ...
CDD:143391	172	PRK	Bacteria:44	cd05401, NT_GlnE_GlnD_like, Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins.  Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS ...
CDD:143392	114	EUK	Invertebrates:24,Mammals:1,Plants:14,Primates:1,Rodents:1,Vertebrates:4	cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases.  Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, ...
CDD:143393	93	PRK	Bacteria:137	cd05403, NT_KNTase_like, Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins.  S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of ...
CDD:176102	197	PRK	Bacteria:196,nodiv:1	cd05466, PBP2_LTTR_substrate, The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily.  This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic ...
CDD:119437	96	EUKprk	Bacteria:12,Invertebrates:5,Mammals:1,Plants:9,Primates:1	cd05467, CBM20, The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. ...
CDD:176472	141	EUKprk	Bacteria:8,Invertebrates:12,Mammals:1,Plants:6,Primates:1,Vertebrates:4,nodiv:1	cd05468, pVHL, von Hippel-Landau (pVHL) tumor suppressor protein.  von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts ...
CDD:133137	109	EUK	Invertebrates:1,Mammals:1,Plants:5,Primates:1,Vertebrates:2,nodiv:1	cd05470, pepsin_retropepsin_like, Cellular and retroviral pepsin-like aspartate proteases.  This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized ...
CDD:133138	283	EUKprk	Bacteria:3,Invertebrates:41,Mammals:6,Plants:52,Primates:1,Vertebrates:4	cd05471, pepsin_like, Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH.  Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, ...
CDD:133139	299	EUK	Plants:7	cd05472, cnd41_like, Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase.  Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco.  CND41 has DNA-binding as well as aspartic ...
CDD:133141	295	EUK	Plants:33	cd05474, SAP_like, SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins.  SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode ...
CDD:133143	265	miss	miss	cd05476, pepsin_A_like_plant, Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants.  This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar ...
CDD:133146	124	EUK	Invertebrates:16,Plants:10,Primates:1,Vertebrates:2	cd05479, RP_DDI, RP_DDI; retropepsin-like domain of DNA damage inducible protein.  The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.
CDD:133148	93	EUK	Invertebrates:3	cd05481, retropepsin_like_LTR_1, Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats.  Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the ...
CDD:133149	87	EUKprk	Bacteria:1,Mammals:5,Primates:1,Rodents:1,Vertebrates:1,Viruses:5	cd05482, HIV_retropepsin_like, Retropepsins, pepsin-like aspartate proteases.  This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are ...
CDD:133150	96	EUKprk	Bacteria:119,Environmental:2,Plants:1	cd05483, retropepsin_like_bacteria, Bacterial aspartate proteases, retropepsin-like protease family.  This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as ...
CDD:133151	91	EUK	Invertebrates:9,Vertebrates:1	cd05484, retropepsin_like_LTR_2, Retropepsins_like_LTR, pepsin-like aspartate proteases.  Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins ...
CDD:133156	362	EUK	Plants:8	cd05489, xylanase_inhibitor_I_like, TAXI-I inhibits degradation of xylan in the cell wall.  Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and ...
CDD:99923	119	EUK	Plants:9	cd05491, Bromo_TBP7_like, Bromodomain; TBP7_like subfamily, limited to fungi. TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
CDD:99924	109	EUK	Invertebrates:5,Primates:2,Vertebrates:2	cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99925	131	EUK	Invertebrates:2,Rodents:1,Vertebrates:2	cd05493, Bromo_ALL-1, Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
CDD:99926	114	EUK	Invertebrates:1,Plants:4,Primates:1,Rodents:1,Vertebrates:2	cd05494, Bromodomain_1, Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
CDD:99930	102	EUK	Invertebrates:6,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99931	102	EUK	Plants:5	cd05499, Bromo_BDF1_2_II, Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99932	103	EUK	Plants:6	cd05500, Bromo_BDF1_2_I, Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99934	109	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:4	cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its ...
CDD:99938	99	EUK	Plants:6	cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99939	104	EUK	Invertebrates:8,Primates:1,Vertebrates:3	cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact ...
CDD:99941	101	EUK	Invertebrates:16,Plants:11,Primates:1,Vertebrates:3	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:99943	112	EUK	Invertebrates:8,Plants:1,Primates:1,Vertebrates:1	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically ...
CDD:99946	105	EUK	Invertebrates:1	cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone ...
CDD:99950	103	EUK	Plants:7	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a ...
CDD:99951	103	EUK	Vertebrates:1	cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone ...
CDD:99952	106	EUK	Plants:9	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that ...
CDD:99953	104	EUK	Plants:3	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, ...
CDD:99957	112	EUK	Invertebrates:4,Plants:1,Primates:1,Vertebrates:2	cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver.
CDD:99958	128	EUK	Invertebrates:9,Plants:5,Vertebrates:3	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
CDD:99914	352	PRK	Bacteria:9	cd05531, POLBc_B2, DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support ...
CDD:99915	400	EUK	Invertebrates:20,Plants:6,Primates:1,Vertebrates:3	cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than ...
CDD:99916	393	EUK	Invertebrates:7,Plants:8,Primates:1,Vertebrates:1	cd05533, POLBc_delta, DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the ...
CDD:99917	451	EUK	Invertebrates:13,Plants:11,Vertebrates:1	cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B ...
CDD:99918	621	EUK	Invertebrates:9,Plants:6,Vertebrates:3	cd05535, POLBc_epsilon, DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is ...
CDD:99919	371	PRK	Bacteria:9	cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are ...
CDD:99920	371	PRK	Bacteria:9	cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In ...
CDD:240187	109	PRK	Bacteria:27	cd05560, Xcc1710_like, Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
CDD:173797	239	PRK	Bacteria:19	cd05561, Peptidases_S8_4, Peptidase S8 family domain, uncharacterized subfamily 4.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173798	275	PRK	Bacteria:16,Environmental:1	cd05562, Peptidases_S53_like, Peptidase domain in the S53 family.  Members of the peptidase S53 (sedolisin) family include endopeptidases and exopeptidases. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different ...
CDD:99905	86	miss	miss	cd05563, PTS_IIB_ascorbate, PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal ...
CDD:99906	96	miss	miss	cd05564, PTS_IIB_chitobiose_lichenan, PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins ...
CDD:99908	89	miss	miss	cd05566, PTS_IIB_galactitol, PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS).  In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) ...
CDD:99909	87	miss	miss	cd05567, PTS_IIB_mannitol, PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain.  The IIA, IIB, and IIC domains are expressed from the mtlA gene as a single protein, also known as the mannitol PTS permease, the mtl transporter, or MtlA. MtlA is only ...
CDD:99910	85	miss	miss	cd05568, PTS_IIB_bgl_like, PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an ...
CDD:99911	96	miss	miss	cd05569, PTS_IIB_fructose, PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. ...
CDD:270722	318	EUK	Invertebrates:7,Plants:3,Primates:1,Rodents:2	cd05570, STKc_PKC, Catalytic domain of the Serine/Threonine Kinase, Protein Kinase C.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. PKCs undergo three phosphorylations in order to take ...
CDD:270724	262	EUK	Invertebrates:17,Plants:2,Vertebrates:3	cd05572, STKc_cGK, Catalytic domain of the Serine/Threonine Kinase, cGMP-dependent protein kinase (cGK or PKG).  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mammals have two cGK isoforms from different genes, cGKI and cGKII. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. cGK consists of an N-terminal regulatory domain containing a dimerization and an ...
CDD:270725	350	EUK	Invertebrates:6,Plants:5,Primates:1	cd05573, STKc_ROCK_NDR_like, Catalytic domain of Rho-associated coiled-coil containing protein kinase (ROCK)- and Nuclear Dbf2-Related (NDR)-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily include ROCK and ROCK-like proteins such as DMPK, MRCK, and CRIK, as well as NDR and NDR-like proteins such as LATS, CBK1 and ...
CDD:270726	316	EUK	Invertebrates:2,Plants:10	cd05574, STKc_phototropin_like, Catalytic domain of Phototropin-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Phototropins are blue-light receptors that control responses such as phototropism, stromatal opening, and chloroplast movement in order to optimize the photosynthetic efficiency of plants. They are light-activated STKs that contain an ...
CDD:270727	323	EUK	Invertebrates:13,Primates:1,Rodents:1,Vertebrates:1	cd05575, STKc_SGK, Catalytic domain of the Serine/Threonine Kinase, Serum- and Glucocorticoid-induced Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SGKs are activated by insulin and growth factors via phosphoinositide 3-kinase and PDK1. They activate ion channels, ion carriers, and the Na-K-ATPase, as well as regulate the activity of enzymes and ...
CDD:270730	257	EUK	Invertebrates:9,Plants:4,Primates:1,Vertebrates:3	cd05578, STKc_Yank1, Catalytic domain of the Serine/Threonine Kinase, Yank1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily contains uncharacterized STKs with similarity to the human protein designated as Yank1 or STK32A. The Yank1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine ...
CDD:270731	272	EUK	Invertebrates:6,Plants:7,Primates:1	cd05579, STKc_MAST_like, Catalytic domain of Microtubule-associated serine/threonine (MAST) kinase-like proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes MAST kinases, MAST-like (MASTL) kinases (also called greatwall kinase or Gwl), and fungal kinases with similarity to Saccharomyces cerevisiae Rim15 and Schizosaccharomyces pombe cek1. MAST ...
CDD:270732	290	EUK	Invertebrates:8,Mammals:2,Plants:8,Primates:1,Rodents:1	cd05580, STKc_PKA_like, Catalytic subunit of the Serine/Threonine Kinases, cAMP-dependent protein kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the cAMP-dependent protein kinases, PKA and PRKX, and similar proteins. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active ...
CDD:270733	278	EUK	Invertebrates:10,Plants:5,Primates:1,Vertebrates:1	cd05581, STKc_PDK1, Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PDK1 carries an N-terminal catalytic domain and a C-terminal pleckstrin homology (PH) domain that binds phosphoinositides. It phosphorylates the activation loop of AGC kinases that are regulated by PI3K ...
CDD:270749	333	EUK	Invertebrates:15,Primates:1	cd05598, STKc_LATS, Catalytic domain of the Serine/Threonine Kinase, Large Tumor Suppressor.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LATS was originally identified in Drosophila using a screen for genes whose inactivation led to overproliferation of cells. In tetrapods, there are two LATS isoforms, LATS1 and LATS2. Inactivation of LATS1 in mice results in the development ...
CDD:270750	324	EUK	Invertebrates:15,Plants:9,Primates:1,nodiv:1	cd05599, STKc_NDR_like, Catalytic domain of Nuclear Dbf2-Related kinase-like Protein Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NDR kinases regulate mitosis, cell growth, embryonic development, and neurological processes. They are also required for proper centrosome duplication. Higher eukaryotes contain two NDR isoforms, NDR1 and ...
CDD:270751	386	EUK	Invertebrates:2,Plants:6	cd05600, STKc_Sid2p_like, Catalytic domain of Fungal Sid2p-like Protein Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This group contains fungal kinases including Schizosaccharomyces pombe Sid2p and Saccharomyces cerevisiae Dbf2p. Group members show similarity to NDR kinases in that they contain an N-terminal regulatory (NTR) domain and an insert within ...
CDD:270752	328	EUK	Invertebrates:10,Vertebrates:2	cd05601, STKc_CRIK, Catalytic domain of the Serine/Threonine Kinase, Citron Rho-interacting kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CRIK (also called citron kinase) is an effector of the small GTPase Rho. It plays an important function during cytokinesis and affects its contractile process. CRIK-deficient mice show severe ataxia and epilepsy as a result of ...
CDD:100059	101	PRK	Bacteria:10	cd05635, LbH_unknown, Uncharacterized proteins, Left-handed parallel beta-Helix (LbH) domain: Members in this group are uncharacterized bacterial proteins containing a LbH domain with multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.
CDD:100060	163	PRK	Bacteria:14	cd05636, LbH_G1P_TT_C_like, Putative glucose-1-phosphate thymidylyltransferase, C-terminal Left-handed parallel beta-Helix (LbH) domain: Proteins in this family show simlarity to glucose-1-phosphate adenylyltransferases in that they contain N-terminal catalytic domains that resemble a dinucleotide-binding Rossmann fold and C-terminal LbH fold domains. Members in this family are predicted to be glucose-1-phosphate thymidylyltransferases, which are involved in the ...
CDD:240188	132	PRK	Bacteria:10	cd05637, SIS_PGI_PMI_2, The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the second SIS domain.
CDD:193519	279	PRK	Bacteria:26	cd05640, M28_like_1, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions.
CDD:193520	348	EUKprk	Bacteria:16,Plants:3	cd05642, M28_AAP_like, M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase (AAP)-like.  Peptidase M28 family; Aeromonas (Vibrio) proteolytica aminopeptidase-like (AAP-like; leucine aminopeptidase from Vibrio proteolyticus; Bacterial leucyl aminopeptidase) subfamily. This group includes uncharacterized proteins with predicted aminopeptidase activity. Leucine aminopeptidases, in general play, important roles in many biological processes such ...
CDD:193521	288	PRK	Bacteria:8	cd05643, M28_like_7, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They typically have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This protein subfamily conserves some of the metal-coordinating residues of the ...
CDD:193522	415	PRK	Bacteria:23,nodiv:1	cd05644, M28_like_3, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They typically have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. Proteins in this subfamily conserve some of the metal-coordinating residues ...
CDD:193524	391	EUK	Invertebrates:8,Mammals:1,Plants:3,Vertebrates:1	cd05646, M20_AcylaseI_like, M20 Aminoacylase-I like subfamily.  Peptidase M20 family, Aminoacylase-I like (AcyI-like; Acylase I; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) subfamily. Acylase I is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate) and is considered as a potential target of antimicrobial agents. Porcine AcyI is also shown to deacetylate certain quorum-sensing ...
CDD:193525	345	PRK	Bacteria:10	cd05647, M20_DapE_actinobac, M20 Peptidase actinobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.  Peptidase M20 family, actinobacterial dapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) subfamily. This group is composed of predominantly actinobacterial DapE proteins. DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. It has been shown that DapE is essential for ...
CDD:193526	376	PRK	Bacteria:14	cd05649, M20_ArgE_DapE_like4, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned peptidases. ...
CDD:193527	393	PRK	Bacteria:7	cd05650, M20_ArgE_DapE_like1, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, ...
CDD:193528	342	PRK	Bacteria:15	cd05651, M20_ArgE_DapE_like5, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, ...
CDD:193529	335	EUKprk	Bacteria:4,Invertebrates:2,Plants:13	cd05652, M20_ArgE_DapE_like_fungal, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a ...
CDD:193530	341	PRK	Bacteria:20	cd05653, M20_ArgE_LysK, M20 Peptidase acetylornithine deacetylase/acetyl-lysine deacetylase.  Peptidase M20 family, acetylornithine deacetylase (ArgE)/acetyl-lysine deacetylase (LysK) subfamily.  Proteins in this subfamily are mainly archaeal with related bacterial species and are deacetylases with specificity for both N-acetyl-ornithine and N-acetyl-lysine found within a lysine biosynthesis operon. ArgE catalyzes the conversion of N-acetylornithine to ornithine, ...
CDD:193531	535	PRK	Bacteria:30	cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein, RocB.  Peptidase M20 family, ArgE RocB (Arginine utilization protein, RocB; arginine degradation protein, RocB) subfamily. This group of proteins is possibly related to acetylornithine deacetylase (ArgE) and may be involved in the arginine and/or ornithine degradation pathway. In Bacillus subtilis, RocB is one of the three genes found in the rocABC operon, which is sigma L dependent and induced by ...
CDD:193532	336	PRK	Bacteria:133,Environmental:3	cd05656, M42_Frv, M42 Peptidase, Endoglucanases.  Peptidase M42 family, Frv (Frv Operon Protein; Endo-1 4-Beta-Glucanase; Cellulase Protein; Endoglucanase; Endo-1 4-Beta-Glucanase Homolog; Glucanase; EC. 3.2.1.4) subfamily. Frv is a co-catalytic metallopeptidase, found in archaea and bacteria, including Pyrococcus horikoshii tetrahedral shaped phTET1 (DAPPh1; FrvX; PhDAP aminopeptidase; PhTET aminopeptidase; deblocking aminopeptidase), phTET2 ...
CDD:193533	336	PRK	Bacteria:39	cd05657, M42_glucanase_like, M42 Peptidase, Endoglucanase-like subfamily.  Peptidase M42 family, glucanase (endo-1 4-beta-glucanase or endoglucanase)-like subfamily. Proteins in this subfamily are co-catalytic metallopeptidases, found in archaea and bacteria. They show similarity to cellulase and endo-1,4-beta-glucanase (endoglucanase) which typically bind two zinc or cobalt atoms. Some of the enzymes exhibit typical aminopeptidase specificity, whereas others are ...
CDD:193534	424	EUKprk	Bacteria:64,Invertebrates:12,Plants:18,Vertebrates:3	cd05658, M18_DAP, M18 Peptidase Aspartyl aminopeptidase.  Peptidase M18 family, Aspartyl aminopeptidase (DAP; EC  3.4.11.21) subfamily. DAP is widely distributed in bacteria and eukaryotes, but only the mammalian aspartyl aminopeptidase has been characterized to date. DAP cleaves only unblocked N-terminal acidic amino-acid residues. It is a cytosolic enzyme and is highly conserved; for example, the human enzyme has 51% ...
CDD:193535	443	PRK	Bacteria:26	cd05659, M18_API, M18 Peptidase Aminopeptidase I.  Peptidase M18 family, Aminopeptidase I (Vacuolar aminopeptidase I; Polypeptidase; Leucine aminopeptidase IV; LAPIV; Aminopeptidase III; Aminopeptidase yscI; EC 3.4.11.22) subfamily. Aminopeptidase I is widely distributed in bacteria and eukaryotes, but only the yeast enzyme has been characterized to date. It is a vacuolar enzyme, synthesized as a cytosolic proform, and proteolytically matured upon arrival in the ...
CDD:193536	306	PRK	Bacteria:21,Environmental:1	cd05660, M28_like_PA_1, M28 Zn-Peptidases containing a PA domain insert.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized ...
CDD:193537	305	PRK	Bacteria:8	cd05661, M28_like_PA_2, M28 Zn-Peptidases containing a PA domain insert.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins ...
CDD:193538	267	PRK	Bacteria:19	cd05662, M28_like_2, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins that do not contain a ...
CDD:193539	260	PRK	Bacteria:15,Environmental:1	cd05663, M28_like_PA_PDZ_associated, M28 Zn-Peptidases containing a PA domain insert and associated with a PDZ domain.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. ...
CDD:193540	398	EUKprk	Bacteria:59,Plants:7	cd05664, M20_Acy1_like6, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of proteins predicted as putative amidohydrolases or hippurate hydrolases. These are a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of ...
CDD:193541	415	EUKprk	Bacteria:28,Invertebrates:1	cd05665, M20_Acy1_IAAspH_bact, M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea.  Peptidase M20 family, Bacterial and archaeal Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase (IAA-Asp hydrolase; IAAspH; IAAH; IAA amidohydrolase; EC 3.5.1.-) subfamily. IAAspH hydrolyzes indole-3-acetyl-N-aspartic acid (IAA or auxin) to indole-3-acetic acid. Genes encoding IAA-amidohydrolases were first ...
CDD:193542	373	PRK	Bacteria:79,nodiv:1	cd05666, M20_Acy1_like1, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of bacterial proteins predicted as putative amidohydrolases or hippurate hydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of ...
CDD:193543	402	PRK	Bacteria:21,Environmental:1	cd05667, M20_Acy1_like2, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of bacterial proteins that have been predicted as N-acyl-L-amino acid amidohydrolase (amaA), thermostable carboxypeptidase (cpsA-1, cpsA-2 in Sulfolobus solfataricus) and abgB (aminobenzoyl-glutamate utilization protein B), and generally are involved in the urea cycle and metabolism of amino groups. Aminoacylases 1 (ACY1s) comprise a ...
CDD:193544	374	PRK	Bacteria:20	cd05668, M20_Acy1_like3, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of bacterial uncharacterized proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be ...
CDD:193545	372	PRK	Bacteria:20	cd05669, M20_Acy1_YxeP_like, M20 Peptidase Aminoacyclase-1 YxeP-like proteins, including YxeP, YtnL, YjiB and HipO2.  Peptidase M20 family, Aminoacyclase-1 YxeP-like subfamily including YxeP, YtnL, YjiB and HipO2, most of which have not been well characterized to date. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on ...
CDD:193546	367	PRK	Bacteria:16	cd05670, M20_Acy1_YkuR_like, M20 Peptidase Aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins.  Peptidase M20 family, Aminoacyclase-1 YkuR-like subfamily including YkuR and Ama/HipO/HyuC proteins, most of which have not been well characterized to date. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be ...
CDD:193547	358	miss	miss	cd05672, M20_ACY1L2_like, M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily.  Peptidase M20 family, Aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase)-like subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli , to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate ...
CDD:193548	434	miss	miss	cd05673, M20_Acy1L2_AbgB, M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily.  Peptidase M20 family, ACY1L2 aminobenzoyl-glutamate utilization protein B (AbgB) subfamily. This group contains mostly bacterial amidohydrolases, including gene products of abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate is a natural ...
CDD:193549	441	EUKprk	Bacteria:18,Invertebrates:2,Plants:22,Primates:1,Vertebrates:3	cd05674, M20_yscS, M20 Peptidase, carboxypeptidase yscS.  Peptidase M20 family, yscS (GlyX-carboxypeptidase, CPS1, carboxypeptidase S, carboxypeptidase a, carboxypeptidase yscS, glycine carboxypeptidase)-like subfamily. This group mostly contains proteins that have been uncharacterized to date, but also includes vacuolar proteins involved in nitrogen metabolism which are essential for use of certain peptides ...
CDD:193550	426	EUKprk	Bacteria:24,Plants:1	cd05675, M20_yscS_like, M20 Peptidase, carboxypeptidase yscS-like.  Peptidase M20 family, yscS (GlyX-carboxypeptidase, CPS1, carboxypeptidase S, carboxypeptidase a, carboxypeptidase yscS, glycine carboxypeptidase)-like subfamily. This group contains proteins that have been uncharacterized to date with similarity to vacuolar proteins involved in nitrogen metabolism which are essential for use of certain peptides that are sole nitrogen sources. YscS ...
CDD:193551	466	EUK	Invertebrates:10,Plants:7,Vertebrates:6	cd05676, M20_dipept_like_CNDP, M20 cytosolic nonspecific dipeptidases including anserinase and serum carnosinase.  Peptidase M20 family, CNDP (cytosolic nonspecific dipeptidase) subfamily including anserinase (Xaa-methyl-His dipeptidase, EC 3.4.13.5), 'serum' carnosinase (beta-alanyl-L-histidine dipeptidase; EC 3.4.13.20), and some uncharacterized proteins. Two genes, CN1 and CN2, coding for proteins that degrade carnosine ...
CDD:193552	434	EUK	Plants:10	cd05677, M20_dipept_like_DUG2_type, M20 Defective in Utilization of Glutathione-type peptidases containing WD repeats.  Peptidase M20 family, Defective in Utilization of Glutathione (DUG2) subfamily. DUG2-type proteins are metallopeptidases containing WD repeats at the N-terminus. DUG2 proteins are involved in the alternative pathway of glutathione (GSH) degradation. GSH, the major low-molecular-weight thiol compound in most eukaryotic cells, is normally degraded ...
CDD:193553	466	PRK	Bacteria:12	cd05678, M20_dipept_like_1, Uncharacterized M20 Dipeptidases.  Peptidase M20 family, unknown dipeptidase-like subfamily 1 (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and  canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly ...
CDD:193554	447	PRK	Bacteria:9	cd05679, M20_dipept_like_2, Uncharacterized M20 Dipeptidases.  Peptidase M20 family, unknown dipeptidase-like subfamily 2 (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and  canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly ...
CDD:193555	437	PRK	Bacteria:46	cd05680, M20_dipept_like_3, Uncharacterized M20 Dipeptidases.  Peptidase M20 family, unknown dipeptidase-like subfamily 3 (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and  canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly ...
CDD:193556	430	PRK	Bacteria:25	cd05681, M20_dipept_like_4, Uncharacterized M20 Dipeptidases.  Peptidase M20 family, unknown dipeptidase-like subfamily 3 (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and  canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly ...
CDD:193557	451	EUKprk	Bacteria:9,Invertebrates:6	cd05682, M20_dipept_like_5, Uncharacterized M20 Dipeptidases.  Peptidase M20 family, unknown dipeptidase-like subfamily 3 (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and  canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, ...
CDD:193558	366	PRK	Bacteria:44	cd05683, M20_peptT_like, M20 Peptidase T like enzymes specifically cleave tripeptides.  Peptidase M20 family, PeptT (tripeptide aminopeptidase; tripeptidase)-like subfamily. This group includes bacterial tripeptidases as well as predicted tripeptidases. Peptidase T acts only on tripeptide substrates, and is thus called a tripeptidase. It catalyzes the release of N-terminal amino acids with hydrophobic side chains from tripeptides with high specificity; dipeptides, ...
CDD:240189	79	EUK	Invertebrates:8,Plants:12,Primates:1,Vertebrates:3	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The  N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide.  The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
CDD:240190	68	EUKprk	Bacteria:16,Invertebrates:5,Primates:1,Vertebrates:2	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined ...
CDD:240192	70	PRK	Bacteria:16	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is ...
CDD:240193	68	PRK	Bacteria:5	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found ...
CDD:240196	73	PRK	Bacteria:9	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found ...
CDD:240198	100	EUK	Invertebrates:6,Plants:11,Vertebrates:1	cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought ...
CDD:240199	74	EUK	Invertebrates:2,Plants:1	cd05694, S1_Rrp5_repeat_hs2_sc2, S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in ...
CDD:240200	66	miss	miss	cd05695, S1_Rrp5_repeat_hs3, S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein ...
CDD:240201	71	EUK	Plants:2	cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein ...
CDD:240202	69	EUK	Plants:3	cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein ...
CDD:240203	70	EUK	Invertebrates:1	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in ...
CDD:240207	70	EUK	Plants:1	cd05702, S1_Rrp5_repeat_hs11_sc8, S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in ...
CDD:240208	73	EUK	Plants:4	cd05703, S1_Rrp5_repeat_hs12_sc9, S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in ...
CDD:240211	73	EUK	Plants:2	cd05706, S1_Rrp5_repeat_sc10, S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein ...
CDD:100078	180	EUKprk	Bacteria:215,Environmental:4,Invertebrates:4,Plants:5,Primates:1,Vertebrates:3,nodiv:1	cd05709, S2P-M50, Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic ...
CDD:240214	120	PRK	Bacteria:10	cd05710, SIS_1, A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
CDD:143188	94	miss	miss	cd05711, Ig_FcalphaRI, Immunoglobulin (IG)-like domain of of FcalphaRI.  IG_FcalphaRI : immunoglobulin (IG)-like domain of of FcalphaRI. FcalphaRI (CD89) is an IgA-specific receptor that is expressed on monocytes, eosinophils, neutrophils and macrophages. FcalphaRI mediates IgA-induced immune effector responses such as phagocytosis, antibody-dependent cell-mediated cytotoxicity and respiratory burst. Both monomeric and dimeric IgA can bind to FcalphaRI, and monomeric or ...
CDD:143190	100	miss	miss	cd05713, Ig_MOG_like, Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG).  Ig_MOG_like:  immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the ...
CDD:143191	106	miss	miss	cd05714, Ig_CSPGs_LP, Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP) and similar proteins.  Ig_CSPGs_LP: immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP).  Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a ...
CDD:143192	116	miss	miss	cd05715, Ig_P0-like, Immunoglobulin (Ig)-like domain of Protein zero (P0) and similar proteins.  Ig_P0ex-like: domain similar to the immunoglobulin (Ig) domain of Protein zero (P0). P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, ...
CDD:143193	98	miss	miss	cd05716, Ig_pIgR, Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR).  Ig_pIgR: Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR). pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their c-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into ...
CDD:143195	98	miss	miss	cd05718, Ig1_PVR_like, First immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155) and similar proteins.  Ig1_PVR_like: domain similar to the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of ...
CDD:143196	95	miss	miss	cd05719, Ig2_PVR_like, Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155) and similar proteins.  Ig2_PVR_like: domain similar to the second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes ...
CDD:143206	85	miss	miss	cd05729, Ig2_FGFR_like, Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor and similar proteins.  Ig2_FGFR_like: domain similar to the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, -2, -3, -4). Receptor diversity ...
CDD:143208	71	miss	miss	cd05731, Ig3_L1-CAM_like, Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM).  Ig3_L1-CAM_like: domain similar to the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed ...
CDD:143210	77	miss	miss	cd05733, Ig6_L1-CAM_like, Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins.  Ig6_L1-CAM_like: domain similar to the sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM).  L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is ...
CDD:143218	92	miss	miss	cd05741, Ig_CEACAM_D1_like, First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins.  Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily-like. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is ...
CDD:143219	84	miss	miss	cd05742, Ig1_VEGFR_like, First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and similar proteins.  Ig1_VEGFR_like: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R) related proteins. The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family ...
CDD:143225	74	miss	miss	cd05748, Ig_Titin_like, Immunoglobulin (Ig)-like domain of titin and similar proteins.  Ig_Titin_like: immunoglobulin (Ig)-like domain found in titin-like proteins. Titin (also called connectin) is a fibrous sarcomeric protein specifically found in vertebrate striated muscle. Titin is gigantic, depending on isoform composition it ranges from 2970 to 3700 kDa, and is of a length that spans half a sarcomere. Titin largely consists of multiple repeats of Ig-like and ...
CDD:143229	78	miss	miss	cd05752, Ig1_FcgammaR_like, Frst immunoglobulin (Ig)-like domain of  Fcgamma-receptors (FcgammaRs) and similar proteins.  Ig1_FcgammaR_like: domain similar to the first immunoglobulin (Ig)-like domain of  Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity ...
CDD:143230	83	miss	miss	cd05753, Ig2_FcgammaR_like, Second immunoglobulin (Ig)-like domain of  Fcgamma-receptors (FcgammaRs) and similar proteins.  Ig2_FcgammaR_like: domain similar to the second immunoglobulin (Ig)-like domain of  Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity ...
CDD:143233	94	miss	miss	cd05756, Ig1_IL1R_like, First immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R) and similar proteins.  Ig1_IL1R_like: domain similar to the first immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with an accessory ...
CDD:143234	92	miss	miss	cd05757, Ig2_IL1R_like, Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R) and similar proteins.  Ig2_IL1R_like: domain similar to the second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R).  IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with an ...
CDD:143238	82	miss	miss	cd05761, Ig2_Necl-1-4_like, Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4 (also known as cell adhesion molecules CADM3, CADM1, CADM2, and CADM4, respectively).  Ig2_Necl-1-4_like: domain similar to the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2) and Necl-4 (CADM4). These nectin-like molecules have similar domain structures ...
CDD:143243	94	miss	miss	cd05766, IgC_MHC_II_beta, Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain.  IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain.  MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for ...
CDD:143244	94	miss	miss	cd05767, IgC_MHC_II_alpha, Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain.  IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain.  MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), ...
CDD:143245	102	miss	miss	cd05768, IgC_CH4, CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin.  IgC_CH4: The fourth immunoglobulin constant domain (IgC), of immunoglobulin (Ig) heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are ...
CDD:143246	115	EUK	Primates:1	cd05769, IgC_TCR_beta, T cell receptor (TCR) beta chain constant immunoglobulin domain.  IgC_TCR_beta: Constant domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments ...
CDD:143251	105	miss	miss	cd05774, Ig_CEACAM_D1, First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM).  IG_CEACAM_D1: immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and ...
CDD:143252	97	miss	miss	cd05775, Ig_SLAM-CD84_like_N, N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like.  Ig_SLAM-CD84_like_N: The N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. Members of this group include proteins such as CD84, SLAM ...
CDD:99819	234	EUK	Invertebrates:11,Plants:9,Vertebrates:2	cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase.  The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha.  DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been ...
CDD:99820	230	EUK	Invertebrates:5,Plants:5	cd05777, DNA_polB_delta_exo, DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase.  The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as ...
CDD:99821	231	EUK	Invertebrates:3,Plants:12	cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase.  The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to ...
CDD:99822	204	EUK	Invertebrates:8,Plants:5,Vertebrates:2	cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase.  The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have ...
CDD:99824	188	PRK	Bacteria:5	cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases.  The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA ...
CDD:99825	208	PRK	Bacteria:31	cd05782, DNA_polB_like1_exo, Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases.  A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This ...
CDD:99826	204	PRK	Bacteria:2	cd05783, DNA_polB_B1_exo, DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases.  The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. ...
CDD:99827	193	PRK	Bacteria:6	cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases.  The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This ...
CDD:100061	79	EUK	Invertebrates:3,Plants:15	cd05787, LbH_eIF2B_epsilon, eIF-2B epsilon subunit, central Left-handed parallel beta-Helix (LbH) domain: eIF-2B is a eukaryotic translation initiator, a guanine nucleotide exchange factor (GEF) composed of five different subunits (alpha, beta, gamma, delta and epsilon). eIF2B is important for regenerating GTP-bound eIF2 during the initiation process. This event is obligatory for eIF2 to bind initiator methionyl-tRNA, forming the ternary initiation ...
CDD:240215	86	EUKprk	Bacteria:6,Invertebrates:12,Plants:5,Vertebrates:2	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of ...
CDD:240216	86	EUK	Invertebrates:9,Plants:6,Vertebrates:3	cd05790, S1_Rrp40, S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA ...
CDD:240217	92	EUK	Invertebrates:8,Plants:6,Vertebrates:2	cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA ...
CDD:240219	77	EUKprk	Bacteria:14,Invertebrates:12,Plants:7,Vertebrates:3	cd05793, S1_IF1A, S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of ...
CDD:240220	56	miss	miss	cd05794, S1_EF-P_repeat_2, S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 ...
CDD:240221	175	miss	miss	cd05795, Ribosomal_P0_L10e, Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as ...
CDD:240222	163	miss	miss	cd05796, Ribosomal_P0_like, Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies ...
CDD:240223	157	miss	miss	cd05797, Ribosomal_L10, Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The ...
CDD:100092	487	EUKprk	Bacteria:79,Environmental:1,Invertebrates:14,Plants:9,Vertebrates:3	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose ...
CDD:100093	461	PRK	Bacteria:29,Environmental:1	cd05800, PGM_like2, This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), ...
CDD:100094	522	PRK	Bacteria:8	cd05801, PGM_like3, This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the ...
CDD:100095	434	PRK	Bacteria:61	cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-acetylglucosamine, an essential precursor to components of the cell envelope.  In order to be active, GlmM must be phosphorylated, which can occur via autophosphorylation or by the Ser/Thr kinase StkP. GlmM ...
CDD:100096	445	EUKprk	Bacteria:4,Invertebrates:3	cd05803, PGM_like4, This PGM-like (phosphoglucomutase-like) domain is located C-terminal to a mannose-1-phosphate guanyltransferase domain in a protein of unknown function that is found in both prokaryotes and eukaryotes. This domain belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include ...
CDD:100115	355	EUKprk	Bacteria:26,Invertebrates:2,Plants:4,Primates:1,Vertebrates:3	cd05804, StaR_like, StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing ...
CDD:100097	441	PRK	Bacteria:17	cd05805, MPG1_transferase, GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity.  The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily.  This subfamily is limited to bacteria and ...
CDD:99883	95	EUKprk	Bacteria:8,Plants:6	cd05808, CBM20_alpha_amylase, Alpha-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in several bacterial and fungal alpha-amylases including the maltopentaose-forming amylases (G5-amylases). Most alpha-amylases have, in addition to the C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13, which hydrolyzes internal alpha-1,4-glucosidic bonds in starch and related ...
CDD:99885	97	PRK	Bacteria:11	cd05810, CBM20_alpha_MTH, Glucan 1,4-alpha-maltotetraohydrolase (alpha-MTH), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Alpha-MTH, also known as maltotetraose-forming exo-amylase or G4-amylase, is an exo-amylase found in bacteria that degrades starch from its non-reducing end. Most alpha-MTHs have, in addition to the C-terminal CBM20 domain, an N-terminal glycosyl hydrolase family 13 catalytic domain. The CBM20 domain is found in a large number ...
CDD:99886	106	EUK	Plants:19	cd05811, CBM20_glucoamylase, Glucoamylase (glucan1,4-alpha-glucosidase), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Glucoamylases are inverting, exo-acting starch hydrolases that hydrolyze starch and related polysaccharides by releasing the nonreducing end glucose. They are mainly active on alpha-1,4-glycosidic bonds but also have some activity towards 1,6-glycosidic bonds occurring in natural oligosaccharides. The ability of glucoamylases to ...
CDD:99888	120	EUK	Invertebrates:5,Vertebrates:3	cd05814, CBM20_Prei4, Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 contains a C-terminal glycerophosphoryl diester phosphodiesterase (GDPD) domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, ...
CDD:99890	99	EUKprk	Bacteria:3,Invertebrates:3,Plants:3	cd05816, CBM20_DPE2_repeat2, Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 2. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on the pathway from starch to sucrose and DPE2 is thought to metabolize the maltose that is exported from the chloroplast. DPE2 has two N-terminal CBM20 domains as ...
CDD:271320	269	EUKprk	Bacteria:103,Environmental:1,Invertebrates:9,Plants:4,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	cd05819, NHL, NHL repeat unit of beta-propeller proteins.  The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the ...
CDD:100114	112	EUKprk	Bacteria:38,Invertebrates:5,Mammals:1,Plants:9,Rodents:1,Vertebrates:2	cd05822, TLP_HIUase, HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). HIUase has high sequence similarity with transthyretins and is a member of the transthyretin-like protein (TLP) family.   HIUase is ...
CDD:100063	107	PRK	Bacteria:24	cd05825, LbH_wcaF_like, wcaF-like: This group is composed of the protein product of the E. coli wcaF gene and similar proteins. WcaF is part of the gene cluster responsible for the biosynthesis of the extracellular polysaccharide colanic acid. The wcaF protein is predicted to contain a left-handed parallel beta-helix (LbH) domain encoded by imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats ...
CDD:99709	209	PRK	Bacteria:33	cd05826, Sortase_B_2, Sortase B (SrtB) or subfamily-2 sortases are membrane cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes ...
CDD:99710	131	PRK	Bacteria:33	cd05827, Sortase_C_3, Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes ...
CDD:99711	127	PRK	Bacteria:30	cd05828, Sortase_D_4, Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, ...
CDD:99712	144	PRK	Bacteria:28	cd05829, Sortase_E, Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function ...
CDD:99713	137	PRK	Bacteria:21	cd05830, Sortase_D_5, Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, ...
CDD:100109	103	EUK	Invertebrates:29,Plants:11,Primates:1,Rodents:1,Vertebrates:3	cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. ...
CDD:100111	109	EUK	Invertebrates:29,Plants:12,Primates:1,Vertebrates:3	cd05833, Ribosomal_P2, Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data ...
CDD:99895	83	EUK	Invertebrates:7,Plants:2,Rodents:1,Vertebrates:4	cd05834, HDGF_related, The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a ...
CDD:99896	87	EUK	Invertebrates:4,Primates:1,Vertebrates:3	cd05835, Dnmt3b_related, The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis.  In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes.  In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome ...
CDD:99898	110	EUK	Invertebrates:4,Primates:1,Vertebrates:2	cd05837, MSH6_like, The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS.   The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans.  The role of the PWWP domain in MSH6 is not clear; MSH6 ...
CDD:99899	95	EUK	Invertebrates:6,Plants:2,Vertebrates:1	cd05838, WHSC1_related, The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS).  When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain.  The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting ...
CDD:99901	93	EUK	Plants:13	cd05840, SPBC215_ISWI_like, The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4.  The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin.   The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in ...
CDD:99902	83	EUK	Invertebrates:3,Primates:1,Vertebrates:2	cd05841, BS69_related, The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions.  BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains.  The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other ...
CDD:100003	367	PRK	Bacteria:20	cd05844, GT1_like_7, Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked ...
CDD:143254	97	miss	miss	cd05846, Ig1_MRC-OX-2_like, First immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200) and similar proteins.  Ig1_ MRC-OX-2_like: domain similar to the first immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200). MRC OX-2 is a membrane glycoprotein expressed in a variety of lymphoid and non-lymphoid cells in rats. It has a similar broad distribution pattern in humans. MRC OX-2 may regulate myeloid cell activity. The protein has an ...
CDD:143255	94	miss	miss	cd05847, IgC_CH2_IgE, CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE).  IgC_CH2_IgE: The second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five types of heavy ...
CDD:143279	91	miss	miss	cd05871, Ig_Semaphorin_classIII, Immunoglobulin (Ig)-like domain of class III semaphorin.  Ig_Semaphorin_class III; Immunoglobulin (Ig)-like domain of class III semaphorins. Semaphorins are classified into various classes on the basis of structural features additional to the Sema domain. Class III semaphorins are a vertebrate class having a Sema domain, an Ig domain, a short basic domain, and are secreted. They have been shown to be axonal guidance cues and have a part in ...
CDD:143280	85	miss	miss	cd05872, Ig_Sema4B_like, Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.  Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of Sema4B_like. Sema4B is a Class IV semaphorin. Semaphorins are classified based on structural features additional to the Sema domain. Sema4B has extracellular Sema and Ig domains, a transmembrane domain and a short cytoplasmic domain. Sema4B has been shown to preferentially regulate the development of the postsynaptic ...
CDD:143285	106	miss	miss	cd05877, Ig_LP_like, Immunoglobulin (Ig)-like domain of human cartilage link protein (LP).  Ig_LP_like: immunoglobulin (Ig)-like domain similar to that that found in human cartilage link protein (LP). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may ...
CDD:143286	110	miss	miss	cd05878, Ig_Aggrecan_like, Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core protein (CSPG).  Ig_Aggrecan_like: immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core protein (CSPG)s. Included in this group are the Ig domains of other CSPGs: versican, and neurocan. In CSPGs this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth ...
CDD:143307	110	miss	miss	cd05899, IgV_TCR_beta, Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) bet a chain.  IgV_TCR_beta: immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. ...
CDD:213271	437	PRK	Bacteria:22	cd05903, CHC_CoA_lg, Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase).  Cyclohexanecarboxylate-CoA ligase activates the aliphatic ring compound, cyclohexanecarboxylate, for degradation. It catalyzes the synthesis of cyclohexanecarboxylate-CoA thioesters in a two-step reaction involving the formation of cyclohexanecarboxylate-AMP anhydride, followed by the nucleophilic substitution of AMP by CoA.
CDD:213272	504	EUKprk	Bacteria:4,Plants:5	cd05904, 4CL, 4-Coumarate-CoA Ligase (4CL).  4-Coumarate:coenzyme A ligase is a key enzyme in the phenylpropanoid metabolic pathway for monolignol and flavonoid biosynthesis. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters in a two-step reaction, involving the formation of hydroxycinnamate-AMP anhydride and the nucleophilic substitution of AMP by CoA. The phenylpropanoid pathway is one of the most important secondary metabolism pathways in ...
CDD:213274	560	EUKprk	Bacteria:14,Plants:2	cd05906, A_NRPS_TubE_like, The adenylation domain (A domain) of a family of nonribosomal peptide synthetases (NRPSs) synthesizing toxins and antitumor agents.  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This ...
CDD:213275	456	EUKprk	Bacteria:49,Plants:2,Vertebrates:1	cd05907, VL_LC_FACS_like, Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases.  This family includes long-chain fatty acid (C12-C20) CoA synthetases and Bubblegum-like very long-chain (>C20) fatty acid CoA synthetases. FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. ...
CDD:213276	499	PRK	Bacteria:9	cd05908, A_NRPS_MycA_like, The adenylation domain of nonribosomal peptide synthetases (NRPS) similar to mycosubtilin synthase subunit A (MycA).  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family includes NRPS similar to ...
CDD:213277	489	PRK	Bacteria:12	cd05909, AAS_C, C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas).  Acyl-acyl carrier protein synthase (Aas) is a membrane protein responsible for a minor pathway of incorporating exogenous fatty acids into membrane phospholipids. Its in vitro activity is characterized by the ligation of free fatty acids between 8 and 18 carbons in length to the acyl carrier protein sulfydryl group ...
CDD:213278	455	PRK	Bacteria:6	cd05910, FACL_like_1, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
CDD:213279	487	EUK	Invertebrates:6,Plants:4	cd05911, Firefly_Luc_like, Firefly luciferase of light emitting insects and 4-Coumarate-CoA Ligase (4CL).  This family contains two functionally unique groups of proteins; one group is insect firefly luciferases and the other is plant 4-coumarate:coenzyme A ligases. However, they share significant sequence similarity in spite of their functional diversity. Luciferase catalyzes the production of light in the presence of MgATP, molecular oxygen, and ...
CDD:213280	407	PRK	Bacteria:31	cd05912, OSB_CoA_lg, O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE).  O-succinylbenzoic acid-CoA synthase catalyzes the coenzyme A (CoA)- and ATP-dependent conversion of o-succinylbenzoic acid to o-succinylbenzoyl-CoA. The reaction is the fourth step of the biosynthesis pathway of menaquinone (vitamin K2). In certain bacteria, menaquinone is used during fumarate reduction in anaerobic respiration. In ...
CDD:213282	448	PRK	Bacteria:13	cd05914, FACL_like_3, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
CDD:213284	347	EUKprk	Bacteria:35,Environmental:2,Invertebrates:2,Plants:1,Primates:1,Vertebrates:1	cd05917, FACL_like_2, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most ...
CDD:213285	447	EUKprk	Bacteria:10,Plants:10	cd05918, A_NRPS_SidN3_like, The adenylation (A) domain of siderophore-synthesizing nonribosomal peptide synthetases (NRPS).  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family of siderophore-synthesizing NRPS ...
CDD:213286	436	PRK	Bacteria:8	cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate forming enzymes.  This family contains benzoate CoA ligase (BCL) and related ligases that catalyze the acylation of benzoate derivatives, 2-aminobenzoate and 4-hydroxybenzoate. Aromatic compounds represent the second most abundant class of organic carbon compounds after carbohydrates. Xenobiotic aromatic compounds are also a major class of man-made pollutants. Some bacteria use benzoate as the sole ...
CDD:213287	483	PRK	Bacteria:24	cd05920, 23DHB-AMP_lg, 2,3-dihydroxybenzoate-AMP ligase.  2,3-dihydroxybenzoate-AMP ligase activates 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. However, it can also catalyze the ATP-PPi exchange for 2,3-DHB analogs, such as salicyclic acid (o-hydrobenzoate), as well as 2,4-DHB and 2,5-DHB, but with less efficiency. Proteins in this family are the stand-alone adenylation components of non-ribosomal peptide synthases ...
CDD:213288	559	PRK	Bacteria:5	cd05921, FCS, Feruloyl-CoA synthetase (FCS).  Feruloyl-CoA synthetase is an essential enzyme in the feruloyl acid degradation pathway and enables some proteobacteria to grow on media containing feruloyl acid as the sole carbon source. It catalyzes the transfer of CoA to the carboxyl group of ferulic acid, which then forms feruloyl-CoA in the presence of ATP and Mg2. The resulting feruloyl-CoA is further degraded to vanillin and acetyl-CoA. Feruloyl-CoA synthetase ...
CDD:213289	350	PRK	Bacteria:17	cd05922, FACL_like_6, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
CDD:213291	365	PRK	Bacteria:5,Environmental:1	cd05924, FACL_like_5, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
CDD:213292	345	EUKprk	Bacteria:13,Plants:6	cd05926, FACL_fum10p_like, Subfamily of fatty acid CoA ligase (FACL) similar to Fum10p of Gibberella moniliformis.  FACL catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, followed by the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Fum10p is a fatty acid CoA ligase involved in the ...
CDD:213293	539	EUK	Invertebrates:6,Plants:7,Primates:1,Vertebrates:3	cd05927, LC-FACS_euk, Eukaryotic long-chain fatty acid CoA synthetase (LC-FACS).  The members of this family are eukaryotic fatty acid CoA synthetases that activate fatty acids with chain lengths of 12 to 20. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. This is a required step before free fatty ...
CDD:213295	342	PRK	Bacteria:63,Environmental:1	cd05929, BACL_like, Bacterial Bile acid CoA ligases and similar proteins.  Bile acid-Coenzyme A ligase catalyzes the formation of bile acid-CoA conjugates in a two-step reaction: the formation of a bile acid-AMP molecule as an intermediate, followed by the formation of a bile acid-CoA. This ligase requires a bile acid with a free carboxyl group, ATP, Mg2+, and CoA for synthesis of the final bile acid-CoA conjugate. The bile acid-CoA ligation is ...
CDD:213296	445	EUKprk	Bacteria:126,Invertebrates:2,Plants:3	cd05930, A_NRPS, The adenylation domain of nonribosomal peptide synthetases (NRPS).  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many ...
CDD:213297	547	EUKprk	Bacteria:63,Plants:2,nodiv:1	cd05931, FAAL, Fatty acyl-AMP ligase (FAAL).  FAAL belongs to the class I adenylate forming enzyme family and is homologous to fatty acyl-coenzyme A (CoA) ligases (FACLs). However, FAALs produce only the acyl adenylate and are unable to perform the thioester-forming reaction, while FACLs perform a two-step catalytic reaction; AMP ligation followed by CoA ligation using ATP and CoA as cofactors. FAALs have insertion motifs between the N-terminal ...
CDD:213298	504	PRK	Bacteria:14	cd05932, LC_FACS_bac, Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase.  The members of this family are bacterial long-chain fatty acid CoA synthetase. Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase in this family is involved in the synthesis of isoprenoid wax ester storage compounds when grown on phytol as the sole carbon source. LC-FACS catalyzes the ...
CDD:213300	421	PRK	Bacteria:32	cd05934, FACL_DitJ_like, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Members of this family include ...
CDD:213301	430	PRK	Bacteria:4	cd05935, LC_FACS_like, Putative long-chain fatty acid CoA ligase.  The members of this family are putative long-chain fatty acyl-CoA synthetases, which catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological ...
CDD:213302	468	PRK	Bacteria:41	cd05936, FC-FACS_FadD_like, Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD.  This subfamily of the AMP-forming adenylation family contains Escherichia coli FadD and similar prokaryotic fatty acid CoA synthetases. FadD was characterized as a long-chain fatty acid CoA synthetase. The gene fadD is regulated by the fatty acid regulatory protein FadR. Fatty acid CoA synthetase catalyzes the formation of fatty acyl-CoA in a two-step ...
CDD:213306	444	EUKprk	Bacteria:9,Environmental:1,Plants:1,Rodents:1	cd05940, FATP_FACS, Fatty acid transport proteins (FATP) play dual roles as fatty acid transporters and its activation enzymes.  Fatty acid transport protein (FATP) transports long-chain or very-long-chain fatty acids across the plasma membrane. FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. At least five copies of FATPs are identified in ...
CDD:213307	430	EUKprk	Bacteria:11,Invertebrates:2,Plants:5,Primates:1,Vertebrates:2	cd05941, MCS, Malonyl-CoA synthetase (MCS).  MCS catalyzes the formation of malonyl-CoA in a two-step reaction consisting of the adenylation of malonate with ATP, followed by malonyl transfer from malonyl-AMP to CoA. Malonic acid and its derivatives are the building blocks of polyketides and malonyl-CoA serves as the substrate of polyketide synthases. Malonyl-CoA synthetase has broad substrate tolerance and can ...
CDD:213308	616	EUKprk	Bacteria:3,Invertebrates:1,Plants:2,Primates:1,Vertebrates:3	cd05943, AACS, Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS).  AACS is a cytosolic ligase that specifically activates acetoacetate to its coenzyme A ester by a two-step reaction. Acetoacetate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is the first step of the mevalonate pathway of isoprenoid biosynthesis via isopentenyl ...
CDD:213309	359	PRK	Bacteria:6	cd05944, FACL_like_4, Uncharacterized subfamily of fatty acid CoA ligase (FACL).  Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
CDD:213310	447	PRK	Bacteria:34	cd05945, DltA, D-alanine:D-alanyl carrier protein ligase (DltA).  DltA belongs to the class I AMP-forming adenylation domain superfamily, which also includes acetyl-CoA synthetase, luciferase, and the adenylation domains of non-ribosomal synthetases. It catalyzes the two-step activation reaction of D-alanine: the formation of a substrate-AMP molecule as an intermediate, and then the transfer of the amino acid adenylate to teichoic acid in the biosynthesis of ...
CDD:213312	506	PRK	Bacteria:9	cd05959, BCL_4HBCL, Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase).  Benzoate CoA ligase and 4-hydroxybenzoate-coenzyme A ligase catalyze the first activating step for benzoate and 4-hydroxybenzoate catabolic pathways, respectively. Although these two enzymes share very high sequence homology, they have their own substrate preference. The reaction proceeds via a two-step process; the first ATP-dependent step forms the ...
CDD:213313	602	EUKprk	Bacteria:18,Invertebrates:4,Plants:4,Primates:1,Vertebrates:1	cd05966, ACS, Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme).  Acetyl-CoA synthetase (ACS) catalyzes the formation of acetyl-CoA from acetate, CoA, and ATP. Synthesis of acetyl-CoA is carried out in a two-step reaction. In the first step, the enzyme catalyzes the synthesis of acetyl-AMP intermediate from acetate and ATP. In the second step, acetyl-AMP reacts with CoA to ...
CDD:213314	607	EUKprk	Bacteria:3,Invertebrates:3,Primates:1,Vertebrates:1	cd05967, PrpE, Propionyl-CoA synthetase (PrpE).  PrpE catalyzes the first step of the 2-methylcitric acid cycle for propionate catabolism. It activates propionate to propionyl-CoA in a two-step reaction, which proceeds through a propionyl-AMP intermediate and requires ATP and Mg2+. In Salmonella enterica, the PrpE protein is required for growth of S. enterica on propionate and can substitute for the acetyl-CoA synthetase ...
CDD:213315	474	PRK	Bacteria:13	cd05968, AACS_like, Uncharacterized acyl-CoA synthetase subfamily similar to Acetoacetyl-CoA synthetase.  This uncharacterized acyl-CoA synthetase family is highly homologous to acetoacetyl-CoA synthetase. However, the proteins in this family exist in only bacteria and archaea. AACS is a cytosolic ligase that specifically activates acetoacetate to its coenzyme A ester by a two-step reaction. Acetoacetate first reacts with ATP to form an acyl-adenylate intermediate, ...
CDD:213318	439	PRK	Bacteria:9	cd05971, MACS_like_3, Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS).  MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria.
CDD:213319	430	EUKprk	Bacteria:5,Primates:1	cd05972, MACS_like, Medium-chain acyl-CoA synthetase (MACS or ACSM).  MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The acyl-CoA is a key intermediate in many important biosynthetic and catabolic processes.
CDD:99716	81	EUK	Invertebrates:14,Mammals:1,Plants:27,Primates:2,Rodents:2,Vertebrates:6	cd05992, PB1, The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring ...
CDD:100076	59	miss	miss	cd06006, R3H_unknown_2, R3H domain of a group of fungal proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA  or ssRNA in a sequence-specific manner.
CDD:100077	59	miss	miss	cd06007, R3H_DEXH_helicase, R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
CDD:100116	49	EUK	Invertebrates:20,Plants:15,Primates:1,Vertebrates:2	cd06008, NF-X1-zinc-finger, Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II ...
CDD:100023	382	EUKprk	Bacteria:1,Invertebrates:4,Plants:1	cd06059, Tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly.  The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, ...
CDD:100024	493	EUK	Invertebrates:6,Plants:1,Vertebrates:2	cd06060, misato, Human Misato shows similarity with Tubulin/FtsZ family of GTPases and is localized to the the outer membrane of mitochondria. It has a role in mitochondrial fusion and in mitochondrial distribution and morphology. Mutations in its Drosophila homolog (misato) lead to irregular chromosome segregation during mitosis. Deletion of the budding yeast homolog DML1 is lethal and unregulate expression of DML1 leads to mitochondrial ...
CDD:100037	298	PRK	Bacteria:34	cd06061, PurM-like1, AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
CDD:99873	146	miss	miss	cd06062, H2MP_MemB-H2up, Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel ...
CDD:99875	150	miss	miss	cd06064, H2MP_F420-Reduc, Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to ...
CDD:99876	139	miss	miss	cd06066, H2MP_NAD-link-bidir, Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the ...
CDD:99877	136	miss	miss	cd06067, H2MP_MemB-H2evol, Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by ...
CDD:99878	144	miss	miss	cd06068, H2MP_like-1, Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal ...
CDD:100117	275	EUK	Invertebrates:16,Plants:7,Rodents:1,Vertebrates:3	cd06071, Beach, BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and ...
CDD:240505	38	EUK	Invertebrates:28,Plants:21,Vertebrates:3	cd06081, KOW_Spt5_1, KOW domain of Spt5, repeat 1.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher ...
CDD:240506	51	EUK	Invertebrates:5,Mammals:1,Plants:20	cd06082, KOW_Spt5_2, KOW domain of Spt5, repeat 2.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic ...
CDD:240507	51	EUK	Invertebrates:4,Plants:9	cd06083, KOW_Spt5_3, KOW domain of Spt5, repeat 3.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 ...
CDD:240508	43	EUK	Invertebrates:4,Plants:7	cd06084, KOW_Spt5_4, KOW domain of Spt5, repeat 4.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 ...
CDD:240509	52	EUK	Plants:10,Vertebrates:1	cd06085, KOW_Spt5_5, KOW domain of Spt5, repeat 5.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins ...
CDD:240510	58	EUK	Invertebrates:6,Plants:3,nodiv:1	cd06086, KOW_Spt5_6, KOW domain of Spt5, repeat 6.  Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 ...
CDD:240511	55	EUKprk	Bacteria:15,Environmental:1,Invertebrates:27,Plants:22,Primates:2,Vertebrates:3	cd06087, KOW_RPS4, KOW motif of Ribosomal Protein S4 (RPS4).  RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the ...
CDD:240512	76	EUKprk	Bacteria:83,Invertebrates:33,Plants:22,Primates:1,Vertebrates:3,nodiv:1	cd06088, KOW_RPL14, KOW motif of Ribosomal Protein L14.  RPL14 is a component of the large ribosomal subunit in both archaea and eukaryotes with KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher ...
CDD:240513	65	EUKprk	Bacteria:138,Environmental:5,Invertebrates:39,Mammals:2,Plants:49,Primates:1,Vertebrates:6,nodiv:1	cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26.  RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic ...
CDD:240514	83	EUK	Invertebrates:28,Mammals:1,Plants:21,Vertebrates:4	cd06090, KOW_RPL27, KOW motif of eukaryotic Ribosomal Protein L27.  RPL27e has a KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. .
CDD:240515	56	EUKprk	Bacteria:196,Plants:5,nodiv:2	cd06091, KOW_NusG, NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus.  KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic ...
CDD:132768	106	EUK	Invertebrates:22,Plants:27,Primates:2,Rodents:2,Vertebrates:3	cd06093, PX_domain, The Phox Homology domain, a phosphoinositide binding module.  The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B ...
CDD:133158	89	EUK	Invertebrates:4,Vertebrates:1	cd06094, RP_Saci_like, RP_Saci_like, retropepsin family.  Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one ...
CDD:133159	86	EUKprk	Invertebrates:2,Mammals:2,Primates:1,Vertebrates:1,Viruses:2	cd06095, RP_RTVL_H_like, Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements.  This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal ...
CDD:133160	326	EUK	Invertebrates:7	cd06096, Plasmepsin_5, Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite.  The family contains a group of aspartic proteinases homologous to plasmepsin 5.  Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins ...
CDD:133161	278	EUK	Plants:15	cd06097, Aspergillopepsin_like, Aspergillopepsin_like, aspartic proteases of fungal origin.  The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive ...
CDD:99853	213	EUKprk	Bacteria:8,Mammals:1,Plants:1,Vertebrates:1	cd06099, CS_ACL-C_CCL, Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved ...
CDD:99854	227	EUKprk	Bacteria:15,Invertebrates:7,Plants:5,Primates:1,Vertebrates:3	cd06100, CCL_ACL-C, Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely ...
CDD:99855	265	EUKprk	Bacteria:1,Vertebrates:1	cd06101, citrate_synt, Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form ...
CDD:99856	282	PRK	Bacteria:27,nodiv:1	cd06102, citrate_synt_like_2, Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form ...
CDD:99857	426	EUKprk	Bacteria:1,Invertebrates:8	cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate ...
CDD:99861	363	EUKprk	Bacteria:10,Invertebrates:3	cd06108, Ec2MCS_like, Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains ...
CDD:99862	349	PRK	Bacteria:8	cd06109, BsCS-I_like, Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial ...
CDD:99863	356	PRK	Bacteria:15	cd06110, BSuCS-II_like, Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial ...
CDD:99866	406	PRK	Bacteria:13	cd06113, citrate_synt_like_1_2, Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form ...
CDD:99867	400	EUKprk	Bacteria:21,Invertebrates:1	cd06114, EcCS_like, Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated ...
CDD:99871	358	PRK	Bacteria:11	cd06118, citrate_synt_like_1, Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form ...
CDD:176647	96	EUKprk	Bacteria:2,Primates:1,Rodents:1	cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily.  The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- ...
CDD:176648	159	EUKprk	Bacteria:235,Environmental:3,Invertebrates:4,Plants:6,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family.  DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are ...
CDD:99834	156	PRK	Bacteria:50	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III.  This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a ...
CDD:99835	167	PRK	Bacteria:33	cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins.  This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and ...
CDD:99836	176	EUKprk	Bacteria:51,Invertebrates:17,Plants:8,Primates:1,Vertebrates:3	cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins.  This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ...
CDD:99837	189	PRK	Bacteria:8	cd06134, RNaseT, DEDDh 3'-5' exonuclease domain of RNase T.  RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two ...
CDD:99838	173	EUKprk	Bacteria:21,Invertebrates:10,Plants:12,Primates:1,Vertebrates:3	cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins.  Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active ...
CDD:99839	177	EUK	Invertebrates:7,Primates:1,Rodents:1	cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins.  Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of ...
CDD:99840	161	EUK	Plants:12,Primates:1	cd06137, DEDDh_RNase, DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins.  This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a ...
CDD:99841	183	PRK	Bacteria:16	cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins.  This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a ...
CDD:176651	193	EUKprk	Bacteria:64,Environmental:1,Invertebrates:2,Plants:3	cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases.  Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ...
CDD:176652	178	PRK	Bacteria:58,Environmental:1	cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases.  Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the ...
CDD:176653	170	EUKprk	Bacteria:16,Environmental:1,Invertebrates:15,Plants:24,Primates:1,Rodents:1,Vertebrates:4	cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar proteins.  WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain ...
CDD:176654	178	EUKprk	Bacteria:81,Environmental:2,Invertebrates:5,Plants:1	cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins.  Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered ...
CDD:99846	174	EUK	Invertebrates:9,Plants:8,Primates:1,Vertebrates:2	cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2.  PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and ...
CDD:99847	152	EUK	Invertebrates:12,Plants:21,Primates:1,Vertebrates:3	cd06144, REX4_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins.  This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus ...
CDD:99848	150	EUK	Invertebrates:19,Plants:20,Vertebrates:5	cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins.  This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ...
CDD:176655	193	EUK	Invertebrates:7,Mammals:1,Plants:4,Vertebrates:1	cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins.  The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a ...
CDD:99850	192	EUK	Invertebrates:14,Plants:7,Primates:1,Vertebrates:3	cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins.  Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing ...
CDD:99851	197	EUK	Invertebrates:6,Plants:3,Primates:1,Vertebrates:3	cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins.  The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a ...
CDD:100007	105	miss	miss	cd06150, YjgF_YER057c_UK114_like_2, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic ...
CDD:100008	126	miss	miss	cd06151, YjgF_YER057c_UK114_like_3, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic ...
CDD:100009	114	miss	miss	cd06152, YjgF_YER057c_UK114_like_4, YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and ...
CDD:100010	114	miss	miss	cd06153, YjgF_YER057c_UK114_like_5, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function.   The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic ...
CDD:100011	119	miss	miss	cd06154, YjgF_YER057c_UK114_like_6, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic ...
CDD:100012	101	miss	miss	cd06155, eu_AANH_C_1, A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to ...
CDD:100013	118	miss	miss	cd06156, eu_AANH_C_2, A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the second of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to ...
CDD:132726	168	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:2	cd06157, NR_LBD, The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators.  Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for ...
CDD:100079	181	miss	miss	cd06158, S2P-M50_like_1, Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another ...
CDD:100080	263	miss	miss	cd06159, S2P-M50_PDZ_Arch, Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in ...
CDD:100081	183	miss	miss	cd06160, S2P-M50_like_2, Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another ...
CDD:100082	208	miss	miss	cd06161, S2P-M50_SpoIVFB, SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA ...
CDD:100084	182	miss	miss	cd06163, S2P-M50_PDZ_RseP-like, RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, ...
CDD:100085	227	miss	miss	cd06164, S2P-M50_SpoIVFB_CBS, SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the ...
CDD:99714	127	PRK	Bacteria:19	cd06165, Sortase_A_1, Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases ...
CDD:99715	126	PRK	Bacteria:11	cd06166, Sortase_D_5, Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, ...
CDD:199895	151	EUKprk	Bacteria:185,Invertebrates:8,Plants:25,Primates:1	cd06167, LabA_like, LabA_like proteins.  A well conserved group of domains found in all three kingdoms of life, with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems ...
CDD:212486	73	EUK	Invertebrates:17,Plants:21,Vertebrates:3	cd06168, LSMD1, LSM domain containing 1.  The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. ...
CDD:132884	62	PRK	Bacteria:14	cd06169, BMC, Bacterial Micro-Compartment (BMC) domain.  Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and ...
CDD:99777	57	PRK	Bacteria:29	cd06170, LuxR_C_like, C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain.  For example ...
CDD:100119	55	PRK	Bacteria:36	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences ...
CDD:119392	352	EUKprk	Bacteria:89,Invertebrates:2,Plants:14,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd06174, MFS, The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the ...
CDD:99779	267	EUK	Invertebrates:3,Plants:1	cd06182, CYPOR_like, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD ...
CDD:99780	234	EUK	Invertebrates:23,Mammals:1,Plants:44,Primates:1,Vertebrates:3	cd06183, cyt_b5_reduct_like, Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound ...
CDD:99781	247	EUKprk	Bacteria:88,Invertebrates:3,Plants:19	cd06184, flavohem_like_fad_nad_binding, FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The hemoglobin domain adopts a globin fold with an embedded heme molecule. Flavohemoglobins also have a C-terminal reductase domain with bindiing sites ...
CDD:99782	211	EUKprk	Bacteria:94,Plants:8	cd06185, PDR_like, Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal  ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur [2Fe-2S] cluster domain. Although structurally homologous to FNR, PDR binds FMN rather than FAD in it's FNR-like domain. Electron transfer between pyrimidines and iron-sulfur clusters ...
CDD:99783	210	EUKprk	Bacteria:2,Invertebrates:16,Plants:51,Primates:1,Vertebrates:4	cd06186, NOX_Duox_like_FAD_NADP, NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the ...
CDD:99784	224	PRK	Bacteria:16,nodiv:1	cd06187, O2ase_reductase_like, The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) ...
CDD:99785	283	EUKprk	Bacteria:13,Invertebrates:1	cd06188, NADH_quinone_reductase, Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The ...
CDD:99786	224	PRK	Bacteria:38	cd06189, flavin_oxioreductase, NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for ...
CDD:99787	232	PRK	Bacteria:16,Environmental:1	cd06190, T4MO_e_transfer_like, Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family.
CDD:99789	243	PRK	Bacteria:19	cd06192, DHOD_e_trans_like, FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD ...
CDD:99790	235	PRK	Bacteria:98	cd06193, siderophore_interacting, Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a ...
CDD:99791	222	PRK	Bacteria:19	cd06194, FNR_N-term_Iron_sulfur_binding, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a ...
CDD:99792	241	PRK	Bacteria:49	cd06195, FNR1, Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of ...
CDD:99793	218	PRK	Bacteria:15	cd06196, FNR_like_1, Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase ...
CDD:99794	220	EUKprk	Bacteria:1,Plants:9	cd06197, FNR_like_2, FAD/NAD(P) binding domain of  ferredoxin reductase-like proteins. Ferredoxin reductase (FNR) was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a ...
CDD:99795	216	PRK	Bacteria:49	cd06198, FNR_like_3, NAD(P) binding domain of  ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The ...
CDD:99796	360	EUKprk	Bacteria:22,Invertebrates:2,Plants:1	cd06199, SiR, Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and ...
CDD:99797	245	PRK	Bacteria:15	cd06200, SiR_like1, Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase ...
CDD:99798	289	PRK	Bacteria:12,Environmental:1	cd06201, SiR_like2, Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide.  Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH.  Cypor (including cyt -450 reductase, nitric oxide synthase, and ...
CDD:99799	406	EUK	Invertebrates:5,Vertebrates:2	cd06202, Nitric_oxide_synthase, The ferredoxin-reductase (FNR) like C-terminal domain of the nitric oxide synthase (NOS) fuses with a heme-containing N-terminal oxidase domain. The reductase portion is similar in structure to NADPH dependent cytochrome-450 reductase (CYPOR), having an  inserted connecting sub-domain within the FAD binding portion of FNR. NOS differs from CYPOR in a requirement for the cofactor tetrahydrobiopterin and unlike most ...
CDD:99800	398	EUK	Invertebrates:9,Vertebrates:2	cd06203, methionine_synthase_red, Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite ...
CDD:99801	416	EUK	Invertebrates:5,Plants:17,Vertebrates:2	cd06204, CYPOR, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins ...
CDD:99802	384	EUKprk	Bacteria:10,Plants:14	cd06206, bifunctional_CYPOR, These bifunctional proteins fuse N-terminal cytochrome p450 with a cytochrome p450 reductase (CYPOR). NADPH cytochrome p450 reductase serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that ...
CDD:99803	382	EUK	Invertebrates:4,Plants:7	cd06207, CyPoR_like, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ...
CDD:99804	286	EUKprk	Bacteria:5,Invertebrates:2,Plants:7	cd06208, CYPOR_like_FNR, These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins, such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a ...
CDD:99805	228	PRK	Bacteria:18	cd06209, BenDO_FAD_NAD, Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain.  In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic ...
CDD:99806	236	PRK	Bacteria:9	cd06210, MMO_FAD_NAD_binding, Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add ...
CDD:99808	232	PRK	Bacteria:7	cd06212, monooxygenase_like, The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.
CDD:99809	227	PRK	Bacteria:10	cd06213, oxygenase_e_transfer_subunit, The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. ...
CDD:99810	241	PRK	Bacteria:70,Environmental:2	cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like domain with an iron-sulfur binding cluster domain. Ferredoxins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a ...
CDD:99811	231	PRK	Bacteria:28	cd06215, FNR_iron_sulfur_binding_1, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic ...
CDD:99812	243	PRK	Bacteria:27	cd06216, FNR_iron_sulfur_binding_2, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain.  Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic ...
CDD:99813	235	PRK	Bacteria:20	cd06217, FNR_iron_sulfur_binding_3, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic ...
CDD:99814	246	PRK	Bacteria:74,Environmental:1	cd06218, DHOD_e_trans, FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 ...
CDD:99815	248	EUKprk	Bacteria:12,Environmental:1,Invertebrates:1	cd06219, DHOD_e_trans_like1, FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are ...
CDD:99816	233	PRK	Bacteria:9	cd06220, DHOD_e_trans_like2, FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 ...
CDD:99817	253	PRK	Bacteria:29	cd06221, sulfite_reductase_like, Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine ...
CDD:259998	121	EUKprk	Bacteria:6,Plants:26,Primates:1,Vertebrates:1,Viruses:1	cd06222, RNase_H_like, Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the ...
CDD:206754	130	EUKprk	Bacteria:362,Environmental:9,Invertebrates:42,Plants:38,Primates:2,Vertebrates:5,nodiv:2	cd06223, PRTases_typeI, Phosphoribosyl transferase (PRT)-type I domain.  Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a ...
CDD:100121	122	EUK	Invertebrates:5,Plants:12,Primates:1,Rodents:2,Vertebrates:2	cd06224, REM, Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins ...
CDD:100122	48	EUKprk	Bacteria:77,Plants:3	cd06225, HAMP, Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this ...
CDD:133084	293	PRK	Bacteria:6	cd06226, M14_CPT_like, Peptidase M14 Carboxypeptidase T-like subfamily.  Peptidase M14-like domain of an uncharacterized group of Peptidase M14 Carboxypeptidase (CP) T (CPT)-like proteins. This group belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of ...
CDD:199854	269	EUK	Invertebrates:4,Plants:3	cd06227, M14-like_2, Peptidase M14-like domain; uncharacterized subfamily.  A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, ...
CDD:199855	256	PRK	Bacteria:12	cd06229, M14_Endopeptidase_I, Peptidase M14 carboxypeptidase family-like domain of Endopeptidase I.  Peptidase M14-like domain of Gamma-D-glutamyl-L-diamino acid endopeptidase 1 (also known as Gamma-D-glutamyl-meso-diaminopimelate peptidase I, and  Endopeptidase I (ENP1); EC 3.4.19.11). ENP1 is a member of the M14 family of metallocarboxypeptidases (MCPs). However it has an exceptional type of activity of hydrolyzing the gamma-D-Glu-(L)meso-diaminopimelic acid ...
CDD:199856	254	EUKprk	Bacteria:20,Primates:1	cd06230, M14_ASTE_ASPA_like, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily.  The Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily belongs to the M14 family of metallocarboxypeptidases (MCPs), and includes ASTE, which catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ...
CDD:199857	234	PRK	Bacteria:14	cd06231, M14-like_4, Peptidase M14-like domain; uncharacterized subfamily.  A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on ...
CDD:133091	283	EUKprk	Bacteria:24,Environmental:1,Invertebrates:3	cd06233, M14-like_6, Peptidase M14-like domain; uncharacterized subfamily.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of ...
CDD:199858	263	EUKprk	Bacteria:9,Invertebrates:1,Plants:1	cd06234, M14_Nna1_like_1, Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup.  A bacterial subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP)-like proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding ...
CDD:199859	258	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:2	cd06235, M14_Nna1_like_2, Peptidase M14-like domain of human Nna1/AGTPBP-1, AGBL2 -5, and related proteins.  Subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which ...
CDD:199860	308	EUK	Invertebrates:7,Mammals:1,Plants:1,Rodents:2,Vertebrates:3	cd06236, M14_AGBL5_like, Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins.  Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-5, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal ...
CDD:199862	270	PRK	Bacteria:15,Environmental:1	cd06238, M14-like_1_1, Peptidase M14-like domain; uncharacterized subgroup.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major ...
CDD:199863	231	PRK	Bacteria:14	cd06239, M14-like_1_2, Peptidase M14-like domain; uncharacterized subgroup.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the ...
CDD:199864	274	PRK	Bacteria:7	cd06240, M14-like_1_3, Peptidase M14-like domain; uncharacterized subgroup.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the ...
CDD:199865	266	PRK	Bacteria:17	cd06241, M14-like_1_4, Peptidase M14-like domain; uncharacterized subgroup.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the ...
CDD:133100	268	EUKprk	Bacteria:4,Plants:4	cd06242, M14-like_1_5, Peptidase M14-like domain; uncharacterized subgroup.  Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major ...
CDD:199869	303	EUK	Plants:16	cd06248, M14_CP_A-B_like_1, Peptidase M14 carboxypeptidase subfamily A/B-like; uncharacterized subgroup.  The Peptidase M14 Carboxypeptidase A/B-like subfamily is one of two main M14 carboxypeptidase subfamilies, defined by sequence and structural homology, the other being N/E. Carboxypeptidases (CPs) hydrolyze single, C-terminal amino acids from polypeptide chains. They have a recognition site for the free C-terminal carboxyl group, which is a key determinant of ...
CDD:199870	359	PRK	Bacteria:27	cd06250, M14_PaAOTO_like, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO.  An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE catalyzes the fifth and last step in arginine ...
CDD:199871	287	EUKprk	Bacteria:43,Environmental:1,Plants:1	cd06251, M14_ASTE_ASPA_like_1, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and ...
CDD:199872	318	PRK	Bacteria:16	cd06252, M14_ASTE_ASPA_like_2, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as ...
CDD:133110	298	PRK	Bacteria:9	cd06253, M14_ASTE_ASPA_like_3, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as ...
CDD:199873	291	PRK	Bacteria:9	cd06254, M14_ASTE_ASPA_like_4, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as ...
CDD:199874	327	PRK	Bacteria:10	cd06256, M14_ASTE_ASPA_like_6, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as ...
CDD:99751	55	EUKprk	Bacteria:15,Invertebrates:10,Mammals:1,Plants:8,Primates:1,Rodents:1	cd06257, DnaJ, DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. ...
CDD:188993	400	EUKprk	Bacteria:13,Plants:2,Rodents:1	cd06258, M3_like, Peptidase M3-like family, a zincin metallopeptidase, includes M3 and M32 families.  The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3 and M32 families of metallopeptidases.  The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, ...
CDD:99750	150	EUKprk	Bacteria:315,Invertebrates:2,Plants:8,nodiv:1	cd06259, YdcF-like, YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX,  which are involved in vancomycin resistance; sfiX may also be involved in ...
CDD:99749	155	PRK	Bacteria:81	cd06260, DUF820, Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of nucleases.
CDD:119394	190	EUKprk	Bacteria:66,Plants:4	cd06261, TM_PBP2, Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs ...
CDD:99706	157	EUK	Invertebrates:8,Mammals:1,Primates:1,Rodents:1,Vertebrates:6,nodiv:1	cd06263, MAM, Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of ...
CDD:119387	115	EUK	Mammals:4,Primates:2,Rodents:1,Vertebrates:8	cd06265, RNase_A_canonical, Canonical RNase A family includes all vertebrate homologues to the bovine pancreatic ribonuclease A (RNase A) that contain the catalytic site, necessary for RNase activity.  In the human genome 8 RNases , refered to as "canonical" RNases, have been identified, pancreatic RNase (RNase 1), Eosinophil Derived Neurotoxin (SEDN/RNASE 2), Eosinophil Cationic Protein (ECP/RNase 3), RNase 4, Angiogenin (RNase 5), ...
CDD:107262	264	PRK	Bacteria:177	cd06267, PBP1_LacI_sugar_binding_like, Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily.  Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily.  In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of ...
CDD:107263	298	PRK	Bacteria:144,Environmental:2,nodiv:1	cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily.  Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from ...
CDD:153137	298	EUK	Invertebrates:16,Mammals:3,Plants:6,Primates:3,Rodents:2,Vertebrates:10	cd06269, PBP1_glutamate_receptors_like, Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domain of the ionotropic glutamate receptors.  This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane ...
CDD:107265	268	PRK	Bacteria:21	cd06270, PBP1_GalS_like, Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism.  Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both ...
CDD:107266	268	PRK	Bacteria:22,nodiv:1	cd06271, PBP1_AglR_RafR_like, Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed ...
CDD:107267	261	PRK	Bacteria:3	cd06272, PBP1_hexuronate_repressor_like, Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators.  Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member ...
CDD:107268	268	PRK	Bacteria:8	cd06273, PBP1_GntR_like_1, This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators.  This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family ...
CDD:107269	264	PRK	Bacteria:10	cd06274, PBP1_FruR, Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs.  Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the ...
CDD:107270	269	EUKprk	Bacteria:10,Plants:1	cd06275, PBP1_PurR, Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli.  Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA ...
CDD:107271	247	PRK	Bacteria:8	cd06276, PBP1_FucR_like, Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability.  Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR ...
CDD:107272	268	PRK	Bacteria:7	cd06277, PBP1_LacI_like_1, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) ...
CDD:107273	266	PRK	Bacteria:26	cd06278, PBP1_LacI_like_2, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) ...
CDD:107274	283	PRK	Bacteria:16	cd06279, PBP1_LacI_like_3, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) ...
CDD:107276	269	PRK	Bacteria:5	cd06281, PBP1_LacI_like_5, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) ...
CDD:107277	266	PRK	Bacteria:9	cd06282, PBP1_GntR_like_2, Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators.  This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription ...
CDD:107278	267	EUKprk	Bacteria:19,Plants:1	cd06283, PBP1_RegR_EndR_KdgR_like, Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR.  Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The ...
CDD:107279	267	PRK	Bacteria:22	cd06284, PBP1_LacI_like_6, Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria.  This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH ...
CDD:107281	260	PRK	Bacteria:21	cd06286, PBP1_CcpB_like, Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species.  This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which ...
CDD:107283	269	PRK	Bacteria:12	cd06288, PBP1_sucrose_transcription_regulator, Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an ...
CDD:107284	268	PRK	Bacteria:24	cd06289, PBP1_MalI_like, Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria.  This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH ...
CDD:107286	265	PRK	Bacteria:27	cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs.  This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its ...
CDD:107287	273	PRK	Bacteria:8	cd06292, PBP1_LacI_like_10, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors.  This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) ...
CDD:107289	270	PRK	Bacteria:29	cd06294, PBP1_ycjW_transcription_regulator_like, Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors.  This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and ...
CDD:107290	275	PRK	Bacteria:21	cd06295, PBP1_CelR, Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators.  This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The ...
CDD:107291	270	PRK	Bacteria:10	cd06296, PBP1_CatR_like, Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation.  This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding ...
CDD:107293	268	PRK	Bacteria:19	cd06298, PBP1_CcpA_like, Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation.  Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence ...
CDD:107294	265	PRK	Bacteria:5	cd06299, PBP1_LacI_like_13, Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia.  This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia.  This regulatory ...
CDD:107295	272	PRK	Bacteria:18	cd06300, PBP1_ABC_sugar_binding_like_1, Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.  Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of ...
CDD:107296	272	PRK	Bacteria:24	cd06301, PBP1_rhizopine_binding_like, Periplasmic binding proteins specific to rhizopines.  Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and ...
CDD:107297	298	PRK	Bacteria:34,nodiv:1	cd06302, PBP1_LsrB_Quorum_Sensing, Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs.  Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and ...
CDD:107298	280	PRK	Bacteria:7	cd06303, PBP1_LuxPQ_Quorum_Sensing, Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs.  Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and ...
CDD:107299	260	PRK	Bacteria:127,Environmental:2	cd06304, PBP1_BmpA_like, Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria.  Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in ...
CDD:107300	273	PRK	Bacteria:13	cd06305, PBP1_methylthioribose_binding_like, Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily.  Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta ...
CDD:107301	268	PRK	Bacteria:6	cd06306, PBP1_TorT-like, TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria.  TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, ...
CDD:107302	275	PRK	Bacteria:23,nodiv:1	cd06307, PBP1_uncharacterized_sugar_binding, Periplasmic sugar-binding domain of uncharacterized transport systems.  Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
CDD:107303	270	miss	miss	cd06308, PBP1_sensor_kinase_like, Periplasmic binding domain of two-component sensor kinase signaling systems.  Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be ...
CDD:107304	273	PRK	Bacteria:21	cd06309, PBP1_YtfQ_like, Periplasmic binding domain of ABC-type YtfQ-like transport systems.  Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing ...
CDD:107305	273	PRK	Bacteria:23,nodiv:1	cd06310, PBP1_ABC_sugar_binding_like_2, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is ...
CDD:107306	274	PRK	Bacteria:8	cd06311, PBP1_ABC_sugar_binding_like_3, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted ...
CDD:107307	271	PRK	Bacteria:25	cd06312, PBP1_ABC_sugar_binding_like_4, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is ...
CDD:107310	280	PRK	Bacteria:10	cd06315, PBP1_ABC_sugar_binding_like_6, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is ...
CDD:107316	271	PRK	Bacteria:10	cd06321, PBP1_ABC_sugar_binding_like_11, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not ...
CDD:107318	268	PRK	Bacteria:27	cd06323, PBP1_ribose_binding, Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs.  Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding ...
CDD:107319	305	miss	miss	cd06324, PBP1_ABC_sugar_binding_like_13, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems.  This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, ...
CDD:107320	281	PRK	Bacteria:65	cd06325, PBP1_ABC_uncharacterized_transporter, Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions.  This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This ...
CDD:107321	336	PRK	Bacteria:40	cd06326, PBP1_STKc_like, Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins.  The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein ...
CDD:107322	334	PRK	Bacteria:37	cd06327, PBP1_SBP_like_1, Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family.  Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are ...
CDD:107324	342	miss	miss	cd06329, PBP1_SBP_like_3, Periplasmic solute-binding domain of active transport proteins.  Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and ...
CDD:107325	346	miss	miss	cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain of active transport proteins.  Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds.  Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the ...
CDD:107326	333	PRK	Bacteria:54,nodiv:1	cd06331, PBP1_AmiC_like, Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF).  This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or ...
CDD:107327	333	PRK	Bacteria:32	cd06332, PBP1_aromatic_compounds_like, Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes.  This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well ...
CDD:107328	312	PRK	Bacteria:35,nodiv:1	cd06333, PBP1_ABC-type_HAAT_like, Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids.  This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type ...
CDD:107329	351	PRK	Bacteria:31	cd06334, PBP1_ABC_ligand_binding_like_1, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107330	347	PRK	Bacteria:24	cd06335, PBP1_ABC_ligand_binding_like_2, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107331	347	PRK	Bacteria:22	cd06336, PBP1_ABC_ligand_binding_like_3, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107332	357	PRK	Bacteria:8	cd06337, PBP1_ABC_ligand_binding_like_4, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107333	345	PRK	Bacteria:24	cd06338, PBP1_ABC_ligand_binding_like_5, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107334	336	PRK	Bacteria:103,Environmental:1	cd06339, PBP1_YraM_LppC_lipoprotein_like, Periplasmic binding component of lipoprotein LppC, an immunodominant antigen.  This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized.  Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).
CDD:107335	347	PRK	Bacteria:15	cd06340, PBP1_ABC_ligand_binding_like_6, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107336	341	PRK	Bacteria:9	cd06341, PBP1_ABC_ligand_binding_like_7, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, ...
CDD:107337	334	PRK	Bacteria:51	cd06342, PBP1_ABC_LIVBP_like, Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine).  This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids ...
CDD:107338	362	PRK	Bacteria:20	cd06343, PBP1_ABC_ligand_binding_like_8, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, ...
CDD:107339	332	PRK	Bacteria:10	cd06344, PBP1_ABC_ligand_binding_like_9, Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, ...
CDD:107340	344	PRK	Bacteria:8,Environmental:1	cd06345, PBP1_ABC_ligand_binding_like_10, Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino ...
CDD:107341	312	PRK	Bacteria:16,Environmental:2	cd06346, PBP1_ABC_ligand_binding_like_11, Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino ...
CDD:107342	334	PRK	Bacteria:44	cd06347, PBP1_ABC_ligand_binding_like_12, Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions.  This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, ...
CDD:153138	348	miss	miss	cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs).  Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are ...
CDD:107346	328	EUK	Invertebrates:1	cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs).  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the ...
CDD:107347	389	EUK	Invertebrates:14,Mammals:3,Primates:1,Rodents:2,Vertebrates:8	cd06352, PBP1_NPR_GC_like, Ligand-binding domain of membrane guanylyl-cyclase receptors.  Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and ...
CDD:107348	258	miss	miss	cd06353, PBP1_BmpA_Med_like, Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea.  Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea.  Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with ...
CDD:107349	265	miss	miss	cd06354, PBP1_BmpA_PnrA_like, Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea.  Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport ...
CDD:107350	348	miss	miss	cd06355, PBP1_FmdD_like, Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF).  This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are ...
CDD:107351	334	PRK	Bacteria:1	cd06356, PBP1_Amide_Urea_BP_like, Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF).  This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
CDD:107352	360	miss	miss	cd06357, PBP1_AmiC, Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family.  This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative ...
CDD:107353	333	PRK	Bacteria:1	cd06358, PBP1_NHase, Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides.  This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and ...
CDD:107354	333	miss	miss	cd06359, PBP1_Nba_like, Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway.  This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
CDD:107355	336	miss	miss	cd06360, PBP1_alkylbenzenes_like, Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene.  This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
CDD:107357	452	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd06362, PBP1_mGluR, Ligand binding domain of the metabotropic glutamate receptors (mGluR).  Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, ...
CDD:107358	410	miss	miss	cd06363, PBP1_Taste_receptor, Ligand-binding domain of the T1R taste receptor.  Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
CDD:107360	469	miss	miss	cd06365, PBP1_Pheromone_receptor, Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily.  Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of ...
CDD:107361	350	miss	miss	cd06366, PBP1_GABAb_receptor, Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA).  Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled ...
CDD:107362	362	miss	miss	cd06367, PBP1_iGluR_NMDA, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors.  While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally ...
CDD:107363	324	miss	miss	cd06368, PBP1_iGluR_non_NMDA_like, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the ...
CDD:107364	380	miss	miss	cd06369, PBP1_GC_C_enterotoxin_receptor, Ligand-binding domain of the membrane guanylyl cyclase C.  Ligand-binding domain of the membrane guanylyl cyclase C (GC-C or StaR). StaR is a key receptor for the STa (Escherichia coli Heat Stable enterotoxin), a potent stimulant of intestinal chloride and bicarbonate secretion that cause acute secretory diarrhea. The catalytic domain of the STa/guanylin receptor type membrane GC is highly similar to those of the natriuretic ...
CDD:107365	404	miss	miss	cd06370, PBP1_Speract_GC_like, Ligand-binding domain of membrane bound guanylyl cyclases.  Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ...
CDD:107366	382	miss	miss	cd06371, PBP1_sensory_GC_DEF_like, Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues.  This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that ...
CDD:107368	396	miss	miss	cd06373, PBP1_NPR_like, Ligand binding domain of natriuretic peptide receptor (NPR) family.  Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or ...
CDD:107373	362	miss	miss	cd06378, PBP1_iGluR_NMDA_NR2, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional ...
CDD:107375	382	miss	miss	cd06380, PBP1_iGluR_AMPA, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system.  While this N-terminal domain ...
CDD:107377	327	miss	miss	cd06382, PBP1_iGluR_Kainate, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate.  While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the ...
CDD:107378	368	miss	miss	cd06383, PBP1_iGluR_AMPA_Like, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors.  N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like ...
CDD:99723	87	miss	miss	cd06402, PB1_p62, The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ...
CDD:99728	82	miss	miss	cd06407, PB1_NLP, A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization ...
CDD:99730	86	miss	miss	cd06409, PB1_MUG70, The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for ...
CDD:99731	97	miss	miss	cd06410, PB1_UP2, Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular ...
CDD:119374	199	EUKprk	Bacteria:8,Plants:3	cd06412, GH25_CH-type, CH-type (Chalaropsis-type) lysozymes represent one of four functionally-defined classes of peptidoglycan hydrolases (also referred to as endo-N-acetylmuramidases) that cleave bacterial cell wall peptidoglycans.  CH-type lysozymes exhibit both lysozyme (acetylmuramidase) and diacetylmuramidase activity. The first member of this family to be described was a muramidase from the fungus Chalaropsis.  However, a majority of the CH-type ...
CDD:119375	191	PRK	Bacteria:14	cd06413, GH25_muramidase_1, Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
CDD:119376	191	EUKprk	Bacteria:25,Invertebrates:1	cd06414, GH25_LytC-like, The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains.   LytC is composed of a C-terminal glycosyl hydrolase family 25 (GH25) domain and an N-terminal choline-binding module (CBM) consisting of eleven homologous repeats that specifically recognizes the ...
CDD:119377	196	PRK	Bacteria:7,Phages:2	cd06415, GH25_Cpl1-like, Cpl-1 lysin (also known as Cpl-9 lysozyme / muramidase) is a bacterial cell wall endolysin encoded by the pneumococcal bacteriophage Cp-1, which cleaves the glycosidic N-acetylmuramoyl-(beta1,4)-N-acetylglucosamine bonds of the pneumococcal glycan chain, thus acting as an enzymatic antimicrobial agent (an enzybiotic) against streptococcal infections. Cpl-1 belongs to the CP family of lysozymes (CPL lysozymes) which includes the ...
CDD:119378	196	EUK	Invertebrates:11,Plants:1	cd06416, GH25_Lys1-like, Lys-1 is a lysozyme encoded by the Caenorhabditis elegans lys-1 gene. This gene is one of a several lysozyme genes upregulated upon infection by the Gram-negative bacterial pathogen Serratia marcescens.  Lys-1 contains a glycosyl hydrolase family 25 (GH25) catalytic domain.  This family also includes Lys-5 from Caenorhabditis elegans.
CDD:119380	212	PRK	Bacteria:23	cd06418, GH25_BacA-like, BacA is a bacterial lysin from Enterococcus faecalis that degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.  BacA is homologous to the YbfG and YkuG lysins of Bacillus subtilis. BacA has a C-terminal catalytic glycosyl hydrolase family 25 (GH25) domain and an N-terminal peptidoglycan-binding domain comprised of three alpha helices which is ...
CDD:119381	190	PRK	Bacteria:8	cd06419, GH25_muramidase_2, Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
CDD:133042	182	PRK	Bacteria:23	cd06420, GT2_Chondriotin_Pol_N, N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase.  Chondroitin polymerase is a two domain, bi-functional protein. The N-terminal domain functions as a GalNAc transferase. The bacterial chondroitin polymerase catalyzes elongation of the chondroitin chain by alternatively transferring the GlcUA and GalNAc moiety from UDP-GlcUA and UDP-GalNAc to the non-reducing ends of the chondroitin chain. The enzyme ...
CDD:133043	234	EUKprk	Bacteria:39,Invertebrates:1,Plants:8	cd06421, CESA_CelA_like, CESA_CelA_like are involved in the elongation of the glucan chain of cellulose.  Family of proteins related to  Agrobacterium tumefaciens CelA and  Gluconacetobacter xylinus BscA. These proteins are involved in the elongation of the glucan chain of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues. They are putative catalytic subunit of cellulose synthase, which is a ...
CDD:133044	221	EUKprk	Bacteria:60,Invertebrates:1,nodiv:1	cd06422, NTP_transferase_like_1, NTP_transferase_like_1 is a member of the nucleotidyl transferase family.  This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, ...
CDD:133045	180	EUKprk	Bacteria:83,Plants:1	cd06423, CESA_like, CESA_like is  the cellulose synthase superfamily.  The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the ...
CDD:133047	233	EUK	Invertebrates:13,Plants:8,Primates:1,Vertebrates:2	cd06425, M1P_guanylylT_B_like_N, N-terminal domain of the M1P-guanylyltransferase B-isoform like proteins.  GDP-mannose pyrophosphorylase  (GTP: alpha-d-mannose-1-phosphate guanyltransferase) catalyzes the formation of GDP-d-mannose from GTP and alpha-d-mannose-1-Phosphate. It contains an N-terminal catalytic domain and a C-terminal Lefthanded-beta-Helix fold domain. GDP-d-mannose is the activated form of mannose for formation ...
CDD:133048	220	EUKprk	Bacteria:20,Invertebrates:1	cd06426, NTP_transferase_like_2, NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family.  This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, ...
CDD:133049	241	PRK	Bacteria:18	cd06427, CESA_like_2, CESA_like_2 is a member of the cellulose synthase superfamily.  The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains.  The members include cellulose synthase catalytic subunit, chitin synthase, Glucan Biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the ...
CDD:133050	257	EUK	Invertebrates:8,Plants:6,Vertebrates:2	cd06428, M1P_guanylylT_A_like_N, N-terminal domain of M1P_guanylyl_A_ like proteins are likely to be a isoform of GDP-mannose pyrophosphorylase.  N-terminal domain of the M1P-guanylyltransferase A-isoform like proteins:  The proteins of this family are likely to be a isoform of GDP-mannose pyrophosphorylase. Their sequences are highly conserved with mannose-1-phosphate guanyltransferase, but  generally about 40-60 bases longer.  ...
CDD:133051	257	EUK	Plants:4,Primates:1,Vertebrates:2	cd06429, GT8_like_1, GT8_like_1 represents a subfamily of GT8 with unknown function.  A subfamily of glycosyltransferase family 8 with unknown function: Glycosyltransferase family 8 comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase  lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase and inositol 1-alpha-galactosyltransferase. It is classified as a retaining glycosyltransferase, ...
CDD:133055	202	PRK	Bacteria:87	cd06433, GT_2_WfgS_like, WfgS and WfeV are involved in O-antigen biosynthesis.  Escherichia coli WfgS and Shigella dysenteriae WfeV are glycosyltransferase 2 family enzymes involved in O-antigen biosynthesis. GT-2 enzymes have GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated ...
CDD:133056	235	EUKprk	Bacteria:8,Plants:7,Primates:1,Vertebrates:3	cd06434, GT2_HAS, Hyaluronan synthases catalyze polymerization of hyaluronan.  Hyaluronan synthases (HASs) are bi-functional glycosyltransferases that catalyze polymerization of hyaluronan. HASs transfer both GlcUA and GlcNAc in beta-(1,3) and beta-(1,4) linkages, respectively to the hyaluronan chain using UDP-GlcNAc and UDP-GlcUA as substrates. HA is made as a free glycan, not attached to a protein or lipid. HASs do not need a ...
CDD:133059	232	EUKprk	Bacteria:6,Invertebrates:1,Plants:4	cd06437, CESA_CaSu_A2, Cellulose synthase catalytic subunit A2 (CESA2) is a catalytic subunit or a catalytic subunit substitute of the cellulose synthase complex.  Cellulose synthase (CESA) catalyzes the polymerization reaction of cellulose using UDP-glucose as the substrate. Cellulose is an aggregate of unbranched polymers of beta-1,4-linked glucose residues, which is an abundant polysaccharide produced by plants and in varying degrees ...
CDD:133060	183	PRK	Bacteria:24	cd06438, EpsO_like, EpsO protein participates in the methanolan synthesis.  The Methylobacillus sp EpsO protein is predicted to participate in the methanolan synthesis. Methanolan is an exopolysaccharide (EPS), composed of glucose, mannose and galactose.  A 21 genes cluster was predicted to participate in the methanolan synthesis. Gene disruption analysis revealed that EpsO is one of the glycosyltransferase enzymes involved in the synthesis of repeating sugar units ...
CDD:133061	251	PRK	Bacteria:42	cd06439, CESA_like_1, CESA_like_1 is a member of the cellulose synthase (CESA) superfamily.  This is a subfamily of cellulose synthase (CESA) superfamily.  CESA superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains.  The members of the superfamily include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other ...
CDD:133062	224	miss	miss	cd06442, DPM1_like, DPM1_like represents putative enzymes similar to eukaryotic DPM1.  Proteins similar to eukaryotic DPM1, including enzymes from bacteria and archaea; DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. DPM ...
CDD:176473	347	EUKprk	Bacteria:10,Plants:1,Primates:1,Vertebrates:1	cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication.  DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I ...
CDD:119438	79	EUKprk	Bacteria:259,Environmental:3,Invertebrates:12,Plants:18,Primates:1,Vertebrates:3	cd06445, ATase, The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many ...
CDD:107207	365	miss	miss	cd06446, Trp-synth_B, Tryptophan synthase-beta:  Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to glyceraldehyde 3-phosphate and indole at the active site of the alpha subunit. In the beta reaction, indole undergoes a PLP-dependent reaction with L-serine to form L-tryptophan at the active site of ...
CDD:107208	404	miss	miss	cd06447, D-Ser-dehyd, D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine  to pyruvate and ammonia.  D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A.  D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes ...
CDD:107209	316	miss	miss	cd06448, L-Ser-dehyd, Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- , D-serine, or L-threonine to pyruvate/ketobutyrate and ammonia.
CDD:99743	345	EUKprk	Bacteria:8,Invertebrates:3,Mammals:1,Plants:4,Primates:1,Vertebrates:2	cd06450, DOPA_deC_like, DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation ...
CDD:99744	356	EUKprk	Bacteria:5,Invertebrates:3,Plants:2	cd06451, AGAT_like, Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, ...
CDD:99746	373	PRK	Bacteria:92,Environmental:1	cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine; and selenocysteine lyase catalyzes the ...
CDD:99747	349	EUKprk	Bacteria:7,Invertebrates:6,Plants:4,Primates:1,Vertebrates:1	cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to ...
CDD:188994	637	EUKprk	Bacteria:16,Invertebrates:9,Plants:18,Primates:1,Vertebrates:3,nodiv:1	cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also includes neurolysin.  Peptidase M3 Thimet oligopeptidase (TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase 24.15; soluble metallo-endopeptidase; EC 3.4.24.15) family also includes neurolysin (endopeptidase 24.16, microsomal endopeptidase, mitochondrial oligopeptidase M, neurotensin endopeptidase, soluble angiotensin II-binding ...
CDD:188995	654	EUKprk	Bacteria:130,Invertebrates:4,Plants:6,nodiv:1	cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase (DCP).  Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. ...
CDD:188996	606	EUK	Invertebrates:13,Plants:24,Primates:1,Vertebrates:3	cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase (MIP).  Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the ...
CDD:188998	484	EUKprk	Bacteria:114,Invertebrates:3,Plants:5	cd06460, M32_Taq, Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP.  Peptidase family M32 is a subclass of metallocarboxypeptidases which are distributed mainly in bacteria and archaea, and contain a HEXXH motif that coordinates a divalent cation such as Zn2+ or Co2+, so far only observed in the active site of neutral metallopeptidases but not in carboxypeptidases. M32 includes the thermostable ...
CDD:188999	562	EUKprk	Bacteria:15,Invertebrates:23,Primates:1,Vertebrates:5,nodiv:2	cd06461, M2_ACE, Peptidase family M2 Angiotensin converting enzyme (ACE).  Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ...
CDD:119396	84	EUKprk	Bacteria:413,Environmental:4,Invertebrates:19,Phages:1,Plants:25,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD ...
CDD:107220	84	miss	miss	cd06463, p23_like, Proteins containing this p23_like domain include p23 and its Saccharomyces cerevisiae (Sc) homolog Sba1. Both are co-chaperones for the heat shock protein (Hsp) 90.  p23 binds Hsp90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis.  Both p23 and Sba1p can regulate telomerase activity. This group ...
CDD:107221	88	miss	miss	cd06464, ACD_sHsps-like, Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain  (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
CDD:107222	108	miss	miss	cd06465, p23_hB-ind1_like, p23_like domain found in human (h) butyrate-induced transcript 1 (B-ind1) and similar proteins. hB-ind1 participates in signaling by the small GTPase Rac1. It binds to Rac1 and enhances different Rac1 effects including activation of nuclear factor (NF) kappaB and activation of c-Jun N-terminal kinase (JNK). hB-ind1 also plays a part in the RNA replication and particle production of Hepatitis C virus (HCV)  through its interaction with heat ...
CDD:107223	84	miss	miss	cd06466, p23_CS_SGT1_like, p23_like domain similar to the C-terminal CHORD-SGT1 (CS) domain of Sgt1 (suppressor of G2 allele of Skp1). Sgt1 interacts with multiple protein complexes and has the features of a cochaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain.  Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required ...
CDD:107224	85	miss	miss	cd06467, p23_NUDC_like, p23_like domain of NUD (nuclear distribution) C and similar proteins. Aspergillus nidulas (An) NUDC is needed for nuclear movement. AnNUDC is localized at the hyphal cortex, and binds NUDF at spindle pole bodies (SPBs) and in the cytoplasm at different stages in the cell cycle. At the SPBs it is part of the dynein molecular motor/NUDF complex that regulates microtubule dynamics.  Mammalian(m) NUDC associates both with the dynein complex and also ...
CDD:107225	92	miss	miss	cd06468, p23_CacyBP, p23_like domain found in proteins similar to Calcyclin-Binding Protein(CacyBP)/Siah-1-interacting protein (SIP). CacyBP/SIP interacts with S100A6 (calcyclin), with some other members of the S100 family, with tubulin, and with Siah-1 and Skp-1. The latter two are components of the ubiquitin ligase that regulates beta-catenin degradation. The beta-catenin gene is an oncogene participating in tumorigenesis in many different cancers. Overexpression of ...
CDD:107226	78	miss	miss	cd06469, p23_DYX1C1_like, p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD susceptibility locus (15q15-21). Independent association studies have reported conflicting results. However, association of short-term memory, which plays a role in DD, with a variant within the ...
CDD:107227	90	miss	miss	cd06470, ACD_IbpA-B_like, Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins.  IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. IbpA and IbpB are produced during high-level production of various heterologous ...
CDD:107228	93	miss	miss	cd06471, ACD_LpsHSP_like, Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of ...
CDD:107229	92	miss	miss	cd06472, ACD_ScHsp26_like, Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large ...
CDD:107238	87	miss	miss	cd06488, p23_melusin_like, p23_like domain similar to the C-terminal (tail) domain of vertebrate Melusin and related proteins. Melusin's tail domain interacts with the cytoplasmic domain of beta1-A and beta1-D isoforms of beta1 integrin, it does not bind other integrin beta subunits. Melusin is a muscle-specific protein expressed in skeletal and cardiac muscles but not in smooth muscle or other tissues. It is needed for heart hypertrophy following mechanical overload. The ...
CDD:107240	87	miss	miss	cd06490, p23_NCB5OR, p23_like domain found in NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR) and similar proteins.  NCB5OR is widely expressed in human organs and tissues and is localized in the ER (endoplasmic reticulum). It appears to play a critical role in maintaining viable pancreatic beta cells. Mice homozygous for a targeted knockout (KO) of the gene encoding NCB5OR develop an early-onset nonautoimmune diabetes phenotype with a non-inflammatory beta-cell ...
CDD:133460	185	EUKprk	Bacteria:8,Invertebrates:1	cd06499, GT_MraY-like, Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate, which is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria. One member, D-N-acetylhexosamine 1-phosphate ...
CDD:99748	338	EUKprk	Bacteria:4,Invertebrates:1,Plants:2	cd06502, TA_like, Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I).  TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway.
CDD:119382	192	PRK	Bacteria:9	cd06522, GH25_AtlA-like, AtlA is an autolysin found in Gram-positive lactic acid bacteria that degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.  This family includes the AtlA and Aml autolysins from Streptococcus mutans which have a C-terminal glycosyl hydrolase family 25 (GH25) catalytic domain as well as six tandem N-terminal repeats of the GBS (group B Streptococcus) ...
CDD:119383	177	PRK	Bacteria:7	cd06523, GH25_PlyB-like, PlyB is a bacteriophage endolysin that displays potent lytic activity toward Bacillus anthracis.  PlyB has an N-terminal glycosyl hydrolase family 25 (GH25) catalytic domain and a C-terminal bacterial SH3-like domain, SH3b.  Both domains are required for effective catalytic activity.  Endolysins are produced by bacteriophages at the end of their life cycle and participate in lysing the bacterial cell in order to release the newly formed ...
CDD:119384	194	PRK	Bacteria:11	cd06524, GH25_YegX-like, YegX is an uncharacterized bacterial protein with a glycosyl hydrolase family 25 (GH25) catalytic domain that is similar in sequence to the CH-type (Chalaropsis-type) lysozymes of the GH25 family of endolysins.
CDD:119385	184	PRK	Bacteria:8	cd06525, GH25_Lyc-like, Lyc muramidase is an autolytic lysozyme (autolysin) from Clostridium acetobutylicum encoded by the lyc gene.  Lyc has a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
CDD:107247	83	miss	miss	cd06526, metazoan_ACD, Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain  (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
CDD:132725	363	PRK	Bacteria:8	cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).  Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence ...
CDD:119397	81	miss	miss	cd06529, S24_LexA-like, Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA ...
CDD:119398	85	miss	miss	cd06530, S26_SPase_I, The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a ...
CDD:133474	128	EUKprk	Bacteria:106,Environmental:1,Invertebrates:9,Plants:8,Rodents:1,Vertebrates:3,nodiv:1	cd06532, Glyco_transf_25, Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of Neisseria gonorrhoeae and Lic2A of Haemophilus influenzae. M. catarrhalis Lgt2 catalyzes the addition of galactose ...
CDD:119439	171	EUKprk	Bacteria:192,Plants:1,nodiv:1	cd06533, Glyco_transf_WecG_TagA, The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the ...
CDD:143395	367	EUKprk	Bacteria:36,Mammals:1,Plants:4,Primates:1,Rodents:1,Vertebrates:2	cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase superfamily.  The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple ...
CDD:119359	255	PRK	Bacteria:13	cd06542, GH18_EndoS-like, Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain.  Some members also have an additional C-terminal glycosyl hydrolase family 20 (GH20) domain while others have an N-terminal domain of unknown function (pfam08522).  Members of this family ...
CDD:119360	294	EUKprk	Bacteria:31,Invertebrates:1	cd06543, GH18_PF-ChiA-like, PF-ChiA is an uncharacterized chitinase found in the hyperthermophilic archaeon Pyrococcus furiosus with a glycosyl hydrolase family 18 (GH18) catalytic domain as well as a cellulose-binding domain.  Members of this domain family are found not only in archaea but also in eukaryotes and prokaryotes. PF-ChiA exhibits hydrolytic activity toward both colloidal and crystalline (beta/alpha) chitins at high temperature.
CDD:119361	253	EUK	Plants:7	cd06544, GH18_narbonin, Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function.  Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity.  Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination.  This ...
CDD:119363	256	EUKprk	Bacteria:1,Plants:6	cd06546, GH18_CTS3_chitinase, GH18 domain of CTS3 (chitinase 3), an uncharacterized protein from the human fungal pathogen Coccidioides posadasii.  CTS3 has a chitinase-like glycosyl hydrolase family 18 (GH18) domain; and has homologs in bacteria as well as fungi.
CDD:119364	339	EUKprk	Bacteria:11,Invertebrates:9,Plants:6,Vertebrates:2	cd06547, GH85_ENGase, Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins.  The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan.  ENGase is a key enzyme in the processing of free oligosaccharides in the ...
CDD:119365	322	EUKprk	Bacteria:39,Environmental:2,Plants:9	cd06548, GH18_chitinase, The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites.  The structure of this domain is an eight-stranded alpha/beta barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.
CDD:119366	298	PRK	Bacteria:6	cd06549, GH18_trifunctional, GH18 domain of an uncharacterized family of bacterial proteins, which share a common three-domain architecture: an N-terminal glycosyl hydrolase family 18 (GH18) domain, a glycosyl transferase family 2 domain, and a C-terminal polysaccharide deacetylase domain.
CDD:119348	261	EUKprk	Bacteria:22,Plants:1	cd06550, TM_ABC_iron-siderophores_like, Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it ...
CDD:153244	187	EUKprk	Bacteria:17,Invertebrates:1,Plants:5,Primates:1,Vertebrates:2	cd06551, LPLAT, Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis.  Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, ...
CDD:119344	100	PRK	Bacteria:34,Environmental:2	cd06552, ASCH_yqfb_like, ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
CDD:119345	127	EUKprk	Bacteria:59,Plants:1	cd06553, ASCH_Ef3133_like, ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
CDD:119346	113	EUKprk	Bacteria:16,Invertebrates:8,Plants:2,Primates:1,Vertebrates:3	cd06554, ASCH_ASC-1_like, ASC-1 homology domain, ASC-1-like subfamily. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, ...
CDD:119347	109	EUKprk	Bacteria:19,Invertebrates:1,Plants:2	cd06555, ASCH_PF0470_like, ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
CDD:119342	254	EUKprk	Bacteria:93,Environmental:5,Invertebrates:3,Plants:17	cd06557, KPHMT-like, Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a precursor to coenzyme A and is required for penicillin biosynthesis.
CDD:119339	195	EUKprk	Bacteria:236,Environmental:3,Invertebrates:20,Plants:30,Primates:1,Rodents:1,Vertebrates:5	cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the ...
CDD:143472	208	EUKprk	Bacteria:86,Invertebrates:13,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd06559, Endonuclease_V, Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases.  Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases.  EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor.  EndoV homologs are conserved throughout all domains of ...
CDD:143473	166	EUKprk	Bacteria:31,Environmental:2,Plants:1	cd06560, PriL, Archaeal/eukaryotic core primase: Large subunit, PriL.  Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. The DNA replication machinery of archaeal organisms contains only the core primase, a simpler arrangement compared to ...
CDD:132880	197	EUKprk	Bacteria:150,Environmental:2,Invertebrates:7,Plants:1	cd06561, AlkD_like, A new structural DNA glycosylase.  This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated ...
CDD:119332	348	EUK	Invertebrates:21,Plants:13,Primates:1,Vertebrates:3	cd06562, GH20_HexA_HexB-like, Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and ...
CDD:119333	357	EUKprk	Bacteria:34,Invertebrates:1	cd06563, GH20_chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin.  Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these ...
CDD:119334	326	EUKprk	Bacteria:21,Invertebrates:1,Plants:3	cd06564, GH20_DspB_LnbB-like, Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides ...
CDD:119335	301	EUKprk	Bacteria:22,Invertebrates:8,Plants:1,Primates:1,Vertebrates:2	cd06565, GH20_GcnA-like, Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA  is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine residues from 4-methylumbelliferylated (4MU) substrates, as well as cleaving NAG from chito-oligosaccharides (i.e. NAG polymers).  In contrast, ...
CDD:143475	224	EUKprk	Bacteria:283,Environmental:4,Invertebrates:1,Plants:10,Primates:1,Vertebrates:4,nodiv:1	cd06567, Peptidase_S41, C-terminal processing peptidase family S41.  Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although ...
CDD:119336	329	PRK	Bacteria:13	cd06568, GH20_SpHex_like, A subgroup of  the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the N-acetylhexosaminidase from Streptomyces plicatus (SpHex).  SpHex catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a ...
CDD:119337	445	EUKprk	Bacteria:3,Invertebrates:1	cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these ...
CDD:119330	90	PRK	Bacteria:136,nodiv:1	cd06571, Bac_DnaA_C, C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
CDD:119329	390	EUKprk	Bacteria:110,Environmental:4,Invertebrates:1,Plants:11	cd06572, Histidinol_dh, Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent oxidation of L-histidinol to L-histidinaldehyde, and (ii) the NAD-dependent oxidation of L-histidinaldehyde to L-histidine. In most fungi and in the ...
CDD:119325	53	PRK	Bacteria:9	cd06573, PASTA, PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
CDD:119320	266	PRK	Bacteria:18	cd06574, TM_PBP1_branched-chain-AA_like, Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of monosaccharides including ribose, galactose, and arabinose. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ...
CDD:119326	54	PRK	Bacteria:105	cd06575, PASTA_Pbp2x-like_2, PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid ...
CDD:119327	55	PRK	Bacteria:19	cd06576, PASTA_Pbp2x-like_1, PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid ...
CDD:119328	62	PRK	Bacteria:221,Environmental:2	cd06577, PASTA_pknB, PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis. PknB is a receptor-like transmembrane protein with an extracellular signal sensor domain (containing multiple PASTA domains) and an intracellular, eukaryotic serine/threonine ...
CDD:119440	239	EUKprk	Bacteria:298,Environmental:7,Invertebrates:8,Plants:22,Primates:1,Vertebrates:3	cd06578, HemD, Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism ...
CDD:119321	263	PRK	Bacteria:108,nodiv:1	cd06579, TM_PBP1_transp_AraH_like, Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group also contains E. coli RbsC, AlsC, and MglC, which are TMs of other monosaccharide transporters, the ribose transporter, the D-allose transporter and the galactose ...
CDD:119322	234	PRK	Bacteria:67,Environmental:1	cd06580, TM_PBP1_transp_TpRbsC_like, Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters, which are mainly involved in the uptake of branched-chain amino acids (AAs) or in the uptake of monosaccharides including ribose, galactose, and ...
CDD:119323	268	PRK	Bacteria:162,Environmental:1	cd06581, TM_PBP1_LivM_like, Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and ...
CDD:119324	272	PRK	Bacteria:152,Environmental:2,nodiv:1	cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ...
CDD:133475	126	EUKprk	Bacteria:146,Invertebrates:26,Mammals:1,Phages:1,Plants:2,Primates:1,Vertebrates:4	cd06583, PGRP, Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and ...
CDD:132915	154	EUKprk	Bacteria:6,Plants:2,Primates:1	cd06586, TPP_enzyme_PYR, Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes.  Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A ...
CDD:211348	110	EUKprk	Bacteria:209,Environmental:1,Invertebrates:5,Plants:2,Primates:1,Rodents:1,nodiv:3	cd06587, Glo_EDI_BRP_like, This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins.  This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic ...
CDD:176658	128	EUKprk	Bacteria:172,Plants:4	cd06588, PhnB_like, Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates.  The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus ...
CDD:269876	265	EUKprk	Bacteria:10,Plants:1,Primates:1	cd06589, GH31, glycosyl hydrolase family 31 (GH31).  GH31 enzymes occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending ...
CDD:260000	207	PRK	Bacteria:74,Environmental:1	cd06590, RNase_HII_bacteria_HIII_like, Bacterial type 2 ribonuclease, HII and HIII-like.  This family includes type 2 RNases H from several bacteria, such as Bacillus subtilis, which have two different RNases, HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) ...
CDD:269877	322	EUKprk	Bacteria:54,Environmental:4,Plants:5	cd06591, GH31_xylosidase_XylS, xylosidase XylS-like.  XylS is a glycosyl hydrolase family 31 (GH31) alpha-xylosidase found in prokaryotes, eukaryotes, and archaea, that catalyzes the release of alpha-xylose from the non-reducing terminal side of the alpha-xyloside substrate. XylS has been characterized in Sulfolobus solfataricus where it hydrolyzes isoprimeverose, the p-nitrophenyl-beta derivative of isoprimeverose, and xyloglucan ...
CDD:269878	364	EUKprk	Bacteria:30,Environmental:6,Invertebrates:20,Plants:6,Primates:1,Vertebrates:3,nodiv:1	cd06592, GH31_NET37, glucosidase NET37.  NET37 (also known as KIAA1161) is a human lamina-associated nuclear envelope transmembrane protein. A member of the glycosyl hydrolase family 31 (GH31) , it has been shown to be required for myogenic differentiation of C2C12 cells. Related proteins are found in eukaryotes and prokaryotes. Enzymes of the GH31 family possess a wide range of different ...
CDD:269879	308	EUKprk	Bacteria:36,Environmental:2,Plants:5	cd06593, GH31_xylosidase_YicI, alpha-xylosidase YicI-like.  YicI alpha-xylosidase is a glycosyl hydrolase family 31 (GH31) enzyme that catalyzes the release of an alpha-xylosyl residue from the non-reducing end of alpha-xyloside substrates such as alpha-xylosyl fluoride and isoprimeverose. YicI forms a homohexamer (a trimer of dimers). All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in ...
CDD:269880	325	EUKprk	Bacteria:17,Invertebrates:9,Plants:10	cd06594, GH31_glucosidase_YihQ, alpha-glucosidase YihQ-like.  YihQ is a bacterial alpha-glucosidase with a conserved glycosyl hydrolase family 31 (GH31) domain that catalyzes the release of an alpha-glucosyl residue from the non-reducing end of alpha-glucoside substrates such as alpha-glucosyl fluoride. Orthologs of YihQ that have not yet been functionally characterized are present in plants and fungi. YihQ has sequence similarity to ...
CDD:269881	304	EUKprk	Bacteria:17,Environmental:26,Invertebrates:2,Plants:6	cd06595, GH31_u1, glycosyl hydrolase family 31 (GH31); uncharacterized subgroup.  This family represents an uncharacterized GH31 enzyme subgroup found in bacteria and eukaryotes. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and ...
CDD:269882	334	EUKprk	Bacteria:12,Invertebrates:2	cd06596, GH31_CPE1046, Clostridium CPE1046-like.  CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type C domain in addition to the GH31 domain. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including ...
CDD:269883	326	EUKprk	Bacteria:12,Environmental:1,Invertebrates:5	cd06597, GH31_transferase_CtsY, CtsY (cyclic tetrasaccharide-synthesizing enzyme Y)-like.  CtsY is a bacterial 3-alpha-isomaltosyltransferase, first identified in Arthrobacter globiformis, that produces cyclic tetrasaccharides together with a closely related enzyme CtsZ. CtsY and CtsZ both have a glycosyl hydrolase family 31 (GH31) catalytic domain; CtsZ belongs to a different subfamily. All GH31 enzymes cleave a terminal ...
CDD:269884	332	PRK	Bacteria:13,Environmental:1	cd06598, GH31_transferase_CtsZ, CtsZ (cyclic tetrasaccharide-synthesizing enzyme Z)-like.  CtsZ is a bacterial 6-alpha-glucosyltransferase, first identified in Arthrobacter globiformis, that produces cyclic tetrasaccharides together with a closely related enzyme CtsY. CtsZ and CtsY both have a glycosyl hydrolase family 31 (GH31) catalytic domain; CtsY belongs to a different subfamily. All GH31 enzymes cleave a terminal carbohydrate moiety from a ...
CDD:269885	319	EUKprk	Bacteria:20,Environmental:2,Invertebrates:2,Plants:4	cd06599, GH31_glycosidase_Aec37, E.coli Aec37-like.  Glycosyl hydrolase family 31 (GH31) domain of a bacterial protein family represented by Escherichia coli protein Aec37. The gene encoding Aec37 (aec-37) is located within a genomic island (AGI-3) isolated from the extraintestinal avian pathogenic Escherichia coli strain BEN2908. The function of Aec37 and its orthologs is unknown; however, deletion of a region of the ...
CDD:269888	367	EUK	Invertebrates:36,Mammals:1,Plants:28,Primates:1,Vertebrates:5,nodiv:1	cd06602, GH31_MGAM_SI_GAA, maltase-glucoamylase, sucrase-isomaltase, lysosomal acid alpha-glucosidase.  This subgroup includes the following three closely related glycosyl hydrolase family 31 (GH31) enzymes: maltase-glucoamylase (MGAM), sucrase-isomaltase (SI), and lysosomal acid alpha-glucosidase (GAA), also known as acid-maltase. MGAM is one of the two enzymes responsible for catalyzing the last ...
CDD:269889	467	EUK	Invertebrates:27,Plants:25,Primates:1,Rodents:1,Vertebrates:3	cd06603, GH31_GANC_GANAB_alpha, neutral alpha-glucosidase C, neutral alpha-glucosidase AB.  This subgroup includes the closely related glycosyl hydrolase family 31 (GH31) isozymes, neutral alpha-glucosidase C (GANC) and the alpha subunit of heterodimeric neutral alpha-glucosidase AB (GANAB). Initially distinguished on the basis of differences in electrophoretic mobility in starch gel, GANC and GANAB have been shown ...
CDD:269890	339	EUKprk	Bacteria:62,Environmental:4,Invertebrates:1,Plants:3	cd06604, GH31_glucosidase_II_MalA, Alpha-glucosidase II-like.  Alpha-glucosidase II (alpha-D-glucoside glucohydrolase) is a glycosyl hydrolase family 31 (GH31) enzyme, found in bacteria and plants, which has exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities. Alpha-glucosidase II has been characterized in Bacillus thermoamyloliquefaciens where it forms a homohexamer. This subgroup also includes the MalA ...
CDD:270782	265	EUK	Plants:2,Primates:1	cd06605, PKc_MAPKK, Catalytic domain of the dual-specificity Protein Kinase, Mitogen-Activated Protein Kinase Kinase.  PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MAPKKs are dual-specificity PKs that phosphorylate their downstream targets, MAPKs, at specific threonine and tyrosine residues. The MAPK signaling pathways are important mediators of cellular responses to ...
CDD:270783	258	EUK	Invertebrates:13,Plants:16,Primates:1	cd06606, STKc_MAPKKK, Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase Kinase Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPKKKs (MKKKs or MAP3Ks) are also called MAP/ERK kinase kinases (MEKKs) in some cases. They phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate ...
CDD:270785	275	EUK	Invertebrates:6,Primates:1	cd06608, STKc_myosinIII_N_like, N-terminal Catalytic domain of Class III myosin-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Class III myosins are motor proteins with an N-terminal kinase catalytic domain and a C-terminal actin-binding motor domain. Class III myosins are present in the photoreceptors of invertebrates and vertebrates and in the ...
CDD:270786	274	EUK	Invertebrates:6,Plants:11,Primates:1	cd06609, STKc_MST3_like, Catalytic domain of Mammalian Ste20-like protein kinase 3-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of MST3, MST4, STK25, Schizosaccharomyces pombe Nak1 and Sid1, Saccharomyces cerevisiae sporulation-specific protein 1 (SPS1), and related proteins. Nak1 is required by fission yeast ...
CDD:270787	267	EUK	Invertebrates:5,Plants:3,Primates:1,Vertebrates:3	cd06610, STKc_OSR1_SPAK, Catalytic domain of the Serine/Threonine Kinases, Oxidative stress response kinase and Ste20-related proline alanine-rich kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SPAK is also referred to as STK39 or PASK (proline-alanine-rich STE20-related kinase). OSR1 and SPAK regulate the activity of cation-chloride cotransporters ...
CDD:132943	256	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd06612, STKc_MST1_2, Catalytic domain of the Serine/Threonine Kinases, Mammalian STe20-like protein kinase 1 and 2.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of MST1, MST2, and related proteins including Drosophila Hippo and Dictyostelium discoideum Krs1 (kinase responsive to stress 1). MST1/2 and Hippo are involved in a conserved ...
CDD:270788	259	EUK	Invertebrates:10,Plants:2,Primates:1,Vertebrates:1	cd06613, STKc_MAP4K3_like, Catalytic domain of Mitogen-activated protein kinase kinase kinase kinase (MAP4K) 3-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes MAP4K3, MAP4K1, MAP4K2, MAP4K5, and related proteins. Vertebrate members contain an N-terminal catalytic domain and a C-terminal citron homology ...
CDD:270789	255	EUK	Invertebrates:7,Plants:2,Primates:1,Vertebrates:1	cd06614, STKc_PAK, Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs are implicated in the regulation of many cellular processes including growth ...
CDD:132954	264	EUK	Invertebrates:9,Plants:7	cd06623, PKc_MAPKK_plant_like, Catalytic domain of Plant dual-specificity Mitogen-Activated Protein Kinase Kinases and similar proteins.  PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. Members of this group include MAPKKs from plants, kinetoplastids, alveolates, and mycetozoa. The MAPKK, LmxPK4, from Leishmania mexicana, is important in differentiation and virulence. ...
CDD:270796	265	EUK	Invertebrates:6,Plants:7,Vertebrates:3	cd06626, STKc_MEKK4, Catalytic domain of the Protein Serine/Threonine Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 4.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MEKK4 is a MAPK kinase kinase that phosphorylates and activates the c-Jun N-terminal kinase (JNK) and p38 MAPK signaling pathways by directly activating ...
CDD:270797	254	EUK	Invertebrates:7,Plants:16	cd06627, STKc_Cdc7_like, Catalytic domain of Cell division control protein 7-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily include Schizosaccharomyces pombe Cdc7, Saccharomyces cerevisiae Cdc15, Arabidopsis thaliana mitogen-activated protein kinase kinase kinase (MAPKKK) epsilon, and related proteins. MAPKKKs phosphorylate ...
CDD:119408	285	EUKprk	Bacteria:375,Environmental:5,Invertebrates:35,Plants:58,Primates:1,Vertebrates:6,nodiv:1	cd06660, Aldo_ket_red, Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid ...
CDD:119400	99	EUKprk	Bacteria:128,Invertebrates:14,Plants:22,Primates:1,Rodents:1,Vertebrates:5	cd06661, GGCT_like, GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle ...
CDD:119401	202	EUKprk	Bacteria:144,Invertebrates:14,Plants:7,Primates:1,Vertebrates:3,nodiv:1	cd06662, SURF1, SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring complex of the respiratory chain, is an assemblage of nuclear and mitochondrially-encoded subunits. Its assembly is mediated by nuclear ...
CDD:143480	123	EUKprk	Bacteria:143,Environmental:3,Invertebrates:14,Plants:11,Primates:1,Vertebrates:3	cd06664, IscU_like, Iron-sulfur cluster scaffold-like proteins.  IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated ...
CDD:143484	211	EUKprk	Bacteria:6,Vertebrates:1	cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes.  The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like ...
CDD:143485	368	PRK	Bacteria:12	cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes.  This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These ...
CDD:143486	382	PRK	Bacteria:15	cd06811, PLPDE_III_yhfX_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX.  This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that ...
CDD:143487	374	PRK	Bacteria:12	cd06812, PLPDE_III_DSD_D-TA_like_1, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1.  This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the ...
CDD:143488	388	PRK	Bacteria:16	cd06813, PLPDE_III_DSD_D-TA_like_2, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2.  This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the ...
CDD:143489	379	PRK	Bacteria:10	cd06814, PLPDE_III_DSD_D-TA_like_3, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3.  This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the ...
CDD:143490	353	PRK	Bacteria:34	cd06815, PLPDE_III_AR_like_1, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1.  This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of ...
CDD:143491	389	EUK	Invertebrates:2,Plants:11,Vertebrates:1	cd06817, PLPDE_III_DSD, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase.  This subfamily is composed of chicken D-serine dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic proteins. Chicken DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. It is a fold type III PLP-dependent enzyme with similarity to bacterial alanine racemase (AR), ...
CDD:143492	382	PRK	Bacteria:18	cd06818, PLPDE_III_cryptic_DSD, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase.  This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel ...
CDD:143493	358	EUKprk	Bacteria:22,Environmental:1,Invertebrates:2,Plants:1	cd06819, PLPDE_III_LS_D-TA, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase.  Low specificity D-threonine aldolase (Low specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene from Arthrobacter sp. strain DK-38, is the prototype of this subfamily. Low specificity D-TAs are fold type III PLP-dependent enzymes that catalyze the interconversion between D-threonine/D-allo-threonine and ...
CDD:143494	353	PRK	Bacteria:12	cd06820, PLPDE_III_LS_D-TA_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like.  This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for ...
CDD:143495	361	PRK	Bacteria:14	cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase.  D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Its activity is present in several genera of bacteria but not in fungi. It requires PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ as cofactors for catalytic ...
CDD:143496	227	EUK	Invertebrates:19,Plants:12,Primates:1,Vertebrates:3	cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins.  This subfamily contains mostly uncharacterized eukaryotic proteins with  similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain ...
CDD:143497	224	EUKprk	Bacteria:31,Invertebrates:1	cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins.  This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is ...
CDD:143499	365	PRK	Bacteria:5	cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2.  This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent ...
CDD:143500	354	PRK	Bacteria:52	cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases.  This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III ...
CDD:143501	373	EUKprk	Bacteria:109,Environmental:2,Invertebrates:3,Plants:5	cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase.  Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to ...
CDD:143502	346	PRK	Bacteria:32,Environmental:1	cd06829, PLPDE_III_CANSDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase.  Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal ...
CDD:143503	409	EUKprk	Bacteria:23,Plants:3	cd06830, PLPDE_III_ADC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase.  This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous ...
CDD:143506	382	PRK	Bacteria:18,nodiv:1	cd06839, PLPDE_III_Btrk_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase.  This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. ...
CDD:143508	379	PRK	Bacteria:18	cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE.  This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, ...
CDD:143509	423	PRK	Bacteria:16	cd06842, PLPDE_III_Y4yA_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA.  This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal ...
CDD:143510	377	PRK	Bacteria:14	cd06843, PLPDE_III_PvsE_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE.  This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich ...
CDD:132900	144	EUK	Invertebrates:17,Mammals:3,Primates:1,Rodents:2,Vertebrates:7,nodiv:1	cd06845, Bcl-2_like, Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) ...
CDD:185704	182	EUKprk	Bacteria:10,Plants:1,Primates:1,Viruses:1	cd06846, Adenylation_DNA_ligase_like, Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases.  ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, ...
CDD:133457	96	EUKprk	Bacteria:74,Environmental:2,Invertebrates:16,Plants:11,Rodents:1,Vertebrates:3	cd06848, GCS_H, Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-proteins) which catalyzes the oxidative cleavage of glycine. The H-protein shuttles the methylamine group of glycine from the P-protein ...
CDD:133458	74	EUKprk	Bacteria:184,Environmental:1,Invertebrates:23,Mammals:1,Plants:20,Primates:1,Vertebrates:4	cd06849, lipoyl_domain, Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl ...
CDD:133459	67	EUKprk	Bacteria:236,Environmental:6,Invertebrates:22,Plants:28,Primates:1,Vertebrates:4,nodiv:1	cd06850, biotinyl_domain, The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain ...
CDD:133462	280	EUKprk	Bacteria:82,Environmental:2,Plants:4	cd06852, GT_MraY, Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with possibly ten transmembrane domains.
CDD:133463	249	PRK	Bacteria:114,nodiv:1	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate molecule and N-acetylglucosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylglucosamine precursor. WecA ...
CDD:133464	253	PRK	Bacteria:40	cd06854, GT_WbpL_WbcO_like, The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor. The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic end products implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or ...
CDD:133465	283	EUKprk	Bacteria:1,Invertebrates:16,Plants:6,Primates:1,Vertebrates:2	cd06855, GT_GPT_euk, UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT) catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-glycosylation. GPT activity has been identified in all eukaryotic cells examined to date. A series of six conserved ...
CDD:133466	280	PRK	Bacteria:16,Environmental:1	cd06856, GT_GPT_archaea, UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT)-like proteins in archaea. Eukaryotic GPT catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-linked glycosylation. Evidence for the existence of the N-glycosylation pathway in archaea has emerged and ...
CDD:271356	407	EUKprk	Bacteria:3,Invertebrates:3	cd06857, SLC5-6-like_sbd, Solute carrier families 5 and 6-like; solute binding domain.  This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, ...
CDD:132769	114	EUK	Invertebrates:9,Plants:15,Primates:1	cd06859, PX_SNX1_2_like, The phosphoinositide binding Phox Homology domain of Sorting Nexins 1 and 2.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein ...
CDD:132770	116	EUK	Invertebrates:9,Primates:1,Vertebrates:1	cd06860, PX_SNX7_30_like, The phosphoinositide binding Phox Homology domain of Sorting Nexins 7 and 30.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the ...
CDD:132772	125	EUK	Invertebrates:7,Plants:1,Primates:1	cd06862, PX_SNX9_18_like, The phosphoinositide binding Phox Homology domain of Sorting Nexins 9 and 18.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein ...
CDD:132773	118	EUK	Plants:11	cd06863, PX_Atg24p, The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs ...
CDD:132774	129	EUK	Invertebrates:7,Primates:1,Vertebrates:1	cd06864, PX_SNX4, The phosphoinositide binding Phox Homology domain of Sorting Nexin 4.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132776	105	EUK	Invertebrates:9,Plants:8,Vertebrates:2	cd06866, PX_SNX8_Mvp1p_like, The phosphoinositide binding Phox Homology domain of Sorting Nexin 8 and yeast Mvp1p.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and ...
CDD:132777	112	EUK	Plants:13	cd06867, PX_SNX41_42, The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched ...
CDD:132779	119	EUK	Plants:17	cd06869, PX_UP2_fungi, The phosphoinositide binding Phox Homology domain of uncharacterized fungal proteins.  The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized fungal proteins containing a PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, ...
CDD:132783	120	EUK	Invertebrates:12,Primates:1,Vertebrates:1	cd06873, PX_SNX13, The phosphoinositide binding Phox Homology domain of Sorting Nexin 13.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132785	116	EUK	Invertebrates:10,Vertebrates:2	cd06875, PX_IRAS, The phosphoinositide binding Phox Homology domain of the Imidazoline Receptor Antisera-Selected.  The PX domain is a phosphoinositide binding (PI) module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Imidazoline Receptor Antisera-Selected (IRAS), also called nischarin, contains an N-terminal PX domain, leucine rich repeats, ...
CDD:132786	133	EUK	Plants:12	cd06876, PX_MDM1p, The phosphoinositide binding Phox Homology domain of yeast MDM1p.  The PX domain is a phosphoinositide binding (PI) module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Yeast MDM1p is a filament-like protein localized in punctate structures distributed throughout the cytoplasm. It plays an important role in nuclear and mitochondrial transmission ...
CDD:132787	119	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd06877, PX_SNX14, The phosphoinositide binding Phox Homology domain of Sorting Nexin 14.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132788	127	EUK	Invertebrates:9,Primates:1,Vertebrates:1	cd06878, PX_SNX25, The phosphoinositide binding Phox Homology domain of Sorting Nexin 25.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132790	110	EUK	Invertebrates:7,Primates:1,Vertebrates:4	cd06880, PX_SNX22, The phosphoinositide binding Phox Homology domain of Sorting Nexin 22.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132791	117	EUK	Invertebrates:8	cd06881, PX_SNX15_like, The phosphoinositide binding Phox Homology domain of Sorting Nexin 15-like proteins.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily have similarity to sorting nexin 15 (SNX15), which contains an N-terminal PX domain and a C-terminal Microtubule ...
CDD:132795	104	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd06885, PX_SNX17_31, The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Members of this subfamily include sorting nexin 17 (SNX17), SNX31, and similar proteins. They contain an N-terminal PX domain followed by a truncated FERM (4.1, ezrin, radixin, and moesin) domain and a unique C-terminal region. SNXs ...
CDD:132800	112	EUK	Plants:17	cd06890, PX_Bem1p, The phosphoinositide binding Phox Homology domain of Bem1p.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 ...
CDD:132801	140	EUK	Plants:13	cd06891, PX_Vps17p, The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps17p.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. ...
CDD:132805	140	EUK	Invertebrates:7,Plants:1,Vertebrates:1	cd06895, PX_PLD, The phosphoinositide binding Phox Homology domain of Phospholipase D.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and ...
CDD:132807	108	EUK	Plants:21	cd06897, PX_SNARE, The phosphoinositide binding Phox Homology domain of SNARE proteins from fungi.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. This subfamily is composed of fungal proteins similar to Saccharomyces cerevisiae Vam7p. They contain an N-terminal PX domain and a C-terminal SNARE domain. The ...
CDD:132808	113	EUK	Invertebrates:3,Vertebrates:4	cd06898, PX_SNX10, The phosphoinositide binding Phox Homology domain of Sorting Nexin 10.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched ...
CDD:173887	236	EUK	Plants:36	cd06899, lectin_legume_LecRK_Arcelin_ConA, legume lectins, lectin-like receptor kinases, arcelin, concanavalinA, and alpha-amylase inhibitor.  This alignment model includes the legume lectins (also known as agglutinins), the arcelin (also known as phytohemagglutinin-L) family of lectin-like defense proteins, the LecRK family of lectin-like receptor kinases, concanavalinA (ConA), and an alpha-amylase inhibitor.  Arcelin is a major seed glycoprotein discovered in ...
CDD:173890	225	EUK	Invertebrates:7,Mammals:1,Rodents:2,Vertebrates:4	cd06902, lectin_ERGIC-53_ERGL, ERGIC-53 and ERGL type 1 transmembrane proteins, N-terminal lectin domain.  ERGIC-53 and ERGL, N-terminal carbohydrate recognition domain. ERGIC-53 and ERGL are eukaryotic mannose-binding type 1 transmembrane proteins of the early secretory pathway that transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC).  ERGIC-53 and ERGL ...
CDD:173891	215	EUK	Plants:17	cd06903, lectin_EMP46_EMP47, EMP46 and EMP47 type 1 transmembrane proteins, N-terminal lectin domain.  EMP46 and EMP47, N-terminal carbohydrate recognition domain. EMP46 and EMP47 are fungal type-I transmembrane proteins that cycle between the endoplasmic reticulum and the golgi apparatus and are thought to function as cargo receptors that transport newly synthesized glycoproteins.  EMP47 is a receptor for EMP46 responsible for the selective transport of EMP46 by ...
CDD:133114	178	PRK	Bacteria:9	cd06904, M14_MpaA_like, Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A and related proteins.  Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A (MpaA) and related proteins. MpaA is a member of the M14 family of metallocarboxypeptidases (MCPs), however it has an exceptional type of activity, it hydrolyzes the gamma-D-glutamyl-meso-diaminopimelic acid (gamma-D-Glu-Dap) bond in murein peptides. MpaA is specific for cleavage ...
CDD:199876	282	EUKprk	Bacteria:5,Invertebrates:2,Primates:1,Rodents:1,Vertebrates:5	cd06909, M14_ASPA, Peptidase M14 Aspartoacylase (ASPA) subfamily.  Aspartoacylase (ASPA) belongs to the Succinylglutamate desuccinylase/aspartoacylase subfamily of the M14 family of metallocarboxypeptidases. ASPA (also known as aminoacylase 2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ...
CDD:199877	272	PRK	Bacteria:14	cd06910, M14_ASTE_ASPA_like_7, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup.  A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as ...
CDD:132874	86	PRK	Bacteria:110,Environmental:1	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system.  VirB9 is a component of the type IV secretion system, which is employed by pathogenic bacteria to export virulence proteins directly from the bacterial cytoplasm into the host cell. Unlike the more common type III secretion system, type IV systems evolved from the conjugative apparatus, which is used to transfer DNA between cells. VirB9 was initially identified ...
CDD:133467	193	PRK	Bacteria:28	cd06912, GT_MraY_like, This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate. This is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan ...
CDD:133064	278	EUK	Plants:6	cd06914, GT8_GNT1, GNT1 is a fungal enzyme that belongs to the GT 8 family.  N-acetylglucosaminyltransferase is a fungal enzyme that catalyzes the addition of N-acetyl-D-glucosamine to mannotetraose side chains by an alpha 1-2 linkage during the synthesis of mannan. The N-acetyl-D-glucosamine moiety in mannan plays a role in the attachment of mannan to asparagine residues in proteins. The mannotetraose and its N-acetyl-D-glucosamine derivative side chains of mannan ...
CDD:133065	223	PRK	Bacteria:28,Environmental:1	cd06915, NTP_transferase_WcbM_like, WcbM_like is a subfamily of nucleotidyl transferases.  WcbM protein of Burkholderia mallei is involved in the biosynthesis, export or translocation of capsule. It is a subfamily of nucleotidyl transferases that transfer nucleotides onto phosphosugars.
CDD:143512	72	EUK	Invertebrates:15,Primates:1,Rodents:1,Vertebrates:2	cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers.  DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a ...
CDD:133476	51	EUK	Invertebrates:6	cd06918, ChtBD1_like, Domain observed in several metazoan proteins. The pattern of conserved cysteine residues resembles that of chitin binding domains found in plants and fungi.
CDD:132994	111	PRK	Bacteria:32,Environmental:3	cd06919, Asp_decarbox, Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent  decarboxylase in beta-alanine production.  Decarboxylation of aspartate is  the major route of beta-alanine production in bacteria, and is catalyzed  by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which  requires a pyruvoyl group for its activity. The pyruvoyl cofactor is  covalently bound to the enzyme. The protein is ...
CDD:132993	117	PRK	Bacteria:31	cd06920, NEAT, NEAr Transport domain, a component of cell surface proteins.  NEAr Transporter (NEAT) domain; used by pathogenic bacteria to to scavenge heme-iron from host hemoproteins. The NEAT domain is a component of cell surface proteins (iron regulated surface determinants, or Isd, such as IsdA and IsdC)  in various gram-positive bacteria, and may be arranged in tandem repeats.
CDD:211313	38	EUK	Plants:7	cd06922, ChtBD1_GH18_1, Hevein or Type 1 chitin binding domain subfamily that co-occurs with family 18 glycosyl hydrolases.  ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in ...
CDD:211314	47	EUK	Plants:7	cd06923, ChtBD1_GH16, Hevein or Type 1 chitin binding domain subfamily that co-occurs with family 16 glycosyl hydrolases.  This subfamily includes Saccharomyces cerevisiae Utr2p, also known as Crh2p, which participates in the cross-linking of chitin to beta(1-3)- and beta(1-6) glucan in the cell wall,  and S. cerevisiae Crr1p, a putative transglycosidase which is needed for proper spore wall assembly. ChtBD1 is a lectin domain found in proteins from plants and fungi ...
CDD:132902	93	EUK	Invertebrates:18,Plants:18,Primates:1,Vertebrates:4	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryotic RNA polymerase II.  The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three ...
CDD:132903	83	PRK	Bacteria:16	cd06927, RNAP_L, L subunit of Archaeal RNA polymerase.  The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the ...
CDD:132904	215	EUKprk	Bacteria:40,Environmental:1,Invertebrates:1,Plants:23	cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of Bacterial RNA polymerase.  The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and ...
CDD:132727	174	EUK	Invertebrates:10	cd06929, NR_LBD_F1, Ligand-binding domain of nuclear receptor family 1.  Ligand-binding domain (LBD) of nuclear receptor (NR) family 1:  This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological ...
CDD:132728	165	EUK	Invertebrates:11,Mammals:1,Primates:2,Vertebrates:7	cd06930, NR_LBD_F2, Ligand-binding domain of nuclear receptor family 2.  Ligand-binding domain (LBD) of nuclear receptor (NR) family 2:  This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear ...
CDD:132737	241	EUK	Invertebrates:4,Mammals:1,Rodents:1,Vertebrates:3	cd06939, NR_LBD_ROR_like, The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily.  The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to ...
CDD:132740	191	EUK	Invertebrates:6	cd06942, NR_LBD_Sex_1_like, The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein.  The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male ...
CDD:132741	207	EUK	Invertebrates:15,Primates:1,Vertebrates:3	cd06943, NR_LBD_RXR_like, The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily.  The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates.  The native ...
CDD:132742	237	EUK	Invertebrates:8,Mammals:1,Primates:1,Rodents:1,Vertebrates:6	cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1 like nuclear receptors.  The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. ...
CDD:132743	239	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:1	cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily.  The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and ...
CDD:132748	206	EUK	Invertebrates:8,Primates:1,Vertebrates:3	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of Tailless-like proteins,  orphan nuclear receptors.  The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR)  like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular ...
CDD:132750	222	EUK	Invertebrates:8,Vertebrates:2	cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan nuclear receptors TR4 and TR2.  The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2):  TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal ...
CDD:143518	76	EUK	Invertebrates:9,Vertebrates:3,nodiv:1	cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers.  DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and ...
CDD:133477	143	PRK	Bacteria:153,Environmental:1	cd06971, PgpA, Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism.  Phosphatidylglycerophosphatase A domain represents a family of bacterial membrane-associated enzymes involved in lipid metabolism. The prototype of this CD is a putative Phosphatidylglycerophosphatase A (PGPase A) from Listeria monocytogenes. PGPase A (EC: 3.1.3.27), encoded by the gene pgpA, specifically catalyzes the formation of ...
CDD:132992	162	EUKprk	Bacteria:73,Invertebrates:7,Plants:3	cd06974, TerD_like, Uncharacterized proteins involved in stress response, similar to tellurium resistance terD.  Tellurium resistance terD like proteins. This family is composed of uncharacterized proteins involved in stress response, such as the tellurium resistance proteins, chemical-damaging agent resistance proteins, and general stress proteins from a variety of organisms. The tellurium resistance proteins are homologous ...
CDD:270234	291	EUKprk	Bacteria:94,Environmental:1,Plants:1	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold.  The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubateria, at least three families of periplasmic binding-protein dependent transporters are known: ...
CDD:132927	160	PRK	Bacteria:96	cd07016, S14_ClpP_1, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease.  Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, ...
CDD:132928	171	EUKprk	Bacteria:56,Invertebrates:14,Plants:32,Primates:2,Vertebrates:2,nodiv:1	cd07017, S14_ClpP_2, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease.  Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded ...
CDD:132929	222	EUKprk	Bacteria:112,Invertebrates:1,Plants:5	cd07018, S49_SppA_67K_type, Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad.  Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the ...
CDD:132931	187	PRK	Bacteria:43	cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease.  Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin ...
CDD:132932	178	PRK	Bacteria:34	cd07021, Clp_protease_NfeD_like, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease.  Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous ...
CDD:132933	214	PRK	Bacteria:52	cd07022, S49_Sppa_36K_type, Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad.  Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes ...
CDD:132934	208	EUKprk	Bacteria:146,Environmental:1,Invertebrates:2,Plants:3	cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad.  Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K ...
CDD:132882	282	EUKprk	Bacteria:163,Environmental:3,Invertebrates:1,Plants:2	cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein.  LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide ...
CDD:197305	106	EUKprk	Bacteria:30,Environmental:2,Invertebrates:9,Mammals:1,Plants:14,Vertebrates:3	cd07026, Ribosomal_L20, Ribosomal protein L20.  The ribosomal protein family L20 contains members from eubacteria, as well as their mitochondrial and plastid homologs. L20 is an assembly protein, required for the first in-vitro reconstitution step of the 50S ribosomal subunit, but does not seem to be essential for ribosome activity. L20 has been shown to partially unfold in the absence of RNA, in ...
CDD:132907	85	EUK	Invertebrates:19,Plants:11,Primates:1,Vertebrates:2	cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III.  The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all ...
CDD:132908	259	PRK	Bacteria:4	cd07030, RNAP_D, D subunit of Archaeal RNA polymerase.  The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the ...
CDD:132909	265	EUK	Invertebrates:18,Plants:13,Rodents:1,Vertebrates:3	cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II.  The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct ...
CDD:132910	291	EUK	Invertebrates:22,Plants:12,Rodents:2,Vertebrates:3	cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III.  The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living ...
CDD:132916	156	EUKprk	Bacteria:153,Invertebrates:14,Mammals:1,Plants:17,Primates:1,Vertebrates:3,nodiv:1	cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins.  Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and the beta subunits of the E1 component of the human pyruvate dehydrogenase complex (E1- PDHc), ...
CDD:132917	160	EUKprk	Bacteria:104,Invertebrates:4,Plants:5	cd07034, TPP_PYR_PFOR_IOR-alpha_like, Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins.  Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain, of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit (IOR-alpha), and related proteins, subfamily. The PYR ...
CDD:132918	155	EUKprk	Bacteria:203,Invertebrates:12,Plants:20,Primates:1,Vertebrates:3	cd07035, TPP_PYR_POX_like, Pyrimidine (PYR) binding domain of POX and related proteins.  Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR ...
CDD:132919	167	EUKprk	Bacteria:41,Invertebrates:6,Plants:11,Vertebrates:3	cd07036, TPP_PYR_E1-PDHc-beta_like, Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins.  Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of the beta subunits of the E1 components of: human pyruvate dehydrogenase complex (E1- PDHc), the acetoin dehydrogenase complex (ADC), and the branched chain alpha-keto ...
CDD:132920	162	EUKprk	Bacteria:70,Plants:7	cd07037, TPP_PYR_MenD, Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins.  Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate (SEPHCHC) synthase (MenD) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. ...
CDD:132921	162	EUKprk	Bacteria:33,Invertebrates:3,Plants:20	cd07038, TPP_PYR_PDC_IPDC_like, Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins.  Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of  pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds ...
CDD:132922	164	PRK	Bacteria:21,nodiv:1	cd07039, TPP_PYR_POX, Pyrimidine (PYR) binding domain of POX.  Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR ...
CDD:132716	153	EUKprk	Bacteria:136,Environmental:2,Invertebrates:22,Plants:51,Primates:1,Rodents:1,Vertebrates:7,nodiv:2	cd07040, HP, Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction.  Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the ...
CDD:132912	109	PRK	Bacteria:39	cd07041, STAS_RsbR_RsbS_like, Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation.  The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress ...
CDD:132913	107	EUKprk	Bacteria:201,Environmental:2,Invertebrates:24,Mammals:1,Plants:35,Primates:1,Rodents:1,Vertebrates:7	cd07042, STAS_SulP_like_sulfate_transporter, Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function.  The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and ...
CDD:132914	99	PRK	Bacteria:229,Environmental:1	cd07043, STAS_anti-anti-sigma_factors, Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation.  Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a ...
CDD:132885	84	PRK	Bacteria:26	cd07045, BMC_CcmK_like, Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain.  Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be ...
CDD:132886	110	PRK	Bacteria:14	cd07046, BMC_PduU-EutS, 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain.  PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits.  PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme ...
CDD:132891	111	PRK	Bacteria:12	cd07051, BMC_like_1_repeat1, Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1.  BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial ...
CDD:132892	79	PRK	Bacteria:3	cd07052, BMC_like_1_repeat2, Bacterial Micro-Compartment (BMC)-like domain 1 repeat 2.  BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial ...
CDD:132893	76	PRK	Bacteria:23	cd07053, BMC_PduT_repeat1, 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1.  PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and ...
CDD:132894	78	PRK	Bacteria:6	cd07054, BMC_PduT_repeat2, 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2.  PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and ...
CDD:132897	88	PRK	Bacteria:11	cd07057, BMC_CcmK, Carbon dioxide concentrating mechanism (CcmK); Bacterial Micro-Compartment (BCM) domain.  CcmK1-4 and CcmL proteins found in Synechocystis sp. strain PCC 6803 make up the beta carboxysome shell.  These CcmK proteins have been shown to form hexameric units, while the CcmL proteins have been shown to form pentameric units.  Together these proteins further assemble into the flat facets of the polyhedral carboxysome shell.  The structures suggest that ...
CDD:132717	242	miss	miss	cd07061, HP_HAP_like, Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction.  Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or ...
CDD:132883	308	miss	miss	cd07062, Peptidase_S66_mccF_like, Microcin C7 self-immunity protein determines resistance to exogenous microcin C7.  Microcin C7 self-immunity protein (mccF): MccF, a homolog of the LD-carboxypeptidase family, mediates resistance against exogenously added microcin C7 (MccC7), a ribosomally-encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. The plasmid-encoded mccF gene is transcribed in the opposite direction ...
CDD:132881	208	miss	miss	cd07064, AlkD_like_1, A new structural DNA glycosylase containing HEAT-like repeats.  This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix).  DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be ...
CDD:143549	119	EUK	Invertebrates:20,Mammals:1,Primates:2,Rodents:2,Vertebrates:2,nodiv:2	cd07066, CRD_FZ, CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain.  CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins ...
CDD:132718	153	miss	miss	cd07067, HP_PGM_like, Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction.  Subgroup of the catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This subgroup contains cofactor-dependent and ...
CDD:132753	221	EUK	Invertebrates:7,Primates:1,Vertebrates:4	cd07068, NR_LBD_ER_like, The ligand binding domain of estrogen receptor and estrogen receptor-related receptors.  The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main ...
CDD:143397	432	PRK	Bacteria:7	cd07078, ALDH, NAD(P)+ dependent aldehyde dehydrogenase family.  The aldehyde dehydrogenase family (ALDH) of NAD(P)+ dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in  ...
CDD:143398	406	EUKprk	Bacteria:98,Environmental:1,Invertebrates:8,Plants:8,Vertebrates:2	cd07079, ALDH_F18-19_ProA-GPR, Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19.  Gamma-glutamyl phosphate reductase (GPR), a L-proline biosynthetic pathway (PBP) enzyme that catalyzes the NADPH dependent reduction of L-gamma-glutamyl  5-phosphate into L-glutamate 5-semialdehyde and phosphate. The glutamate route of the PBP involves two enzymatic steps catalyzed by ...
CDD:143399	422	PRK	Bacteria:25	cd07080, ALDH_Acyl-CoA-Red_LuxC, Acyl-CoA reductase LuxC.  Acyl-CoA reductase, LuxC, (EC=1.2.1.50) is the fatty acid reductase enzyme responsible for synthesis of the aldehyde  substrate for the luminescent reaction catalyzed by luciferase. The fatty acid reductase, a luminescence-specific, multienzyme complex (LuxCDE), reduces myristic acid to generate the long chain fatty aldehyde required for the luciferase-catalyzed reaction resulting in the emission of ...
CDD:143401	473	EUKprk	Bacteria:20,Plants:3	cd07082, ALDH_F11_NP-GAPDH, NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11.  NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9) catalyzes the irreversible oxidation of glyceraldehyde 3-phosphate to 3-phosphoglycerate generating NADPH for biosynthetic reactions.  This CD also includes the Arabidopsis thaliana osmotic-stress-inducible ALDH family 11, ALDH11A3 ...
CDD:143404	478	EUKprk	Bacteria:28,Environmental:1,Invertebrates:8,Plants:8,Primates:1,Vertebrates:3	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2.  Methylmalonate semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27) [acylating] from Bacillus subtilis is involved in valine metabolism and catalyses the NAD+- and CoA-dependent oxidation of methylmalonate semialdehyde into propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and Arabidopsis MMSDH ...
CDD:143405	478	EUKprk	Bacteria:13,Invertebrates:11,Plants:4,Primates:1,Vertebrates:2	cd07086, ALDH_F7_AASADH-like, NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase and related proteins.  ALDH subfamily which includes the NAD+-dependent, alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as Antiquitin-1, ALDH7A1, ALDH7B or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), and other similar sequences, such as the uncharacterized aldehyde dehydrogenase ...
CDD:143406	426	EUKprk	Bacteria:30,Environmental:1,Invertebrates:5	cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl aldehyde dehydrogenase, ALDH families 3, 13, and 14, and other related proteins.  ALDH subfamily which includes NAD(P)+-dependent, aldehyde dehydrogenase, family 3 member A1 and B1  (ALDH3A1, ALDH3B1,  EC=1.2.1.5) and fatty aldehyde dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3), and also plant ALDH family members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14 ...
CDD:143407	468	PRK	Bacteria:14,Environmental:1	cd07088, ALDH_LactADH-AldA, Escherichia coli lactaldehyde dehydrogenase AldA-like.  Lactaldehyde dehydrogenase from Escherichia coli (AldA, LactADH, EC=1.2.1.22), an NAD(+)-dependent enzyme involved in the metabolism of L-fucose and L-rhamnose, and other similar sequences are present in this CD.
CDD:143408	459	PRK	Bacteria:14	cd07089, ALDH_CddD-AldA-like, Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins.  The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD.
CDD:143409	457	EUKprk	Bacteria:4,Invertebrates:6,Plants:1,Primates:1,Vertebrates:2	cd07090, ALDH_F9_TMBADH, NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1.  NAD+-dependent, 4-trimethylaminobutyraldehyde dehydrogenase (TMABADH, EC=1.2.1.47), also known as aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in humans, is a cytosolic tetramer which catalyzes the oxidation of gamma-aminobutyraldehyde involved in 4-aminobutyric acid (GABA) biosynthesis  and also oxidizes ...
CDD:143410	476	EUKprk	Bacteria:2,Invertebrates:4,Plants:7	cd07091, ALDH_F1-2_Ald2-like, ALDH subfamily: ALDH families 1and 2, including 10-formyltetrahydrofolate dehydrogenase, NAD+-dependent retinal dehydrogenase 1 and related proteins.  ALDH subfamily which includes the NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36), also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1), in humans, a homotetrameric, cytosolic enzyme that catalyzes the oxidation of ...
CDD:143411	450	PRK	Bacteria:10	cd07092, ALDH_ABALDH-YdcW, Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like.  NAD+-dependent, tetrameric, gamma-aminobutyraldehyde dehydrogenase (ABALDH), YdcW of Escherichia coli K12, catalyzes the oxidation of gamma-aminobutyraldehyde to gamma-aminobutyric acid. ABALDH can also oxidize n-alkyl medium-chain aldehydes, but with a lower catalytic efficiency.
CDD:143412	455	EUKprk	Bacteria:26,Invertebrates:4,Plants:1,Primates:1,Vertebrates:2	cd07093, ALDH_F8_HMSADH, Human aldehyde dehydrogenase family 8 member A1-like.  In humans, the  aldehyde dehydrogenase family 8 member A1 (ALDH8A1) protein functions to convert 9-cis-retinal to 9-cis-retinoic acid and has a preference for NAD+. Also included in this CD is the 2-hydroxymuconic semialdehyde dehydrogenase (HMSADH) which catalyzes the conversion of 2-hydroxymuconic semialdehyde to 4-oxalocrotonate, a ...
CDD:143414	431	PRK	Bacteria:18	cd07095, ALDH_SGSD_AstD, N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like.  N-succinylglutamate 5-semialdehyde dehydrogenase or succinylglutamic semialdehyde dehydrogenase (SGSD, E. coli AstD, EC=1.2.1.71) involved in L-arginine degradation via the arginine succinyltransferase (AST) pathway and catalyzes the NAD+-dependent reduction of succinylglutamate semialdehyde into succinylglutamate.
CDD:143415	473	PRK	Bacteria:17	cd07097, ALDH_KGSADH-YcbD, Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like.  Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, ...
CDD:143416	465	EUKprk	Bacteria:1,Invertebrates:3,Plants:8	cd07098, ALDH_F15-22, Aldehyde dehydrogenase family 15A1 and 22A1-like.  Aldehyde dehydrogenase family members ALDH15A1 (Saccharomyces cerevisiae YHR039C) and ALDH22A1 (Arabidopsis thaliana, EC=1.2.1.3), and similar sequences, are in this CD. Significant improvement of stress tolerance in tobacco plants was observed by overexpressing the ALDH22A1 gene from maize (Zea mays) and was accompanied by a reduction of malondialdehyde  derived ...
CDD:143417	453	EUKprk	Bacteria:21,Invertebrates:1	cd07099, ALDH_DDALDH, Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like.  The 4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH) involved in C30 carotenoid synthesis in Methylomonas sp. strain 16a and other similar sequences are present in this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde into 4,4'-diapolycopene-diacid.
CDD:143418	429	EUKprk	Bacteria:80,Invertebrates:2	cd07100, ALDH_SSADH1_GabD1, Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like.  Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde (SSA)  to succinate.  SSADH activity in Mycobacterium tuberculosis (Mtb) is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731).  The Mtb GabD1 SSADH1 reportedly is an enzyme of the gamma-aminobutyrate shunt, which ...
CDD:143419	454	PRK	Bacteria:3	cd07101, ALDH_SSADH2_GabD2, Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 2-like.  Succinate-semialdehyde dehydrogenase 2 (SSADH2) and similar proteins are in this CD. SSADH1 (GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate.  SSADH activity in Mycobacterium tuberculosis is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1 was shown to be much higher than that of ...
CDD:143420	452	EUKprk	Bacteria:12,Invertebrates:1,Plants:6	cd07102, ALDH_EDX86601, Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (EDX86601).  Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (locus EDX86601) and other similar sequences, are present in this CD.
CDD:143421	451	EUKprk	Bacteria:75,Environmental:1,Invertebrates:12,Plants:17,Rodents:1,Vertebrates:3,nodiv:1	cd07103, ALDH_F5_SSADH_GabD, Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like.  Succinate-semialdehyde dehydrogenase, mitochondrial (SSADH, GabD, EC=1.2.1.24) catalyzes the NAD+-dependent oxidation of succinate semialdehyde (SSA) to succinate. This group includes the human aldehyde dehydrogenase family 5 member A1 (ALDH5A1) which is a ...
CDD:143422	431	PRK	Bacteria:33	cd07104, ALDH_BenzADH-like, ALDH subfamily: NAD(P)+-dependent benzaldehyde dehydrogenase II, vanillin dehydrogenase, p-hydroxybenzaldehyde dehydrogenase and related proteins.  ALDH subfamily which includes the NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28)  involved in the oxidation of benzyl alcohol to benzoate; p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes the oxidation of p-hydroxybenzaldehyde to ...
CDD:143423	432	EUKprk	Bacteria:11,Plants:18	cd07105, ALDH_SaliADH, Salicylaldehyde dehydrogenase, DoxF-like.  Salicylaldehyde dehydrogenase (DoxF, SaliADH, EC=1.2.1.65) involved in the upper naphthalene catabolic pathway of Pseudomonas strain C18 and other similar sequences are present in this CD.
CDD:143424	446	EUKprk	Bacteria:30,Plants:10	cd07106, ALDH_AldA-AAD23400, Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like.  Putative aldehyde dehydrogenase, AldA, from Streptomyces aureofaciens (locus AAD23400) and other similar sequences are present in this CD.
CDD:143427	454	PRK	Bacteria:21	cd07109, ALDH_AAS00426, Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like.  Uncharacterized aldehyde dehydrogenase of Saccharopolyspora spinosa (AAS00426) and other similar sequences, are present in this CD.
CDD:143430	462	PRK	Bacteria:24,nodiv:1	cd07112, ALDH_GABALDH-PuuC, Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like.  NADP+-dependent, gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (GABALDH) PuuC of  Escherichia coli which catalyzes the conversion of putrescine to 4-aminobutanoate and other similar sequences are present in this CD.
CDD:143432	457	EUKprk	Bacteria:27,Plants:3,nodiv:1	cd07114, ALDH_DhaS, Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like.  Uncharacterized aldehyde dehydrogenase from Candidatus pelagibacter (DhaS) and other related sequences are present in this CD.
CDD:143437	482	EUKprk	Bacteria:10,Plants:1	cd07119, ALDH_BADH-GbsA, Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like.  Included in this CD is the NAD+-dependent, betaine aldehyde dehydrogenase (BADH, GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the synthesis of the osmoprotectant glycine betaine from choline or glycine betaine aldehyde.
CDD:143438	455	PRK	Bacteria:9,nodiv:1	cd07120, ALDH_PsfA-ACA09737, Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like.  Included in this CD is the aldehyde dehydrogenase (PsfA, locus ACA09737) of Pseudomonas putida involved in furoic acid metabolism. Transcription of psfA was induced in response to 2-furoic acid, furfuryl alcohol, and furfural.
CDD:143439	429	PRK	Bacteria:11	cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.  Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), converts acetaldehyde into acetyl-CoA.  This CD is limited to such monofunctional enzymes as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium.  Mutations in eutE abolish the ability to utilize ethanolamine as a carbon source.
CDD:143440	436	EUKprk	Bacteria:39,Invertebrates:4,Plants:2	cd07122, ALDH_F20_ACDH, Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like.  Coenzyme A acylating aldehyde dehydrogenase (ACDH, EC=1.2.1.10), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, functions as a single enzyme (such as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium) or as part of a multifunctional enzyme to convert acetaldehyde into acetyl-CoA . The E. coli aldehyde-alcohol ...
CDD:143441	522	EUKprk	Bacteria:12,Invertebrates:8,Plants:4,Vertebrates:2	cd07123, ALDH_F4-17_P5CDH, Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17.  Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), families 4 and 17: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily.  Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), also known as ALDH4A1 in humans,  is a mitochondrial  homodimer involved in proline degradation and ...
CDD:143442	512	PRK	Bacteria:16,Environmental:1	cd07124, ALDH_PutA-P5CDH-RocA, Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA.  Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), RocA: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. The proline catabolic enzymes, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate ...
CDD:143443	518	PRK	Bacteria:20,Environmental:1	cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA.  The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two ...
CDD:143446	513	PRK	Bacteria:11	cd07128, ALDH_MaoC-N, N-terminal domain of the monoamine oxidase C dehydratase.  The N-terminal domain of the MaoC dehydratase, a monoamine oxidase regulatory protein. Orthologs of MaoC include PaaZ (Escherichia coli) and PaaN (Pseudomonas putida), which are putative ring-opening enzymes of the aerobic phenylacetic acid (PA) catabolic pathway. The C-terminal domain of MaoC has sequence similarity to enoyl-CoA hydratase. Also included in this CD is a novel ...
CDD:143447	454	PRK	Bacteria:43	cd07129, ALDH_KGSADH, Alpha-Ketoglutaric Semialdehyde Dehydrogenase.  Alpha-Ketoglutaric Semialdehyde (KGSA) Dehydrogenase (KGSADH, EC 1.2.1.26) catalyzes the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. This CD contains such sequences as those seen in Azospirillum brasilense, KGSADH-II (D-glucarate/D-galactarate-inducible) and KGSADH-III (hydroxy-L-proline-inducible). Both show similar high substrate specificity for KGSA and different coenzyme ...
CDD:143448	474	miss	miss	cd07130, ALDH_F7_AASADH, NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B.  Alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as ALDH7A1, Antiquitin-1, ALDH7B, or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), is a NAD+-dependent ALDH. Human ALDH7A1 is involved in the pipecolic acid pathway of lysine catabolism, catalyzing the oxidation of alpha-aminoadipic semialdehyde to ...
CDD:143450	443	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:4	cd07132, ALDH_F3AB, Aldehyde dehydrogenase family 3 members A1, A2, and B1 and related proteins.  NAD(P)+-dependent, aldehyde dehydrogenase, family 3 members A1 and B1  (ALDH3A1, ALDH3B1,  EC=1.2.1.5) and fatty aldehyde dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3), and similar sequences are included in this CD. Human ALDH3A1 is a homodimer with a critical role in cellular defense against oxidative stress; it ...
CDD:143451	434	PRK	Bacteria:59	cd07133, ALDH_CALDH_CalB, Coniferyl aldehyde dehydrogenase-like.  Coniferyl aldehyde dehydrogenase (CALDH, EC=1.2.1.68) of Pseudomonas sp. strain HR199 (CalB) which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid, and similar sequences, are present in this CD.
CDD:143452	433	PRK	Bacteria:21	cd07134, ALDH_AlkH-like, Pseudomonas putida Aldehyde dehydrogenase AlkH-like.  Aldehyde dehydrogenase AlkH (locus name P12693, EC=1.2.1.3) of the alkBFGHJKL operon that allows Pseudomonas putida to metabolize alkanes and the aldehyde dehydrogenase AldX of Bacillus subtilis (locus P46329, EC=1.2.1.3), and similar sequences, are present in this CD.
CDD:143453	436	EUK	Plants:17	cd07135, ALDH_F14-YMR110C, Saccharomyces cerevisiae aldehyde dehydrogenase family 14 and related proteins.  Aldehyde dehydrogenase family 14 (ALDH14), isolated mainly from the mitochondrial outer membrane of Saccharomyces cerevisiae (YMR110C) and most closely related to the plant and animal ALDHs and fatty ALDHs family 3 members, and similar fungal sequences, are present in this CD.
CDD:143454	449	PRK	Bacteria:44,Environmental:1	cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde dehydrogenase ywdH-like.  Uncharacterized Bacillus subtilis ywdH aldehyde dehydrogenase (locus P39616)  most closely related to the ALDHs and fatty ALDHs of families 3 and 14, and similar sequences, are included in this CD.
CDD:143456	466	EUKprk	Bacteria:48,Plants:1,nodiv:1	cd07138, ALDH_CddD_SSP0762, Rhodococcus ruber 6-oxolauric acid dehydrogenase-like.  The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid, and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and other similar sequences, are included in this CD.
CDD:143457	471	PRK	Bacteria:21	cd07139, ALDH_AldA-Rv0768, Mycobacterium tuberculosis aldehyde dehydrogenase  AldA-like.  The Mycobacterium tuberculosis NAD+-dependent, aldehyde dehydrogenase  PDB structure,  3B4W, and the Mycobacterium tuberculosis H37Rv aldehyde dehydrogenase  AldA (locus Rv0768) sequence, as well as the Rhodococcus rhodochrous ALDH involved in haloalkane catabolism, and other similar sequences, are included in this CD.
CDD:143465	452	EUKprk	Bacteria:16,Invertebrates:1	cd07147, ALDH_F21_RNP123, Aldehyde dehydrogenase family 21A1-like.  Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was first described in the moss Tortula ruralis and is believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and ALDH21A1 expression represents a unique stress tolerance mechanism. So far, of plants, only the bryophyte sequence has been observed, but ...
CDD:143467	453	PRK	Bacteria:22	cd07149, ALDH_y4uC, Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1.  Uncharacterized aldehyde dehydrogenase (ORF name y4uC) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD.
CDD:143468	451	miss	miss	cd07150, ALDH_VaniDH_like, Pseudomonas putida vanillin dehydrogenase-like.  Vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid and other related  sequences are included in this CD.  The E. coli vanillin dehydrogenase (LigV) preferred NAD+ to NADP+  and exhibited a broad substrate preference, including vanillin,  benzaldehyde, protocatechualdehyde, m-anisaldehyde, and p-hydroxybenzaldehyde.
CDD:143469	465	miss	miss	cd07151, ALDH_HBenzADH, NADP+-dependent p-hydroxybenzaldehyde dehydrogenase-like.  NADP+-dependent, p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic acid and other related sequences are included in this CD.
CDD:143470	443	miss	miss	cd07152, ALDH_BenzADH, NAD-dependent benzaldehyde dehydrogenase II-like.  NAD-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28) is involved in the oxidation of benzyl alcohol to benzoate. In Acinetobacter calcoaceticus, this process is carried out by the chromosomally encoded, benzyl alcohol dehydrogenase (xylB) and benzaldehyde dehydrogenase II (xylC) enzymes; whereas in Pseudomonas putida they are encoded by TOL plasmids.
CDD:133478	116	PRK	Bacteria:239,Environmental:1	cd07153, Fur_like, Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators.  Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism.  A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) ...
CDD:143580	111	PRK	Bacteria:71,nodiv:1	cd07176, terB, tellurite resistance protein terB.  This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown.
CDD:143581	104	PRK	Bacteria:181,Environmental:1,nodiv:1	cd07177, terB_like, tellurium resistance terB-like protein.  This family consists of tellurium resistance terB proteins, N-terminal domain of heat shock DnaJ-like proteins, N-terminal domain of Mo-dependent nitrogenase-like proteins, C-terminal domain of ABC transporter ATP-binding proteins, C-terminal domain of serine/threonine protein kinase, and many hypothetical bacterial proteins. The function of this family is unknown.
CDD:143582	95	miss	miss	cd07178, terB_like_YebE, tellurium resistance terB-like protein, subgroup 3.  This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
CDD:260001	204	EUKprk	Bacteria:53,Environmental:4,Invertebrates:2	cd07180, RNase_HII_archaea_like, Archaeal Ribonuclease HII.  This family includes type 2 RNases H from archaea, some of which show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one is involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology ...
CDD:260002	221	EUK	Invertebrates:35,Plants:27,Primates:1,Rodents:1,Vertebrates:2	cd07181, RNase_HII_eukaryota_like, Eukaryotic RNase HII.  This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and ...
CDD:260003	177	EUKprk	Bacteria:370,Environmental:5,Invertebrates:2,Plants:11,nodiv:1	cd07182, RNase_HII_bacteria_HII_like, Bacterial Ribonuclease HII-like.  This family includes mostly bacterial type 2 RNases H, with some eukaryotic members. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII ...
CDD:199892	86	PRK	Bacteria:34	cd07184, E_set_Isoamylase_like_N, N-terminal Early set domain associated with the catalytic domain of isoamylase-like (also called glycogen 6-glucanohydrolase) proteins.  E or "early" set domains are associated with the catalytic domain of isoamylase-like proteins at the N-terminal end. Isoamylase is one of the starch-debranching enzymes that catalyze the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. ...
CDD:143586	106	EUKprk	Bacteria:396,Invertebrates:1,nodiv:1	cd07185, OmpA_C-like, Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA.  OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli ...
CDD:132872	303	PRK	Bacteria:13,Environmental:1	cd07186, CofD_like, LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis.  CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of ...
CDD:132873	308	EUKprk	Bacteria:35,Environmental:1,Plants:7	cd07187, YvcK_like, family of mostly uncharacterized proteins similar to B.subtilis YvcK.  One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been ...
CDD:143587	253	EUKprk	Bacteria:109,Invertebrates:3,Plants:6,Vertebrates:1	cd07197, nitrilase, Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes.  This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the ...
CDD:132837	172	EUKprk	Bacteria:5,Plants:4,Primates:1	cd07198, Patatin, Patatin-like phospholipase.  Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. ...
CDD:132838	258	EUKprk	Bacteria:41,Invertebrates:7,Plants:18,Primates:1	cd07199, Pat17_PNPLA8_PNPLA9_like, Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17.  Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a ...
CDD:132840	541	miss	miss	cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF cytosolic phospholipase A2; catalytic domain; Ca-dependent.  Group IVB, IVD, IVE, and IVF cPLA2 consists of two domains: the regulatory C2 domain and alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE, and IVF cPLA2 are also referred to as cPLA2-beta, -delta, -epsilon, and -zeta respectively. cPLA2-beta is approximately 30% identical to cPLA2-alpha and it shows low enzymatic activity compared to ...
CDD:132842	552	miss	miss	cd07203, cPLA2_Fungal_PLB, Fungal Phospholipase B-like; cPLA2 GrpIVA homologs; catalytic domain.  Fungal phospholipase B are Group IV cPLA2 homologs. Aspergillus PLA2 is Ca-dependent, yet it does not contain a C2 domain. PLB deacylates both sn-1 and sn-2 chains of phospholipids and are abundantly expressed in fungi. It shows lysophospholipase (lysoPL) and transacylase activities. The active site residues from cPLA2 are also conserved in PLB. Like cPLA2, PLB also has a ...
CDD:132843	243	EUK	Invertebrates:3	cd07204, Pat_PNPLA_like, Patatin-like phospholipase domain containing protein family.  Members of this family share a patain domain, initially discovered in potato tubers. PNPLA protein members show non-specific hydrolase activity with a variety of substrates such as triacylglycerol, phospholipids, and retinylesters. It contains the lipase consensus sequence (Gly-X-Ser-X-Gly). Nomenclature of PNPLA family could be misleading as some of the mammalian members of ...
CDD:132844	175	PRK	Bacteria:26	cd07205, Pat_PNPLA6_PNPLA7_NTE1_like, Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1.  Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are included in this family. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows ...
CDD:132845	298	EUKprk	Bacteria:14,Invertebrates:2	cd07206, Pat_TGL3-4-5_SDP1, Triacylglycerol lipase 3, 4, and 5 and Sugar-Dependent 1 lipase.  Triacylglycerol lipases are involved in triacylglycerol mobilization and degradation; they are found in lipid particles. TGL4 is 30% homologus to TGL3, whereas TGL5 is 26% homologus to TGL3. Sugar-Dependent 1 (SDP1) lipase has a patatin-like acyl-hydrolase domain that initiates the breakdown of storage oil in germinating Arabidopsis seeds. This family ...
CDD:132846	194	EUKprk	Bacteria:22,Invertebrates:4	cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2.  ExoU, a 74-kDa enzyme, is a potent virulence factor of Pseudomonas aeruginosa. One of the pathogenic mechanisms of P. aeruginosa is to induce cytotoxicity by the injection of effector proteins (e.g. ExoU) using the type III secretion (T3S) system. ExoU is homologus to patatin and also has the conserved catalytic residues of mammalian ...
CDD:132847	266	EUKprk	Bacteria:42,Plants:1	cd07208, Pat_hypo_Ecoli_yjju_like, Hypothetical patatin similar to yjju protein of Escherichia coli.  Patatin-like phospholipase similar to yjju protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins, and some representatives from eukaryotes and archaea.  The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic ...
CDD:132848	215	EUKprk	Bacteria:46,Invertebrates:1	cd07209, Pat_hypo_Ecoli_Z1214_like, Hypothetical patatin similar to Z1214 protein of Escherichia coli.  Patatin-like phospholipase similar to Z1214 protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins and some representatives from eukaryotes and archaea. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic ...
CDD:132849	221	EUKprk	Bacteria:9,Plants:1	cd07210, Pat_hypo_W_succinogenes_WS1459_like, Hypothetical patatin similar to WS1459 of Wolinella succinogenes.  Patatin-like phospholipase. This family predominantly consists of bacterial patatin glycoproteins. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. ...
CDD:132850	308	EUK	Invertebrates:11,Mammals:1,Plants:4,Rodents:1,Vertebrates:2	cd07211, Pat_PNPLA8, Patatin-like phospholipase domain containing protein 8.  PNPLA8 is a Ca-independent myocardial phospholipase which maintains mitochondrial integrity. PNPLA8 is also known as iPLA2-gamma. In humans, it is predominantly expressed in heart tissue. iPLA2-gamma can catalyze both phospholipase A1 and A2 reactions (PLA1 and PLA2 respectively). This family includes PNPLA8 (iPLA2-gamma) from Homo sapiens ...
CDD:132851	312	EUK	Invertebrates:6,Primates:1,Rodents:2,Vertebrates:3	cd07212, Pat_PNPLA9, Patatin-like phospholipase domain containing protein 9.  PNPLA9 is a Ca-independent phospholipase that catalyzes the hydrolysis of glycerophospholipids at the sn-2 position. PNPLA9 is also known as PLA2G6 (phospholipase A2 group VI) or iPLA2beta. PLA2G6 is stimulated by ATP and inhibited by bromoenol lactone (BEL). In humans, PNPLA9 in expressed ubiquitously and is involved in signal transduction, cell ...
CDD:132852	288	EUKprk	Bacteria:6,Invertebrates:3	cd07213, Pat17_PNPLA8_PNPLA9_like1, Patatin-like phospholipase.  Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of ...
CDD:132855	309	EUK	Plants:14	cd07216, Pat17_PNPLA8_PNPLA9_like3, Patatin-like phospholipase.  Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The ...
CDD:132863	233	EUK	Invertebrates:6,Plants:5	cd07224, Pat_like, Patatin-like phospholipase.  Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
CDD:132866	175	PRK	Bacteria:8	cd07228, Pat_NTE_like_bacteria, Bacterial patatin-like phospholipase domain containing protein 6.  Bacterial patatin-like phospholipase domain containing protein 6. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and ...
CDD:132867	391	EUK	Invertebrates:2,Plants:15	cd07229, Pat_TGL3_like, Triacylglycerol lipase 3.  Triacylglycerol lipase 3 (TGL3) are responsible for all the TAG lipase activity of the lipid particle. Triacylglycerol (TAG) lipases are also necessary for the mobilization of TAG stored in lipid particles. TGL3 contains the consensus sequence motif GXSXG, which is found in lipolytic enzymes. This family includes Tgl3p from Saccharomyces cerevisiae.
CDD:132868	421	EUK	Plants:26	cd07230, Pat_TGL4-5_like, Triacylglycerol lipase 4 and 5.  TGL4 and TGL5 are triacylglycerol lipases that are involved in triacylglycerol mobilization and degradation; they are found in lipid particles. Tgl4 is a functional ortholog of mammalian adipose TG lipase (ATGL) and is phosphorylated and activated by cyclin-dependent kinase 1 (Cdk1/Cdc28). TGL4 is 30% homologus to TGL3, whereas TGL5 is 26% homologus to TGL3. This family includes TGL4 (STC1) and TGL5 (STC2) ...
CDD:132870	407	EUK	Invertebrates:2,Plants:23	cd07232, Pat_PLPL, Patain-like phospholipase.  Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants and fungi. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
CDD:176659	121	EUKprk	Bacteria:32,Invertebrates:10,Plants:14,Vertebrates:3	cd07233, Glyoxalase_I, Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione.  Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes ...
CDD:176660	122	PRK	Bacteria:14	cd07235, MRD, Mitomycin C resistance protein (MRD).  Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance ...
CDD:176661	154	PRK	Bacteria:36	cd07237, BphC1-RGP6_C_like, C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins.  This subfamily contains the C-terminal, catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs ...
CDD:176662	112	PRK	Bacteria:13	cd07238, Glo_EDI_BRP_like_5, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members ...
CDD:176665	125	PRK	Bacteria:17	cd07241, Glo_EDI_BRP_like_3, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members ...
CDD:176666	128	EUKprk	Bacteria:38,Plants:1	cd07242, Glo_EDI_BRP_like_6, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for ...
CDD:176669	114	EUKprk	Bacteria:83,Plants:7	cd07245, Glo_EDI_BRP_like_9, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for ...
CDD:211349	123	EUKprk	Bacteria:71,Plants:3	cd07246, Glo_EDI_BRP_like_8, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for ...
CDD:176671	114	EUKprk	Bacteria:181,Environmental:1,Invertebrates:1,Plants:7,nodiv:1	cd07247, SgaA_N_like, N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains.  SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor ...
CDD:211350	128	EUKprk	Bacteria:80,Invertebrates:9,Plants:2,Primates:1,Vertebrates:3,nodiv:1	cd07249, MMCE, Methylmalonyl-CoA epimerase (MMCE).  MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, ...
CDD:176673	191	EUKprk	Bacteria:30,Invertebrates:12,Plants:9,Primates:1,Vertebrates:4	cd07250, HPPD_C_like, C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS).  HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of 4-hydroxyphenylpyruvate to homogentisate ...
CDD:211351	120	EUKprk	Bacteria:48,Plants:1	cd07251, Glo_EDI_BRP_like_10, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities ...
CDD:176675	120	PRK	Bacteria:24	cd07252, BphC1-RGP6_N_like, N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins.  This subfamily contains the N-terminal, non-catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs ...
CDD:176676	125	EUKprk	Bacteria:42,Invertebrates:5,Plants:6,Primates:1,Vertebrates:3,nodiv:1	cd07253, Glo_EDI_BRP_like_2, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound ...
CDD:176677	120	PRK	Bacteria:16	cd07254, Glo_EDI_BRP_like_20, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and types I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:211352	125	PRK	Bacteria:40	cd07255, Glo_EDI_BRP_like_12, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:176679	161	PRK	Bacteria:12	cd07256, HPCD_C_class_II, C-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD), which catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate; belongs to the type I class II family of extradiol dioxygenases.  This subfamily contains the C-terminal, catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of ...
CDD:176680	153	EUKprk	Bacteria:11,Plants:3	cd07257, THT_oxygenase_C, The C-terminal domain of 2,4,5-Trihydroxytoluene (THT) oxygenase, which is an extradiol dioxygenease in the 2,4-dinitrotoluene (DNT) degradation pathway.  This subfamily contains the C-terminal, catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, ...
CDD:176682	114	PRK	Bacteria:25	cd07261, Glo_EDI_BRP_like_11, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:176683	123	EUKprk	Bacteria:92,Plants:13	cd07262, Glo_EDI_BRP_like_19, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities ...
CDD:211353	120	EUKprk	Bacteria:64,Invertebrates:1	cd07263, Glo_EDI_BRP_like_16, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein ...
CDD:176685	125	EUKprk	Bacteria:18,Plants:1	cd07264, Glo_EDI_BRP_like_15, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities ...
CDD:176686	122	PRK	Bacteria:7	cd07265, 2_3_CTD_N, N-terminal domain of catechol 2,3-dioxygenase.  This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase  (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered ...
CDD:211354	121	PRK	Bacteria:4	cd07266, HPCD_N_class_II, N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); belongs to the type I class II family of extradiol dioxygenases.  This subfamily contains the N-terminal, non-catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, ...
CDD:176688	113	EUKprk	Bacteria:6,Plants:10	cd07267, THT_Oxygenase_N, N-terminal domain of 2,4,5-trihydroxytoluene (THT) oxygenase.  This subfamily contains the N-terminal, non-catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by ...
CDD:176689	149	EUKprk	Bacteria:5,Invertebrates:1	cd07268, Glo_EDI_BRP_like_4, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein ...
CDD:132810	118	EUK	Invertebrates:9,Vertebrates:2	cd07277, PX_RUN, The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains.  The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized proteins containing an N-terminal RUN domain and a C-terminal PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell ...
CDD:132812	112	EUK	Invertebrates:6,Primates:1	cd07279, PX_SNX20_21_like, The phosphoinositide binding Phox Homology domain of Sorting Nexins 20 and 21.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:132813	120	EUK	Plants:12	cd07280, PX_YPT35, The phosphoinositide binding Phox Homology domain of the fungal protein YPT35.  The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. This subfamily is composed of YPT35 proteins from the fungal subkingdom Dikarya. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may ...
CDD:143636	177	EUKprk	Bacteria:255,Invertebrates:41,Mammals:2,Plants:7,Primates:1,Rodents:1,Vertebrates:6,nodiv:2	cd07302, CHD, cyclase homology domain.  Catalytic domains of the mononucleotidyl cyclases (MNC's), also called cyclase homology domains (CHDs), are part of the class III nucleotidyl cyclases. This class includes eukaryotic and prokaryotic adenylate cyclases (AC's) and guanylate cyclases (GC's). They seem to share a common catalytic mechanism in their requirement for two magnesium ...
CDD:143612	344	EUKprk	Bacteria:88,Environmental:4,Invertebrates:4,Plants:10,nodiv:1	cd07304, Chorismate_synthase, Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway.  Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the ...
CDD:132766	279	EUK	Invertebrates:24,Plants:19,Rodents:1,Vertebrates:2,nodiv:1	cd07305, Porin3_Tom40, Translocase of outer mitochondrial membrane 40 (Tom40).  Tom40 forms a channel in the mitochondrial outer membrane with a pore about 1.5 to 2.5 nanometers wide. It functions as a transport channel for unfolded protein chains and forms a complex with Tom5, Tom6, Tom7, and Tom22. The primary receptors Tom20 and Tom70 recruit the unfolded precursor protein from the mitochondrial-import stimulating ...
CDD:132767	276	EUK	Invertebrates:21,Plants:18,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd07306, Porin3_VDAC, Voltage-dependent anion channel of the outer mitochondrial membrane.  The voltage-dependent anion channel (VDAC) regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane, which is highly permeable to small molecules. VDAC is the most abundant protein in the outer membrane, and membrane potentials can toggle VDAC between open or high-conducting and closed ...
CDD:153271	194	EUK	Invertebrates:7,Plants:12,Primates:1,Rodents:2,Vertebrates:1	cd07307, BAR, The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to ...
CDD:173892	218	EUK	Invertebrates:10,Plants:13	cd07308, lectin_leg-like, legume-like lectins: ERGIC-53, ERGL, VIP36, VIPL, EMP46, and EMP47.  The legume-like (leg-like) lectins are eukaryotic intracellular sugar transport proteins with a carbohydrate recognition domain similar to that of the legume lectins.  This domain binds high-mannose-type oligosaccharides for transport from the endoplasmic reticulum to the Golgi complex.  These leg-like lectins include ERGIC-53, ERGL, VIP36, VIPL, EMP46, ...
CDD:213985	88	PRK	Bacteria:5	cd07309, PHP, Polymerase and Histidinol Phosphatase domain.  The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in ...
CDD:143584	104	miss	miss	cd07313, terB_like_2, tellurium resistance terB-like protein, subgroup 2.  This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
CDD:143585	106	miss	miss	cd07316, terB_like_DjlA, N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins.  Tellurium resistance terB-like domain of the DnaJ-like DjlA proteins. This family represents the terB-like domain of DjlA-like proteins, a subgroup of heat shock DnaJ-like proteins.  Escherichia coli DjlA is a type III membrane protein with a small N-terminal transmembrane region and DnaJ-like domain on the extreme C-terminus.  Overproduction has been ...
CDD:153390	77	PRK	Bacteria:12	cd07321, Extradiol_Dioxygenase_3A_like, Subunit A of Class III extradiol dioxygenases.  Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings.  There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes ...
CDD:143474	390	EUK	Invertebrates:26,Plants:13,Primates:1,Vertebrates:1,nodiv:1	cd07322, PriL_PriS_Eukaryotic, Eukaryotic core primase: Large subunit, PriL.  Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic ...
CDD:153396	75	EUK	Invertebrates:13,Plants:22,Primates:1,Vertebrates:1	cd07323, LAM, LA motif RNA-binding domain.  This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins ...
CDD:259818	78	EUK	Invertebrates:3,Primates:1,Rodents:1	cd07347, harmonin_N_like, N-terminal protein-binding module of harmonin and similar domains, also known as HHD (harmonin homology domain).  This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the ...
CDD:259820	80	EUK	Invertebrates:5,Primates:1,Vertebrates:1	cd07354, HN_L-delphilin-R1_like, first harmonin_N_like domain (repeat 1) of L-delphilin, and related domains.  This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel ...
CDD:259823	81	EUK	Invertebrates:6,Vertebrates:1	cd07357, HN_L-whirlin_R2_like, second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains.  This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte ...
CDD:153372	271	PRK	Bacteria:20	cd07359, PCA_45_Doxase_B_like, Subunit B of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and simlar enzymes.  This subfamily of class III extradiol dioxygenases consists of a number of proteins with known enzymatic activities: Protocatechuate (PCA) 4,5-dioxygenase (LigAB), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), 3-O-Methylgallate Dioxygenase, 2-aminophenol 1,6-dioxygenase, as well as proteins without any known enzymatic ...
CDD:153373	266	EUKprk	Bacteria:101,Environmental:1,Invertebrates:21,Plants:27,Primates:1,Vertebrates:3,nodiv:1	cd07361, MEMO_like, Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility.  This subfamily is composed of Memo (mediator of ErbB2-driven cell motility) and similar proteins. Memo is a protein that is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility. It is required for the ...
CDD:153375	253	EUKprk	Bacteria:148,Invertebrates:7,Plants:31	cd07363, 45_DOPA_Dioxygenase, The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine.  This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine ...
CDD:153377	310	PRK	Bacteria:14	cd07365, MhpB_like, Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate.  2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB) catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate, yielding the product 2-hydroxy-6-oxo-nona-2,4-diene 1,9-dicarboxylate.  It is an essential ...
CDD:153378	328	PRK	Bacteria:8	cd07366, 3MGA_Dioxygenase, Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate.  3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to ...
CDD:153382	280	PRK	Bacteria:13	cd07370, HPCD, The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate.  3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, ...
CDD:143620	174	EUKprk	Bacteria:23,Invertebrates:1,Plants:6,Primates:1	cd07374, CYTH-like_Pase, CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases.  CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class ...
CDD:153408	117	PRK	Bacteria:2,Synthetic:1	cd07375, Anticodon_Ia_like, Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains.  This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino ...
CDD:143511	345	miss	miss	cd07376, PLPDE_III_DSD_D-TA_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase.  This family includes eukaryotic D-serine dehydratases (DSD), cryptic DSDs from bacteria, D-threonine aldolases (D-TA), low specificity D-TAs, and similar uncharacterized proteins. DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the ...
CDD:153418	66	EUKprk	Bacteria:225,Invertebrates:2,Plants:2,nodiv:2	cd07377, WHTH_GntR, Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators.  This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all ...
CDD:163621	277	EUKprk	Bacteria:12,Invertebrates:14,Mammals:1,Plants:4,Rodents:1,Vertebrates:2,nodiv:1	cd07378, MPP_ACP5, Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain.  Acid phosphatase 5 (ACP5) removes the mannose 6-phosphate recognition marker from lysosomal proteins.  The exact site of dephosphorylation is not clear. Evidence suggests dephosphorylation may take place in a prelysosomal compartment as well as in the lysosome.  ACP5 belongs to the ...
CDD:163622	135	EUKprk	Bacteria:4,Invertebrates:12,Plants:11,Primates:1,Vertebrates:3	cd07379, MPP_239FB, Homo sapiens 239FB and related proteins, metallophosphatase domain.  239FB (Fetal brain protein 239) is thought to play a role in central nervous system development, but its specific role in unknown.  239FB is expressed predominantly in human fetal brain from a gene located in the chromosome 11p13 region associated with the mental retardation component of the WAGR (Wilms tumor, Aniridia, ...
CDD:163623	150	EUK	Invertebrates:13,Plants:16,Vertebrates:3	cd07380, MPP_CWF19_N, Schizosaccharomyces pombe CWF19 and related proteins, N-terminal metallophosphatase domain.  CWF19 cell cycle control protein (also known as CWF19-like 1 (CWF19L1) in Homo sapiens), N-terminal metallophosphatase domain.   CWF19 contains C-terminal domains similar to that found in the CwfJ cell cycle control protein.   The metallophosphatase domain belongs to the metallophosphatase (MPP) superfamily.  MPPs are ...
CDD:163624	239	EUKprk	Bacteria:134,Invertebrates:2,Plants:2,nodiv:2	cd07381, MPP_CapA, CapA and related proteins, metallophosphatase domain.  CapA is one of three membrane-associated enzymes in Bacillus anthracis that is required for synthesis of gamma-polyglutamic acid (PGA), a major component of the bacterial capsule.  The YwtB and PgsA proteins of Bacillus subtilis are closely related to CapA and are also included in this alignment model.  CapA belongs to the metallophosphatase (MPP) ...
CDD:163625	255	PRK	Bacteria:68,Environmental:1	cd07382, MPP_DR1281, Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain.  DR1281 is an uncharacterized Deinococcus radiodurans protein with a domain that belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, ...
CDD:163626	199	EUKprk	Bacteria:14,Invertebrates:2,Plants:22	cd07383, MPP_Dcr2, Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain.  DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2.  DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic ...
CDD:163627	171	EUK	Invertebrates:1,Plants:9,Primates:1	cd07384, MPP_Cdc1_like, Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain.  Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen.  In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization.  Cdc1 mutant cells accumulate ...
CDD:163628	223	EUKprk	Bacteria:68,Invertebrates:5,Primates:1,Vertebrates:2	cd07385, MPP_YkuE_C, Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain.  YkuE is an uncharacterized Bacillus subtilis protein with a C-terminal metallophosphatase domain and an N-terminal twin-arginine (RR) motif. An RR-signal peptide derived from the Bacillus subtilis YkuE protein can direct Tat-dependent secretion of agarase in Streptomyces lividans. This is an indication that YkuE is ...
CDD:163629	243	PRK	Bacteria:1,Environmental:2	cd07386, MPP_DNA_pol_II_small_archeal_C, archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain.  The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain.  This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact.  The archeal replicative DNA polymerases are thought to ...
CDD:163630	257	EUK	Invertebrates:14,Plants:11,Primates:1,Vertebrates:2	cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2), C-terminal domain.  PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits.  PolD2 is catalytically inactive and lacks the active site residues required for ...
CDD:163632	228	EUKprk	Bacteria:89,Invertebrates:10,Plants:20	cd07389, MPP_PhoD, Bacillus subtilis PhoD and related proteins, metallophosphatase domain.  PhoD (also known as alkaline phosphatase D/APaseD  in Bacillus subtilis) is a secreted phosphodiesterase encoded by phoD of the Pho regulon in Bacillus subtilis.  PhoD homologs are found in prokaryotes, eukaryotes, and archaea.  PhoD contains a twin arginine (RR) motif and is transported by the Tat (Twin-arginine translocation) translocation ...
CDD:163633	168	PRK	Bacteria:31	cd07390, MPP_AQ1575, Aquifex aeolicus AQ1575 and related proteins, metallophosphatase domain.  This family includes bacterial and archeal proteins homologous to AQ1575, an uncharacterized Aquifex aeolicus protein.  AQ1575 may play an accessory role in DNA repair, based on the close proximity of its gene to Holliday junction resolvasome genes.  The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally ...
CDD:163634	172	PRK	Bacteria:22	cd07391, MPP_PF1019, Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain.  This family includes bacterial and archeal proteins homologous to PF1019, an uncharacterized Pyrococcus furiosus protein.  The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) ...
CDD:163635	188	PRK	Bacteria:10	cd07392, MPP_PAE1087, Pyrobaculum aerophilum PAE1087 and related proteins, metallophosphatase domain.  PAE1087 is an uncharacterized Pyrobaculum aerophilum protein with a metallophosphatase domain.  The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with ...
CDD:163636	232	EUKprk	Bacteria:7,Invertebrates:1	cd07393, MPP_DR1119, Deinococcus radiodurans DR1119 and related proteins, metallophosphatase domain.  DR1119 is an uncharacterized Deinococcus radiodurans protein with a metallophosphatase domain.  The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) ...
CDD:163637	178	EUK	Invertebrates:17,Plants:10,Primates:1,Vertebrates:3	cd07394, MPP_Vps29, Homo sapiens Vps29 and related proteins, metallophosphatase domain.  Vps29 (vacuolar sorting protein 29), also known as vacuolar membrane protein Pep11, is a subunit of the retromer complex which is responsible for the retrieval of mannose-6-phosphate receptors (MPRs) from the endosomes for retrograde transport back to the Golgi. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold ...
CDD:163638	262	EUKprk	Bacteria:2,Invertebrates:8,Plants:1,Vertebrates:3	cd07395, MPP_CSTP1, Homo sapiens CSTP1 and related proteins, metallophosphatase domain.  CSTP1 (complete S-transactivated protein 1) is an uncharacterized Homo sapiens protein with a metallophosphatase domain, that is transactivated by the complete S protein of hepatitis B virus.  CSTP1 belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site ...
CDD:163639	267	EUKprk	Bacteria:10,Invertebrates:2,Plants:5,Primates:1,Vertebrates:2,nodiv:1	cd07396, MPP_Nbla03831, Homo sapiens Nbla03831 and related proteins, metallophosphatase domain.  Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated ...
CDD:163640	238	EUKprk	Bacteria:3,Plants:3	cd07397, MPP_DevT, Myxococcus xanthus DevT and related proteins, metallophosphatase domain.  DevT is a component in the C-signal response pathway in Myxococcus xanthus that stimulates the developmentally regulated expression of the FruA response regulator protein and is required for methylation of FrzCD during fruiting body formation.  DevT mutants having an in-frame deletion in the devT gene, display delayed aggregation and a cell autonomous sporulation ...
CDD:163641	217	EUKprk	Bacteria:123,Environmental:1,Invertebrates:1,nodiv:1	cd07398, MPP_YbbF-LpxH, Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain.  YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP.  YbbF belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally ...
CDD:163642	214	EUKprk	Bacteria:13,Plants:1	cd07399, MPP_YvnB, Bacillus subtilis YvnB and related proteins, metallophosphatase domain.  YvnB (BSU35040) is an uncharacterized Bacillus subtilis protein with a metallophosphatase domain.  This family includes bacterial and eukaryotic proteins similar to YvnB.  YvnB belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, ...
CDD:163643	144	EUKprk	Bacteria:52,Environmental:1,Plants:1	cd07400, MPP_YydB, Bacillus subtilis YydB and related proteins, metallophosphatase domain.  YydB (BSU40220) is an uncharacterized Bacillus subtilis protein that  belongs to the following Bacillus subtilis gene cluster yydB-yydC-yydD-yydG-yydH-yydI-yydJ.  YydB belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually ...
CDD:163644	256	EUK	Invertebrates:7,Mammals:1,Vertebrates:2	cd07401, MPP_TMEM62_N, Homo sapiens TMEM62, N-terminal metallophosphatase domain.  TMEM62 (transmembrane protein 62) is an uncharacterized Homo sapiens transmembrane protein with an N-terminal metallophosphatase domain.  TMEM62 belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated ...
CDD:163645	240	EUKprk	Bacteria:78,Environmental:1,Plants:1,nodiv:1	cd07402, MPP_GpdQ, Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain.  GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents.  The GpdQ homolog, ...
CDD:163646	129	PRK	Bacteria:12	cd07403, MPP_TTHA0053, Thermus thermophilus TTHA0053 and related proteins, metallophosphatase domain.  TTHA0053 is an uncharacterized Thermus thermophilus protein with a domain that belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and ...
CDD:163647	166	EUKprk	Bacteria:12,Invertebrates:1,Plants:3,nodiv:1	cd07404, MPP_MS158, Microscilla MS158 and related proteins, metallophosphatase domain.  MS158 is an uncharacterized Microscilla protein with a metallophosphatase domain.  Microscilla proteins MS152, and MS153 are also included in this family.  The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site ...
CDD:163649	257	EUKprk	Bacteria:9,Environmental:1,Invertebrates:8,Plants:4,Rodents:1	cd07406, MPP_CG11883_N, Drosophila melanogaster CG11883 and related proteins, N-terminal metallophosphatase domain.  CG11883 is an uncharacterized Drosophila melanogaster UshA-like protein with two domains, an N-terminal metallophosphatase domain and  a C-terminal nucleotidase domain.  The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that ...
CDD:163650	282	EUK	Invertebrates:1,Plants:8	cd07407, MPP_YHR202W_N, Saccharomyces cerevisiae YHR202W and related proteins, N-terminal metallophosphatase domain.  YHR202W is an uncharacterized Saccharomyces cerevisiae UshA-like protein with two domains, an N-terminal metallophosphatase domain and  a C-terminal nucleotidase domain.  The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, ...
CDD:163651	257	PRK	Bacteria:13	cd07408, MPP_SA0022_N, Staphylococcus aureus SA0022 and related proteins, N-terminal metallophosphatase domain.  SA0022 is an uncharacterized Staphylococcus aureus UshA-like protein with two putative domains, an N-terminal metallophosphatase domain and  a C-terminal nucleotidase domain.  SA0022 also contains a putative C-terminal cell wall anchor domain.  The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related ...
CDD:163652	281	EUKprk	Bacteria:12,Invertebrates:18,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related proteins, N-terminal metallophosphatase domain.  CD73 is a mammalian ecto-5'-nucleotidase expressed in endothelial cells and lymphocytes that catalyzes the conversion of 5'-AMP to adenosine in the final step of a pathway that generates adenosine from ATP.  This pathway also includes a CD39 nucleoside triphosphate dephosphorylase that mediates the ...
CDD:163653	277	PRK	Bacteria:50	cd07410, MPP_CpdB_N, Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain.  CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain.  This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and ...
CDD:163654	264	PRK	Bacteria:14	cd07411, MPP_SoxB_N, Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain.  SoxB (sulfur oxidation protein B) is a periplasmic thiosulfohydrolase and an essential component of the sulfur oxidation pathway in archaea and bacteria.  SoxB has a dinuclear manganese cluster and is thought to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate.  SoxB is expressed from the sox (sulfur oxidation) gene cluster, which ...
CDD:163655	288	PRK	Bacteria:22	cd07412, MPP_YhcR_N, Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain.  YhcR is a Bacillus subtilis sugar-nonspecific endonuclease. It cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to Staphylococcus aureus micrococcal nuclease. YhcR appears to be located in the cell wall, and is thought to be a substrate for a Bacillus subtilis sortase. YhcR is the major calcium-activated nuclease of ...
CDD:163656	222	PRK	Bacteria:13	cd07413, MPP_PA3087, Pseudomonas aeruginosa PA3087 and related proteins, metallophosphatase domain.  PA3087 is an uncharacterized protein from Pseudomonas aeruginosa with a metallophosphatase domain that belongs to the phosphoprotein phosphatase (PPP) family.  The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, ...
CDD:163658	285	EUK	Invertebrates:15,Plants:11,Primates:1,Vertebrates:3	cd07415, MPP_PP2A_PP4_PP6, PP2A, PP4, and PP6 phosphoprotein phosphatases, metallophosphatase domain.  PP2A-like family of phosphoprotein phosphatases (PPP's) including PP4 and PP6.  PP2A (Protein phosphatase 2A) is a critical regulator of many cellular activities.  PP2A comprises about 1% of total cellular proteins.  PP2A, together with protein phosphatase 1 (PP1), accounts for more than 90% of all serine/threonine ...
CDD:163659	305	EUK	Invertebrates:12,Mammals:1,Plants:4,Primates:1,Vertebrates:3,nodiv:1	cd07416, MPP_PP2B, PP2B, metallophosphatase domain.  PP2B (calcineurin) is a unique serine/threonine protein phosphatase in its regulation by a second messenger (calcium and calmodulin).  PP2B is involved in many biological processes including immune responses, the second messenger cAMP pathway, sodium/potassium ion transport in the nephron, cell cycle progression in lower eukaryotes, cardiac hypertrophy, and ...
CDD:163660	316	EUK	Invertebrates:9,Plants:8,Primates:1,Vertebrates:1,nodiv:1	cd07417, MPP_PP5_C, PP5, C-terminal metallophosphatase domain.  Serine/threonine protein phosphatase-5 (PP5) is a member of the PPP gene family of protein phosphatases that is highly conserved among eukaryotes and widely expressed in mammalian tissues. PP5 has a C-terminal phosphatase domain and an extended N-terminal TPR (tetratricopeptide repeat) domain containing three TPR motifs.  The PPP (phosphoprotein ...
CDD:163665	257	EUKprk	Bacteria:25,Plants:1	cd07422, MPP_ApaH, Escherichia coli ApaH and related proteins, metallophosphatase domain.  ApaH (also known as symmetrically cleaving Ap4A hydrolase and bis(5'nucleosyl)-tetraphosphatase) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases that hydrolyzes the nucleotide-signaling molecule diadenosine tetraphosphate (Ap(4)A) into two ADP and also hydrolyzes Ap(5)A, Gp(4)G, and other extending compounds.  ...
CDD:163666	234	PRK	Bacteria:10	cd07423, MPP_PrpE, Bacillus subtilis PrpE and related proteins, metallophosphatase domain.  PrpE (protein phosphatase E) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases and a key signal transduction pathway component controlling the expression of spore germination receptors GerA and GerK in Bacillus subtilis. PrpE is closely related to ApaH (also known symmetrical Ap(4)A hydrolase and ...
CDD:163667	207	PRK	Bacteria:20	cd07424, MPP_PrpA_PrpB, PrpA and PrpB, metallophosphatase domain.  PrpA and PrpB are bacterial type I serine/threonine and tyrosine phosphatases thought to modulate the expression of proteins that protect the cell upon accumulation of misfolded proteins in the periplasm.  The PPP (phosphoprotein phosphatase) family, to which PrpA and PrpB belong, is one of two known protein phosphatase families specific for serine and threonine.  This family also includes: PP1, ...
CDD:163668	208	EUKprk	Bacteria:10,Invertebrates:7,Plants:4	cd07425, MPP_Shelphs, Shewanella-like phosphatases, metallophosphatase domain.  This family includes bacterial, eukaryotic, and archeal proteins orthologous to the Shewanella cold-active protein-tyrosine phosphatase, CAPTPase.  CAPTPase is an uncharacterized protein that belongs to the Shelph (Shewanella-like phosphatase) family of PPP (phosphoprotein phosphatases).  The PPP family is one of two known protein phosphatase families ...
CDD:143631	108	EUK	Invertebrates:11,Mammals:1,Primates:1,Vertebrates:3,nodiv:1	cd07429, Cby_like, Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins.  Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By ...
CDD:143632	260	PRK	Bacteria:38,nodiv:1	cd07430, GH15_N, Glycoside hydrolase family 15, N-terminal domain.  Members of this family are N-terminal domains uniquely found in bacterial and archaeal glucoamylases and glucodextranases. Glucoamylase (glucan 1,4-alpha-glucosidase; 4-alpha-D-glucan glucohydrolase; amyloglucosidase; exo-1,4-alpha-glucosidase; gamma-amylase; lysosomal alpha-glucosidase; EC 3.2.1.3) hydrolyzes beta-1,4-glucosidic linkages of starch, glycogen and malto-oligosaccharides, ...
CDD:213986	179	PRK	Bacteria:121,nodiv:4	cd07431, PHP_PolIIIA, Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III.  PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA ...
CDD:213987	129	PRK	Bacteria:151,Environmental:3	cd07432, PHP_HisPPase, Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase.  HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the ...
CDD:213988	277	EUKprk	Bacteria:61,Environmental:1,Invertebrates:1	cd07433, PHP_PolIIIA_DnaE1, Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1.  PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, ...
CDD:213989	260	PRK	Bacteria:87,Environmental:1	cd07434, PHP_PolIIIA_DnaE2, Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene.  PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, ...
CDD:213990	268	PRK	Bacteria:67,nodiv:1	cd07435, PHP_PolIIIA_POLC, Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene.  DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. The PHP (also called histidinol phosphatase-2/HIS2) domain is ...
CDD:213991	237	PRK	Bacteria:118,Environmental:2,nodiv:1	cd07436, PHP_PolX, Polymerase and Histidinol Phosphatase domain of bacterial polymerase X.  The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA ...
CDD:213992	233	PRK	Bacteria:95	cd07437, PHP_HisPPase_Ycdx_like, Polymerase and Histidinol Phosphatase domain of Ycdx like.  PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. ...
CDD:213993	155	EUKprk	Bacteria:328,Environmental:2,Plants:4	cd07438, PHP_HisPPase_AMP, Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound.  The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA ...
CDD:143633	254	EUK	Invertebrates:4,Mammals:1,Plants:5,Primates:1,Vertebrates:3	cd07439, FANCE_c-term, Fanconi anemia complementation group E protein, C-terminal domain.  Fanconi Anemia (FA) is an autosomal recessive disorder associated with increased susceptibility to various cancers, bone marrow failure, cardiac, renal, and limb malformations, and other characteristics. Cells are highly sensitive to DNA damaging agents. A multi-subunit protein complex, the FA core complex, is responsible for ...
CDD:188659	113	EUK	Invertebrates:8,Mammals:1,Plants:14,Primates:1,Rodents:2,Vertebrates:3	cd07440, RGS, Regulator of G protein signaling (RGS) domain superfamily.  The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric ...
CDD:143560	132	EUK	Invertebrates:9,Vertebrates:3	cd07451, CRD_SMO, Cysteine-rich domain of the smoothened receptor (Smo) integral membrane protein.  The cysteine-rich domain (CRD) is part of the smoothened receptor (Smo), an integral membrane protein and one of the key players in the Hedgehog (Hh) signaling pathway, critical for development, cell growth and migration, as well as stem cell maintenance. The CRD of Smo is conserved in vertebrates and can also be identified in invertebrates. The ...
CDD:143568	135	EUK	Invertebrates:12,Rodents:1,Vertebrates:2,nodiv:2	cd07459, CRD_TK_ROR_like, Cysteine-rich domain of tyrosine kinase-like orphan receptors.  The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror) proteins, a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a ...
CDD:143578	147	EUK	Invertebrates:5,Mammals:1,Vertebrates:2	cd07469, CRD_TK_ROR_related, Cysteine-rich domain of proteins similar to tyrosine kinase-like orphan receptors.  The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror) proteins, a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key ...
CDD:143621	243	EUKprk	Invertebrates:8,Plants:17,Viruses:1	cd07470, CYTH-like_mRNA_RTPase, CYTH-like mRNA triphosphatase (RTPase) component of the mRNA capping apparatus.  This subgroup includes fungal and protozoal RTPases. RTPase catalyzes the first step in the mRNA cap formation process, the removal of the gamma-phosphate of  triphosphate terminated pre-mRNA. This activity is metal-dependent. The 5'-end of the resulting mRNA diphosphate is subsequently capped with GMP by RNA ...
CDD:173799	259	EUKprk	Bacteria:28,Invertebrates:7,Plants:1	cd07473, Peptidases_S8_Subtilisin_like, Peptidase S8 family domain in Subtilisin-like proteins.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members ...
CDD:173800	295	PRK	Bacteria:13,Environmental:1	cd07474, Peptidases_S8_subtilisin_Vpr-like, Peptidase S8 family domain in Vpr-like proteins.  The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide.  Vpr was identified as one of the proteases,  along with WprA, that are capable of processing subtilin.    Asp, Ser, His triadPeptidases S8 or Subtilases are ...
CDD:173801	346	PRK	Bacteria:19	cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases.  Streptococcal C5a peptidase (SCP), is a highly specific protease and adhesin/invasin.  The subtilisin-like protease domain is located at the N-terminus and contains a protease-associated domain inserted into a loop.  There are three fibronectin type III (Fn) domains at the C-terminus. SCP binds to integrins with the help of Arg-Gly-Asp motifs which are thought to ...
CDD:173802	267	PRK	Bacteria:10,Environmental:1	cd07476, Peptidases_S8_thiazoline_oxidase_subtilisin-like_protease, Peptidase S8 family domain in Thiazoline oxidase/subtilisin-like proteases.  Thiazoline oxidase/subtilisin-like protease is produced by the symbiotic bacteria Prochloron spp. that inhabit didemnid family ascidians.  The cyclic peptides of the patellamide class found in didemnid extracts are now known to be synthesized by the Prochloron spp.  The prepatellamide is heterocyclized to ...
CDD:173803	229	EUKprk	Bacteria:37,Plants:2	cd07477, Peptidases_S8_Subtilisin_subset, Peptidase S8 family domain in Subtilisin proteins.  This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain.  TK-subtilisin is ...
CDD:173804	455	PRK	Bacteria:34	cd07478, Peptidases_S8_CspA-like, Peptidase S8 family domain in CspA-like proteins.  GSP (germination-specific protease) converts the spore peptidoglycan hydrolase (SleC) precursor to an active enzyme during germination of Clostridium perfringens S40 spores.  Analysis of an enzyme fraction of GSP showed that it was composed of a gene cluster containing the processed forms of products of cspA, cspB, and cspC which are positioned in a tandem array just upstream of ...
CDD:173806	297	PRK	Bacteria:16	cd07480, Peptidases_S8_12, Peptidase S8 family domain, uncharacterized subfamily 12.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173807	264	EUKprk	Bacteria:8,Plants:1	cd07481, Peptidases_S8_BacillopeptidaseF-like, Peptidase S8 family domain in BacillopeptidaseF-like proteins.  Bacillus subtilis produces and secretes proteases and other types of exoenzymes at the end of the exponential phase of growth. The ones that make up this group is known as bacillopeptidase F, encoded by bpr,  a serine protease with high esterolytic activity which is inhibited by PMSF.  Like other members of the peptidases S8 family these have a ...
CDD:173808	294	PRK	Bacteria:12	cd07482, Peptidases_S8_Lantibiotic_specific_protease, Peptidase S8 family domain in Lantiobiotic (lanthionine-containing antibiotics) specific proteases.  Lantiobiotic (lanthionine-containing antibiotics) specific proteases are very similar in structure to serine proteases.  Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides with antimicrobial activities against Gram-positive bacteria. The proteases that ...
CDD:173809	291	EUKprk	Bacteria:7,Invertebrates:1	cd07483, Peptidases_S8_Subtilisin_Novo-like, Peptidase S8 family domain in Subtilisin_Novo-like proteins.  Subtilisins are a group of alkaline proteinases originating from different strains of Bacillus subtilis.  Novo is one of the strains that produced enzymes belonging to this group.  The enzymes obtained from the Novo and BPN' strains are identical.  The Carlsburg and Novo subtilisins are thought to have arisen from a common ancestral protein.  ...
CDD:173810	260	PRK	Bacteria:14	cd07484, Peptidases_S8_Thermitase_like, Peptidase S8 family domain in Thermitase-like proteins.  Thermitase is a non-specific, trypsin-related serine protease with a very high specific activity.  It contains a subtilisin like domain. The tertiary structure of thermitase is similar to that of subtilisin BPN'.  It contains a Asp/His/Ser catalytic triad. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and  ...
CDD:173812	264	PRK	Bacteria:34	cd07487, Peptidases_S8_1, Peptidase S8 family domain, uncharacterized subfamily 1.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173813	247	PRK	Bacteria:2	cd07488, Peptidases_S8_2, Peptidase S8 family domain, uncharacterized subfamily 2.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173814	312	EUKprk	Bacteria:2,Plants:9	cd07489, Peptidases_S8_5, Peptidase S8 family domain, uncharacterized subfamily 5.  gap in seq This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to ...
CDD:173816	247	EUK	Plants:9	cd07491, Peptidases_S8_7, Peptidase S8 family domain, uncharacterized subfamily 7.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173817	222	PRK	Bacteria:10	cd07492, Peptidases_S8_8, Peptidase S8 family domain, uncharacterized subfamily 8.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173818	261	EUKprk	Bacteria:7,Invertebrates:1	cd07493, Peptidases_S8_9, Peptidase S8 family domain, uncharacterized subfamily 9.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up ...
CDD:173820	285	PRK	Bacteria:19	cd07496, Peptidases_S8_13, Peptidase S8 family domain, uncharacterized subfamily 13.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:173822	242	PRK	Bacteria:14	cd07498, Peptidases_S8_15, Peptidase S8 family domain, uncharacterized subfamily 15.  This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via ...
CDD:143637	133	miss	miss	cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.  Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the ...
CDD:143638	92	EUKprk	Bacteria:168,Environmental:1,Invertebrates:16,Mammals:5,Plants:17,Primates:1,Vertebrates:3,Viruses:2,nodiv:3	cd07557, trimeric_dUTPase, Trimeric dUTP diphosphatases.  Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and ...
CDD:143476	211	miss	miss	cd07560, Peptidase_S41_CPP, C-terminal processing peptidase; serine protease family S41.  The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa ...
CDD:143477	256	miss	miss	cd07561, Peptidase_S41_CPP_like, C-terminal processing peptidase-like; serine protease family S41.  Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP).  CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at ...
CDD:143478	266	miss	miss	cd07562, Peptidase_S41_TRI, Tricorn protease; serine protease family S41.  The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 ...
CDD:143479	250	miss	miss	cd07563, Peptidase_S41_IRBP, Interphotoreceptor retinoid-binding protein; serine protease family S41.  Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium ...
CDD:143588	297	EUKprk	Bacteria:69,Invertebrates:1,Plants:20	cd07564, nitrilases_CHs, Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases).  Nitrilases (nitrile aminohydrolases, EC:3.5.5.1) hydrolyze nitriles (RCN) to ammonia and the corresponding carboxylic acid. Most nitrilases prefer aromatic nitriles, some prefer arylacetonitriles and others aliphatic nitriles. This group includes the nitrilase cyanide dihydratase (CDH), which hydrolyzes inorganic cyanide (HCN) to ...
CDD:143589	291	EUKprk	Bacteria:18,Plants:4	cd07565, aliphatic_amidase, aliphatic amidases (class 2 nitrilases).  Aliphatic amidases catalyze the hydrolysis of short-chain aliphatic amides to form ammonia and the corresponding organic acid. This group includes Pseudomonas aeruginosa (Pa) AmiE, the amidase from Geobacillus pallidus RAPc8 (RAPc8 amidase), and Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and HpAmiE hydrolyze various very short aliphatic amides, including propionamide, acetamide ...
CDD:143590	295	EUK	Plants:18	cd07566, ScNTA1_like, Saccharomyces cerevisiae N-terminal amidase NTA1, and related proteins (class 3 nitrilases).  Saccharomyces cerevisiae NTA1 functions in the N-end rule protein degradation pathway. It specifically deaminates the N-terminal asparagine and glutamine residues of substrates of this pathway, to aspartate and glutamate respectively, these latter are the destabilizing residues. This subgroup belongs to a larger nitrilase superfamily comprised of ...
CDD:143591	299	EUK	Invertebrates:13,Mammals:1,Primates:1,Vertebrates:4	cd07567, biotinidase_like, biotinidase and vanins (class 4 nitrilases).  These secondary amidases participate in vitamin recycling. Biotinidase (EC 3.5.1.12) has both a hydrolase and a transferase activity. It hydrolyzes free biocytin or small biotinyl-peptides produced during the proteolytic degradation of biotin-dependent carboxylases, to release free biotin (vitamin H), and it can transfer biotin to acceptor molecules such ...
CDD:143593	302	EUKprk	Bacteria:13,Plants:3	cd07569, DCase, N-carbamyl-D-amino acid amidohydrolase (DCase, class 6 nitrilases).  DCase hydrolyses N-carbamyl-D-amino acids to produce D-amino acids. It is an important biocatalyst in the pharmaceutical industry, producing useful D-amino acids for example in the preparation of beta-lactam antibiotics. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend ...
CDD:143594	261	EUKprk	Bacteria:194,Environmental:2,Invertebrates:9,Plants:9,Primates:1,Vertebrates:3,nodiv:1	cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases).  Glutamine-dependent NAD synthetases are bifunctional enzymes, which have an N-terminal GAT domain and a C-terminal NAD+ synthetase domain. The GAT domain is a glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to L-glutamate and ammonia. ...
CDD:143595	270	EUKprk	Bacteria:234,Environmental:1,Plants:1	cd07571, ALP_N-acyl_transferase, Apolipoprotein N-acyl transferase (class 9 nitrilases).  ALP N-acyl transferase (Lnt), is an essential membrane-bound enzyme in gram-negative bacteria, which catalyzes the N-acylation of apolipoproteins, the final step in lipoprotein maturation. This is a reverse amidase (i.e. condensation) reaction. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing ...
CDD:143596	265	EUKprk	Bacteria:118,Environmental:2,Invertebrates:24,Plants:31,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd07572, nit, Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases).  This subgroup includes mammalian Nit1 and Nit2, the Nit1-like domain of the invertebrate NitFhit, and various uncharacterized bacterial and archaeal Nit-like proteins. Nit1 and Nit2 are candidate tumor suppressor proteins. In NitFhit, the Nit1-like domain is encoded as ...
CDD:143597	284	EUKprk	Bacteria:34,Plants:5	cd07573, CPA, N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases).  CPA (EC 3.5.1.53, also known as N-carbamoylputrescine amidase and carbamoylputrescine hydrolase) converts N-carbamoylputrescine to putrescine, a step in polyamine biosynthesis in plants and bacteria. This subgroup includes Arabidopsis thaliana CPA, also known as nitrilase-like 1 (NLP1), and Pseudomonas aeruginosa AguB. This subgroup belongs to a larger nitrilase superfamily ...
CDD:143598	280	PRK	Bacteria:36	cd07574, nitrilase_Rim1_like, Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases).  Some members of this subgroup are implicated in post-translational modification, as they contain an N-terminal GCN5-related N-acetyltransferase (GNAT) protein RimI family domain. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which ...
CDD:143599	252	EUKprk	Bacteria:41,Environmental:2,Invertebrates:2,nodiv:1	cd07575, Xc-1258_like, Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases).  Uncharacterized subgroup belonging to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure ...
CDD:143600	254	PRK	Bacteria:30,Environmental:1	cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases).  Pseudomonas sp. MCI3434 R-amidase hydrolyzes (R,S)-piperazine-2-tert-butylcarboxamide to form (R)-piperazine-2-carboxylic acid. It does so with strict R-stereoselectively. Its preferred substrates are carboxamide compounds which have the amino or imino group connected to their beta- or gamma-carbon. This subgroup belongs to a larger ...
CDD:143601	259	PRK	Bacteria:12	cd07577, Ph0642_like, Pyrococcus horikoshii Ph0642 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases).  Uncharacterized subgroup of the nitrilase superfamily. This superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. Pyrococcus horikoshii Ph0642 is a hypothetical protein belonging to this subgroup. This superfamily has been classified in ...
CDD:143604	268	PRK	Bacteria:10	cd07580, nitrilase_2, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins ...
CDD:143605	255	PRK	Bacteria:44,Environmental:2	cd07581, nitrilase_3, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 ...
CDD:143606	294	PRK	Bacteria:8	cd07582, nitrilase_4, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that ...
CDD:143607	253	PRK	Bacteria:69,Environmental:1	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 ...
CDD:143609	261	PRK	Bacteria:12	cd07585, nitrilase_7, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins ...
CDD:143610	269	PRK	Bacteria:14	cd07586, nitrilase_8, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases).  The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins ...
CDD:153272	211	EUK	Invertebrates:8,Vertebrates:1	cd07588, BAR_Amphiphysin, The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. ...
CDD:153273	195	EUK	Invertebrates:3,Mammals:1,Plants:11,Primates:1,Rodents:1,Vertebrates:4	cd07589, BAR_DNMBP, The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. DyNamin Binding Protein (DNMBP), also called Tuba, is a Cdc42-specific Guanine nucleotide Exchange Factor (GEF) that binds dynamin and various actin regulatory proteins. It serves as a link ...
CDD:153274	225	EUK	Invertebrates:6,Vertebrates:2,nodiv:1	cd07590, BAR_Bin3, The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 3.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 3 (Bin3) is widely expressed in many tissues except in the brain. It plays roles in regulating filamentous actin localization and in cell division. In humans, the Bin3 gene is located in chromosome 8p21.3, a ...
CDD:153276	223	EUK	Invertebrates:9,Primates:1,Vertebrates:2,nodiv:1	cd07592, BAR_Endophilin_A, The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins, localized at synapses, which interact with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact ...
CDD:153277	215	EUK	Plants:8	cd07593, BAR_MUG137_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of Schizosaccharomyces pombe Meiotically Up-regulated Gene 137 protein and similar proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This subfamily is composed predominantly of uncharacterized fungal proteins with ...
CDD:153278	229	EUK	Invertebrates:9,Rodents:1	cd07594, BAR_Endophilin_B, The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an ...
CDD:153279	244	EUK	Invertebrates:9,Primates:1	cd07595, BAR_RhoGAP_Rich-like, The Bin/Amphiphysin/Rvs (BAR) domain of Rich-like Rho GTPase Activating Proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to GAP interacting with CIP4 homologs proteins (Rich). Members contain an N-terminal BAR domain, followed by a Rho ...
CDD:153280	218	EUK	Invertebrates:4,Plants:13,Primates:1,Vertebrates:1	cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding ...
CDD:153281	246	EUK	Invertebrates:2,Plants:9,Vertebrates:1	cd07597, BAR_SNX8, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, ...
CDD:153282	211	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd07598, BAR_FAM92, The Bin/Amphiphysin/Rvs (BAR) domain of Family with sequence similarity 92 (FAM92).  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of proteins from the family with sequence similarity 92 ...
CDD:153283	216	EUK	Plants:21	cd07599, BAR_Rvs167p, The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 ...
CDD:153284	242	EUK	Plants:14	cd07600, BAR_Gvp36, The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular ...
CDD:153286	207	EUK	Invertebrates:7,Primates:1,Rodents:1,nodiv:1	cd07602, BAR_RhoGAP_OPHN1-like, The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin1-like Rho GTPase Activating Proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to oligophrenin1 (OPHN1). Members contain an N-terminal BAR domain, followed by a ...
CDD:153287	200	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd07603, BAR_ACAPs, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an ...
CDD:153289	223	EUK	Invertebrates:5,Primates:1	cd07605, I-BAR_IMD, Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), a dimerization module that binds and bends membranes.  Inverse (I)-BAR (or IMD) is a member of the Bin/Amphiphysin/Rvs (BAR) domain family. It is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. IMD domains are ...
CDD:153292	192	EUK	Plants:10	cd07608, BAR_ArfGAP_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized fungal Arf GAP proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of uncharacterized fungal proteins containing an N-terminal BAR domain, followed by a Pleckstrin homology ...
CDD:153293	214	EUK	Plants:24	cd07609, BAR_SIP3_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of fungal Snf1p-interacting protein 3.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of mostly uncharacterized fungal proteins with similarity to Saccharomyces cerevisiae Snf1p-interacting protein 3 ...
CDD:153294	191	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:1	cd07610, FCH_F-BAR, The Extended FES-CIP4 Homology (FCH) or F-BAR (FCH and Bin/Amphiphysin/Rvs) domain, a dimerization module that binds and bends membranes.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. F-BAR domain containing proteins, also known as Pombe Cdc15 homology (PCH) family proteins, include Fes and Fer tyrosine ...
CDD:153305	219	EUK	Invertebrates:13,Primates:1,Vertebrates:1,nodiv:1	cd07621, BAR_SNX5_6, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their ...
CDD:153306	201	EUK	Invertebrates:4,Vertebrates:1	cd07622, BAR_SNX4, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular ...
CDD:153307	224	EUK	Invertebrates:8,Vertebrates:1,nodiv:1	cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 1 and 2.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding ...
CDD:153308	200	EUK	Invertebrates:2,Primates:1,nodiv:1	cd07624, BAR_SNX7_30, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding ...
CDD:153309	230	EUK	Plants:4	cd07625, BAR_Vps17p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps17p.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular ...
CDD:153310	199	EUK	Invertebrates:8,Primates:1,Rodents:1,nodiv:1	cd07626, BAR_SNX9_like, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9 and Similar Proteins.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their ...
CDD:153311	216	EUK	Plants:9	cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular ...
CDD:153312	185	EUK	Plants:6	cd07628, BAR_Atg24p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg24p.  BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular ...
CDD:153332	261	EUK	Invertebrates:12,Primates:1	cd07648, F-BAR_FCHO, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proteins in this group have been named FCH domain Only (FCHO) proteins. Vertebrates have two members, FCHO1 and FCHO2. These proteins contain an F-BAR domain and a C-terminal domain of ...
CDD:153334	228	EUK	Plants:17	cd07650, F-BAR_Syp1p_like, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Syp1p is associated with septins, a family of GTP-binding proteins that serve as elements of septin filaments, which are required for cell morphogenesis and division. Syp1p regulates cell-cycle dependent ...
CDD:153335	236	EUK	Plants:13	cd07651, F-BAR_PombeCdc15_like, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe Cdc15, and similar proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Schizosaccharomyces pombe Cdc15 and Imp2, and similar proteins. These proteins contain an N-terminal F-BAR domain and a C-terminal SH3 ...
CDD:153336	234	EUK	Plants:13	cd07652, F-BAR_Rgd1, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Saccharomyces cerevisiae  Rho GTPase activating protein Rgd1 and similar proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Saccharomyces cerevisiae Rgd1 is a GTPase activating protein (GAP) with activity towards Rho3p and Rho4p, which are involved in bud growth and ...
CDD:153337	251	EUK	Invertebrates:11,Primates:1,Vertebrates:1	cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein 4 and similar proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and ...
CDD:153339	258	EUK	Invertebrates:10,Primates:1,Vertebrates:3,nodiv:1	cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated ...
CDD:153340	241	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:3	cd07656, F-BAR_srGAP, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Proteins.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are ...
CDD:153341	237	EUK	Invertebrates:5,Primates:1	cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases.  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), and Fer (Fes related) are cytoplasmic (or nonreceptor) tyrosine kinases that play roles ...
CDD:153342	239	EUK	Invertebrates:7,Vertebrates:2	cd07658, F-BAR_NOSTRIN, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Nitric Oxide Synthase TRaffic INducer (NOSTRIN).  F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Nitric Oxide Synthase TRaffic INducer (NOSTRIN) is expressed in endothelial and epithelial cells and is involved in the regulation, trafficking and targeting of ...
CDD:153343	215	EUK	Invertebrates:11,Rodents:1,Vertebrates:3	cd07659, BAR_PICK1, The Bin/Amphiphysin/Rvs (BAR) domain of Protein Interacting with C Kinase 1.  The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Protein Interacting with C Kinase 1 (PICK1), also called Protein kinase C-alpha-binding protein, is highly expressed in brain and testes. PICK1 plays a key role in the ...
CDD:153344	201	EUK	Invertebrates:10,Primates:1,Vertebrates:4,nodiv:1	cd07660, BAR_Arfaptin, The Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin.  The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Arfaptins are ubiquitously expressed proteins implicated in mediating cross-talk between Rac, a member of the Rho family GTPases, and Arf (ADP-ribosylation factor) small GTPases. Arfaptins bind ...
CDD:143312	81	miss	miss	cd07688, IgC_TCR_alpha, T cell receptor (TCR) alpha chain immunoglobulin domain.  IgC_TCR_alpha: Constant domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by ...
CDD:143320	96	miss	miss	cd07696, IgC_CH3, CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin.  IgC_CH3: The third immunoglobulin constant domain (IgC) of immunoglobulin (Ig) heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five ...
CDD:143322	93	miss	miss	cd07698, IgC_MHC_I_alpha3, Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain.  IgC_MHC_I_alpha3;  Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes.  Class I molecules consist of a transmembrane alpha chain and a small chain called the beta2 microglobulin. The alpha chain contains three extracellular domains, ...
CDD:143323	100	miss	miss	cd07699, IgC_L, Immunoglobulin Constant domain.  IgC_L: Immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of ...
CDD:143327	95	miss	miss	cd07703, Ig2_Nectin-2_like, Second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112) and similar proteins.  Ig2_Nectin-2_like: domain similar to the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112). Nectin-2 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through 4). Nectins are synaptic cell adhesion molecules (CAMs) which ...
CDD:143622	214	EUKprk	Bacteria:62,Environmental:1,Plants:1	cd07750, PolyPPase_VTC_like, Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, -3 and- 4, and similar proteins.  Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2, -3, and -4 contain polyP polymerase domains. For S. cerevisiae VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This ...
CDD:143623	290	EUK	Invertebrates:3,Plants:11	cd07751, PolyPPase_VTC4_like, Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) protein VTC4, and similar proteins.  Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2,-3, and -4 contain polyP polymerase domains. S. cerevisiae VTC4 belongs to this subgroup. For VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This ...
CDD:143624	197	PRK	Bacteria:63,Environmental:1	cd07756, CYTH-like_Pase_CHAD, Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain.  This subgroup belongs to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily. Members of this superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the ...
CDD:143625	196	EUK	Invertebrates:4,Plants:8,Rodents:1,Vertebrates:2	cd07758, ThTPase, Thiamine Triphosphatase.  ThTPase is a soluble cytosolic enzyme which converts thiamine triphosphate (ThTP) to thiamine diphosphate. This catalytic activity depends on a divalent metal cofactor, for example Mg++. ThTPase regulates the intracellular concentration of ThTP, maintaining it at a low concentration in vivo. ThTP acts as a messenger in cell signaling in response to cellular stress, and in addition, can ...
CDD:143626	146	PRK	Bacteria:24	cd07761, CYTH-like_CthTTM-like, Clostridium thermocellum (Cth)TTM and similar proteins, a subgroup of the CYTH-like superfamily.  CthTTM is a metal dependent tripolyphosphatase, nucleoside triphosphatase, and nucleoside tetraphosphatase. It hydrolyzes the beta-gamma phosphoanhydride linkage of triphosphate-containing substrates including tripolyphosphate, nucleoside triphosphates and nucleoside tetraphosphates. These substrates are hydrolyzed, releasing Pi. Mg++ or ...
CDD:143627	180	PRK	Bacteria:36	cd07762, CYTH-like_Pase_1, Uncharacterized subgroup 1 of the CYTH-like superfamily.  Enzymes belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for ...
CDD:143639	40	EUK	Mammals:5,Primates:2,Rodents:2,Vertebrates:4	cd07765, KRAB_A-box, KRAB (Kruppel-associated box) domain -A box.  The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in ...
CDD:173927	332	PRK	Bacteria:7,nodiv:1	cd07766, DHQ_Fe-ADH, Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH).  Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing  alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate ...
CDD:163686	116	EUKprk	Bacteria:2,Invertebrates:1,Primates:1,Vertebrates:2	cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains.  MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ...
CDD:198347	484	EUKprk	Bacteria:9,Invertebrates:6,Plants:4,Primates:1,Vertebrates:1	cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily includes glycerol kinases (GK; EC 2.7.1.30) and glycerol kinase-like proteins from all three kingdoms of living organisms. Glycerol is an important intermediate of energy metabolism and it plays fundamental roles in several vital physiological processes. GKs are involved in the entry of external glycerol ...
CDD:212659	440	EUKprk	Bacteria:36,Invertebrates:1,Plants:1	cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is composed of a group of gluconate kinases (GntK, also known as gluconokinase; EC 2.7.1.12) encoded by the gntK gene, which catalyzes the ATP-dependent phosphorylation of D-gluconate and produce 6-phospho-D-gluconate and ADP. The presence of Mg2+ might be required for catalytic activity. The prototypical member of this ...
CDD:198349	440	PRK	Bacteria:70,nodiv:1	cd07771, FGGY_RhuK, L-rhamnulose kinases; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is predominantly composed of bacterial L-rhamnulose kinases (RhuK, also known as rhamnulokinase; EC 2.7.1.5), which are encoded by the rhaB gene and catalyze the ATP-dependent phosphorylation of L-rhamnulose to produce L-rhamnulose-1-phosphate and ADP. Some uncharacterized homologous sequences are also included in this subfamily. The ...
CDD:198350	419	PRK	Bacteria:9	cd07772, FGGY_NaCK_like, Novosphingobium aromaticivorans carbohydrate kinase-like proteins; belongs to the FGGY family of carbohydrate kinases.  This subfamily is predominantly composed of uncharacterized bacterial proteins with similarity to carbohydrate kinase from Novosphingobium aromaticivorans (NaCK). These proteins may catalyze the transfer of a phosphate group from ATP to their carbohydrate substrates. They belong to the FGGY family of carbohydrate kinases, ...
CDD:198352	430	PRK	Bacteria:8	cd07774, FGGY_1, uncharacterized subgroup; belongs to the FGGY family of carbohydrate kinases.  This subfamily is composed of uncharacterized carbohydrate kinases. They are sequence homologous to bacterial glycerol kinase and have been classified as members of the FGGY family of carbohydrate kinases. The monomers of FGGY proteins contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, ...
CDD:212660	480	EUK	Invertebrates:11,Plants:14,Vertebrates:2,nodiv:1	cd07776, FGGY_D-XK_euk, eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is composed of eukaryotic D-xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17), which catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. They belong to the FGGY family of carbohydrate kinases, the monomers of ...
CDD:212661	448	EUKprk	Bacteria:3,Invertebrates:11,Vertebrates:1,nodiv:1	cd07777, FGGY_SHK_like, sedoheptulokinase-like proteins; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is predominantly composed of uncharacterized bacterial and eukaryotic proteins with similarity to human sedoheptulokinase (SHK, also known as D-altro-heptulose or heptulokinase, EC 2.7.1.14) encoded by the carbohydrate kinase-like (CARKL/SHPK) gene. SHK catalyzes the ATP-dependent phosphorylation ...
CDD:198356	466	PRK	Bacteria:16	cd07778, FGGY_L-RBK_like, L-ribulokinase-like proteins; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is composed of a group of putative bacterial L-ribulokinases (RBK; EC 2.7.1.16) and similar proteins. L-RBK catalyzes the MgATP-dependent phosphorylation of a variety of sugar substrates. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a ...
CDD:212662	488	PRK	Bacteria:24	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins.  This subfamily consists of uncharacterized hypothetical bacterial proteins with similarity to Escherichia coli sugar kinase ygcE , whose functional roles are not yet clear. Escherichia coli ygcE is recognized by this model, but is not present in the alignment as it contains a deletion relative to other members of the group. These proteins belong to the FGGY family of carbohydrate kinases, the monomers of ...
CDD:198358	498	EUKprk	Bacteria:21,Invertebrates:1	cd07781, FGGY_RBK, Ribulokinases; belongs to the FGGY family of carbohydrate kinases.  This subgroup is predominantly composed of bacterial ribulokinases (RBK) which catalyze the MgATP-dependent phosphorylation of L(or D)-ribulose to produce L(or D)-ribulose 5-phosphate and ADP. RBK also phosphorylates a variety of other sugar substrates including ribitol and arabitol. The reason why L-RBK can phosphorylate so many different substrates is not yet ...
CDD:212663	536	EUKprk	Bacteria:12,Invertebrates:7,Plants:7,Primates:1,Vertebrates:3	cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis carbohydrate kinase-like subgroup; belongs to the FGGY family of carbohydrate kinases.  This subgroup is composed of the uncharacterized Yersinia Pseudotuberculosis carbohydrate kinase that has been named glyerol/xylulose kinase and similar uncharacterized proteins from bacteria and eukaryota. Carbohydrate kinases catalyze the ATP-dependent phosphorylation ...
CDD:198360	484	EUKprk	Bacteria:6,Plants:4	cd07783, FGGY_CarbK-RPE_like, Carbohydrate kinase and ribulose-phosphate 3-epimerase fusion proteins-like; belongs to the FGGY family of carbohydrate kinases.  This subgroup is composed of uncharacterized proteins with similarity to carbohydrate kinases. Some members are carbohydrate kinase and ribulose-phosphate 3-epimerase fusion proteins. Carbohydrate kinases catalyze the ATP-dependent phosphorylation of their carbohydrate substrate to produce ...
CDD:198361	486	PRK	Bacteria:69,Environmental:2,nodiv:1	cd07786, FGGY_EcGK_like, Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases.  This subgroup is composed of mostly bacterial and archaeal glycerol kinases (GK), including the well characterized proteins from Escherichia coli (EcGK), Thermococcus kodakaraensis (TkGK), and Enterococcus casseliflavus (EnGK). GKs contain two large domains separated by a deep cleft that forms the active site. This ...
CDD:212664	504	EUK	Invertebrates:8,Primates:1,Vertebrates:1,nodiv:1	cd07792, FGGY_GK1-3_metazoa, Metazoan glycerol kinase 1 and 3-like proteins; belongs to the FGGY family of carbohydrate kinases.  This subgroup corresponds to a group of metazoan glycerol kinases (GKs), coded by X chromosome-linked GK genes, and glycerol kinase (GK)-like proteins, coded by autosomal testis-specific GK-like genes (GK-like genes, GK1 and GK3).  Sequence comparison shows that metazoan GKs and GK-like proteins in ...
CDD:212665	504	EUKprk	Bacteria:1,Invertebrates:9,Vertebrates:1	cd07793, FGGY_GK5_metazoa, metazoan glycerol kinase 5-like proteins; belongs to the FGGY family of carbohydrate kinases.  This subgroup corresponds to a group of metazoan putative glycerol kinases (GK), which may be coded by the GK-like gene, GK5. Sequence comparison shows members of this group are homologs of bacterial GKs, and they retain all functionally important residues. However, GK-like proteins in this family do not have ...
CDD:212666	447	PRK	Bacteria:31	cd07802, FGGY_L-XK, L-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases.  This subfamily is composed of bacterial L-xylulose kinases (L-XK, also known as L-xylulokinase; EC 2.7.1.53), which catalyze the ATP-dependent phosphorylation of L-xylulose to produce L-xylulose 5-phosphate and ADP. The presence of Mg2+ might be required for catalytic activity. Some uncharacterized sequences are also included in this subfamily. L-XKs belong to the FGGY ...
CDD:198371	482	PRK	Bacteria:11	cd07803, FGGY_D-XK, D-xylulose kinases; a subgroup of the FGGY family of carbohydrate kinases.  This subfamily is predominantly composed of bacterial D-xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17), which catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. Some uncharacterized sequences are also included in this subfamily. The prototypical member of this subfamily is ...
CDD:198372	492	PRK	Bacteria:27	cd07804, FGGY_XK_like_1, uncharacterized xylulose kinase-like proteins; a subgroup of the FGGY family of carbohydrate kinases.  This subgroup is composed of uncharacterized bacterial and archaeal xylulose kinases-like proteins with similarity to bacterial D-xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17), which catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. The ...
CDD:198373	514	EUKprk	Bacteria:22,Plants:3	cd07805, FGGY_XK_like_2, uncharacterized xylulose kinase-like proteins; a subgroup of the FGGY family of carbohydrate kinases.  This subgroup is composed of uncharacterized proteins with similarity to bacterial D-Xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17), which catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+ is required ...
CDD:198374	482	EUKprk	Bacteria:61,Invertebrates:1,Plants:1	cd07808, FGGY_D-XK_EcXK-like, Escherichia coli xylulokinase-like D-xylulose kinases; a subgroup of the FGGY family of carbohydrate kinases.  This subgroup is predominantly composed of bacterial D-xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17), which catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. D-xylulose has been used as a source of ...
CDD:198375	487	EUKprk	Bacteria:12,Invertebrates:1	cd07809, FGGY_D-XK_1, D-xylulose kinases, subgroup 1; members of the FGGY family of carbohydrate kinases.  This subgroup is composed of D-xylulose kinases (XK, also known as xylulokinase; EC 2.7.1.17) from bacteria and eukaryota. They share high sequence similarity with Escherichia coli xylulokinase (EcXK), which catalyzes the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P) and ADP. ...
CDD:176854	141	EUKprk	Bacteria:118,Environmental:1,Plants:4,Primates:1	cd07812, SRPBCC, START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily.  SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type ...
CDD:176855	138	EUKprk	Bacteria:102,Environmental:1,Invertebrates:21,Plants:29,Primates:1,Vertebrates:4,nodiv:1	cd07813, COQ10p_like, Coenzyme Q-binding protein COQ10p and similar proteins.  Coenzyme Q-binding protein COQ10p and similar proteins. COQ10p is a hydrophobic protein located in the inner membrane of mitochondria that binds coenzyme Q (CoQ), also called ubiquinone, which is an essential electron carrier of the respiratory chain. Deletion of the gene encoding COQ10p (COQ10 or YOL008W) in ...
CDD:176856	139	EUKprk	Bacteria:151,Environmental:2,Primates:1	cd07814, SRPBCC_CalC_Aha1-like, Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins.  This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Micromonospora echinospora CalC, human Aha1, and related proteins. Proteins in this group belong to the SRPBCC domain superfamily of proteins, which bind hydrophobic ligands. SRPBCC domains have a deep ...
CDD:176857	251	EUK	Invertebrates:4,Plants:3,Primates:1,Rodents:1	cd07815, SRPBCC_PITP, Lipid-binding SRPBCC domain of Class I and Class II Phosphatidylinositol Transfer Proteins.  This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the phosphatidylinositol transfer protein (PITP) family of lipid transfer proteins. This family of proteins includes Class 1 PITPs (PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator and related proteins), Class IIA  PITPs ...
CDD:176858	148	EUK	Plants:43	cd07816, Bet_v1-like, Ligand-binding bet_v_1 domain of major pollen allergen of white birch (Betula verrucosa), Bet v 1, and related proteins.  This family includes the ligand binding domain of Bet v 1 (the major pollen allergen of white birch, Betula verrucosa) and related proteins. In addition to birch Bet v 1, this family includes other plant intracellular pathogenesis-related class 10 (PR-10) proteins, norcoclaurine synthases (NCSs), cytokinin binding proteins ...
CDD:176859	139	EUKprk	Bacteria:55,Plants:7	cd07817, SRPBCC_8, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains ...
CDD:176860	150	EUKprk	Bacteria:60,Environmental:1,Plants:1	cd07818, SRPBCC_1, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal ...
CDD:176861	140	EUKprk	Bacteria:27,Invertebrates:1	cd07819, SRPBCC_2, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic ...
CDD:176862	137	PRK	Bacteria:66,Environmental:1	cd07820, SRPBCC_3, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic ...
CDD:176863	140	EUKprk	Bacteria:99,Environmental:2,Invertebrates:1,Plants:12	cd07821, PYR_PYL_RCAR_like, Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins.  The PYR/PYL/RCAR-like family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. PYR/PYL/RCAR plant proteins are receptors involved ...
CDD:176864	141	EUKprk	Bacteria:44,Environmental:1,Plants:24	cd07822, SRPBCC_4, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal ...
CDD:176865	146	PRK	Bacteria:24	cd07823, SRPBCC_5, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the ...
CDD:176866	146	PRK	Bacteria:22	cd07824, SRPBCC_6, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the ...
CDD:176867	144	PRK	Bacteria:12	cd07825, SRPBCC_7, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the ...
CDD:176868	142	PRK	Bacteria:27	cd07826, SRPBCC_CalC_Aha1-like_9, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:143640	174	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:1	cd07827, RHD-n, N-terminal sub-domain of the Rel homology domain (RHD).  Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module ...
CDD:143652	148	EUKprk	Bacteria:44,Invertebrates:12,Plants:2,Primates:1,Vertebrates:2	cd07828, nitrobindin, nitrobindin heme-binding domain.  Nitrobindin is a heme-containing lipocalin that may reversibly bind nitric oxide. This heme-binding domain forms a beta barrel structure, and in a small family of proteins from tetrapods, it is found C-terminal to a THAP zinc finger domain (a sequence-specific DNA binding domain). Members of this group are putatively related to fatty acid-binding proteins (FABPs).
CDD:270823	282	EUK	Invertebrates:19,Plants:4,Primates:1	cd07829, STKc_CDK_like, Catalytic domain of Cyclin-Dependent protein Kinase-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. CDKs are partly regulated ...
CDD:270824	283	EUK	Invertebrates:14,Plants:15,Primates:1,Vertebrates:3	cd07830, STKc_MAK_like, Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of human MAK and MAK-related kinase (MRK), Saccharomyces cerevisiae Ime2p, Schizosaccharomyces pombe Mei4-dependent protein 3 (Mde3) and Pit1, Caenorhabditis elegans dyf-5, ...
CDD:270825	282	EUK	Invertebrates:12,Plants:3,Vertebrates:3	cd07831, STKc_MOK, Catalytic domain of the Serine/Threonine Kinase, MAPK/MAK/MRK Overlapping Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MOK, also called Renal tumor antigen 1 (RAGE-1), is widely expressed and is enriched in testis, kidney, lung, and brain. It is expressed in approximately 50% of renal cell carcinomas (RCC) and is a potential target for ...
CDD:270826	287	EUK	Invertebrates:8,Plants:2,Vertebrates:2	cd07832, STKc_CCRK, Catalytic domain of the Serine/Threonine Kinase, Cell Cycle-Related Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CCRK was previously called p42. It is a Cyclin-Dependent Kinase (CDK)-Activating Kinase (CAK) which is essential for the activation of CDK2. It is indispensable for cell growth and has been implicated in the progression of ...
CDD:270827	288	EUK	Invertebrates:4,Plants:2,Primates:1	cd07833, STKc_CDKL, Catalytic domain of Cyclin-Dependent protein Kinase Like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDKL1-5 and similar proteins. Some CDKLs, like CDKL1 and CDKL3, may be implicated in transformation and others, like CDKL3 and CDKL5, are associated with mental retardation when impaired. CDKL2 ...
CDD:270828	329	EUK	Invertebrates:15,Plants:7,Primates:1,Rodents:2,Vertebrates:1	cd07834, STKc_MAPK, Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPKs serve as important mediators of cellular responses to extracellular signals. They control critical cellular functions including differentiation, proliferation, migration, and apoptosis. They ...
CDD:270829	283	EUK	Invertebrates:4,Plants:11,Primates:1,Vertebrates:1	cd07835, STKc_CDK1_CdkB_like, Catalytic domain of Cyclin-Dependent protein Kinase 1-like Serine/Threonine Kinases and of Plant B-type Cyclin-Dependent protein Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK, CDK2, and CDK3. CDK1 is also called Cell division control protein 2 (Cdc2) or p34 protein kinase, and is ...
CDD:270831	287	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd07838, STKc_CDK4_6_like, Catalytic domain of Cyclin-Dependent protein Kinase 4 and 6-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK4 and CDK6 partner with D-type cyclins to regulate the early G1 phase of the cell cycle. They are the first kinases activated by mitogenic signals to release cells from the G0 arrested state. CDK4 ...
CDD:270832	291	EUK	Invertebrates:5,Plants:20,Primates:1,Vertebrates:1	cd07840, STKc_CDK9_like, Catalytic domain of Cyclin-Dependent protein Kinase 9-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK9 and CDK12 from higher eukaryotes, yeast BUR1, C-type plant CDKs (CdkC), and similar proteins. CDK9, BUR1, and CdkC are functionally equivalent. They act as a kinase ...
CDD:270833	298	EUK	Invertebrates:13,Plants:11,Vertebrates:3	cd07841, STKc_CDK7, Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 7.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK7 plays essential roles in the cell cycle and in transcription. It associates with cyclin H and MAT1 and acts as a CDK-Activating Kinase (CAK) by phosphorylating and activating cell cycle CDKs (CDK1/2/4/6). In the ...
CDD:270834	316	EUK	Invertebrates:7,Plants:7,Primates:1,nodiv:1	cd07842, STKc_CDK8_like, Catalytic domain of Cyclin-Dependent protein Kinase 8-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK8, CDC2L6, and similar proteins. CDK8 functions as a negative or positive regulator of transcription, depending on the scenario. Together with its regulator, cyclin C, it ...
CDD:173741	293	EUK	Invertebrates:14,Plants:11,Vertebrates:3	cd07843, STKc_CDC2L1, Catalytic domain of the Serine/Threonine Kinase, Cell Division Cycle 2-like 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDC2L1, also called PITSLRE, exists in different isoforms which are named using the alias CDK11(p). The CDC2L1 gene produces two protein products, CDK11(p110) and CDK11(p58). CDC2L1 is also represented by the ...
CDD:270839	336	EUK	Invertebrates:7,Plants:8,Primates:1,Rodents:1,Vertebrates:3	cd07849, STKc_ERK1_2_like, Catalytic domain of Extracellular signal-Regulated Kinase 1 and 2-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the mitogen-activated protein kinases (MAPKs) ERK1, ERK2, baker's yeast Fus3, and similar proteins. MAPK pathways are important mediators of ...
CDD:143356	343	EUK	Invertebrates:10,Primates:1,Rodents:1,Vertebrates:2	cd07851, STKc_p38, Catalytic domain of the Serine/Threonine Kinase, p38 Mitogen-Activated Protein Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38 kinases are mitogen-activated protein kinases (MAPKs), serving as important mediators of cellular responses to extracellular signals. They function in the regulation of the cell cycle, cell ...
CDD:270841	337	EUK	Invertebrates:23,Plants:10,Primates:1,Vertebrates:2	cd07852, STKc_MAPK15-like, Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase 15 and similar MAPKs.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Human MAPK15 is also called Extracellular signal Regulated Kinase 8 (ERK8) while the rat protein is called ERK7. ERK7 and ERK8 display both similar and different biochemical ...
CDD:270849	311	EUK	Plants:10	cd07866, STKc_BUR1, Catalytic domain of the Serine/Threonine Kinase, Fungal Cyclin-Dependent protein Kinase (CDK), Bypass UAS Requirement 1, and similar proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BUR1, also called SGV1, is a yeast CDK that is functionally equivalent to mammalian CDK9. It associates with the cyclin BUR2. BUR genes were orginally identified in a genetic screen as ...
CDD:143628	169	EUKprk	Bacteria:65,Invertebrates:13,Vertebrates:1	cd07890, CYTH-like_AC_IV-like, Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily.  This subgroup contains class IV ACs and similar proteins. AC catalyzes the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. cAMP is a key signaling molecule which conveys a variety of signals in different cell types. In prokaryotes, cAMP is a catabolite derepression signal which triggers the expression of metabolic ...
CDD:143629	148	PRK	Bacteria:71,nodiv:2	cd07891, CYTH-like_CthTTM-like_1, CYTH-like Clostridium thermocellum TTM-like subgroup 1.  This subgroup contains the triphosphate tunnel metalloenzyme (TTM) from Clostridium thermocellum (CthTTM) and similar proteins. These are found primarily in bacteria. CthTTM is a metal dependent tripolyphosphatase, nucleoside triphosphatase, and nucleoside tetraphosphatase. It hydrolyzes the beta-gamma phosphoanhydride linkage of triphosphate-containing substrates ...
CDD:143630	303	EUK	Plants:8	cd07892, PolyPPase_VTC2-3_like, Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, and -3 , and similar proteins.  Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2, -3, and -4 contain polyP polymerase domains. S. cerevisiae VTC-2,and -3 belong to this subgroup. For VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. ...
CDD:153435	129	EUKprk	Bacteria:6,Vertebrates:1	cd07893, OBF_DNA_ligase, The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA ...
CDD:185705	342	PRK	Bacteria:26	cd07894, Adenylation_RNA_ligase, Adenylation domain of RNA circularization proteins.  RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that ...
CDD:185706	215	EUK	Invertebrates:30,Plants:28,Primates:1,Vertebrates:3,nodiv:1	cd07895, Adenylation_mRNA_capping, Adenylation domain of GTP-dependent mRNA capping enzymes.  RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation ...
CDD:185707	174	EUKprk	Bacteria:36,Invertebrates:5,Plants:3,Viruses:2	cd07896, Adenylation_kDNA_ligase_like, Adenylation domain of kDNA ligases and similar proteins.  The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and ...
CDD:185708	207	EUKprk	Bacteria:30,Plants:1	cd07897, Adenylation_DNA_ligase_Bac1, Adenylation domain of putative bacterial ATP-dependent DNA ligases.  Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ...
CDD:185709	201	EUKprk	Bacteria:8,Plants:1	cd07898, Adenylation_DNA_ligase, Adenylation domain of ATP-dependent DNA Ligases.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, ...
CDD:185710	219	EUK	Invertebrates:21,Plants:18,Vertebrates:1,nodiv:1	cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of eukaryotic DNA Ligase I.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many ...
CDD:185711	207	PRK	Bacteria:33,Environmental:2	cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of archaeal and bacterial LigB-like DNA ligases.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in ...
CDD:185712	213	EUK	Invertebrates:12,Vertebrates:2	cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA Ligase III.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, ...
CDD:185713	225	EUK	Invertebrates:22,Plants:26,Vertebrates:2,nodiv:1	cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA Ligase IV.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms ...
CDD:185714	194	PRK	Bacteria:14,nodiv:1	cd07905, Adenylation_DNA_ligase_LigC, Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases.  Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is ...
CDD:185715	190	EUKprk	Bacteria:120,Plants:1,nodiv:1	cd07906, Adenylation_DNA_ligase_LigD_LigC, Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases.  Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, ...
CDD:153117	154	PRK	Bacteria:17	cd07908, Mn_catalase_like, Manganese catalase-like protein, ferritin-like diiron-binding domain.  This uncharacterized bacterial protein family has a ferritin-like domain similar to that of the manganese catalase protein of Lactobacillus plantarum and the bll3758 protein of Bradyrhizobium japonicum.  Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These ...
CDD:153118	147	PRK	Bacteria:29,nodiv:1	cd07909, YciF, YciF bacterial stress response protein, ferritin-like iron-binding domain.  YciF is a bacterial protein of unknown function that is up-regulated when bacteria experience stress conditions, and is highly conserved in a broad range of bacterial species.  YciF has a ferritin-like domain.  Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. ...
CDD:153119	180	PRK	Bacteria:33	cd07910, MiaE, MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain.  MiaE is a nonheme diiron monooxygenase that catalyzes the posttranscriptional allylic hydroxylation of a modified nucleoside in tRNA called 2-methylthio-N-6-isopentenyl adenosine (ms2i6A).  ms2i6A is found at position 37, next to the anticodon at the 3' position in almost all eukaryotic and bacterial tRNA's that read codons beginning with uridine. The miaE gene is ...
CDD:153120	280	PRK	Bacteria:6	cd07911, RNRR2_Rv0233_like, Ribonucleotide Reductase R2-like protein, Mn/Fe-binding domain.  Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a  heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases.  ...
CDD:143653	418	EUK	Invertebrates:6,Primates:1,Vertebrates:3	cd07912, Tweety_N, N-terminal domain of the protein encoded by the Drosophila tweety gene and related proteins, a family of chloride ion channels.  The protein product of the Drosophila tweety (tty) gene is thought to form a trans-membrane protein with five membrane-spanning regions and a cytoplasmic C-terminus. This N-terminal domain contains the putative transmembrane spanning regions. Tweety has been suggested as a candidate for a ...
CDD:153419	190	EUKprk	Bacteria:117,Environmental:2,Plants:7	cd07914, IGPD, Imidazoleglycerol-phosphate dehydratase.  Imidazoleglycerol-phosphate dehydratase (IGPD; EC 4.2.1.19) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ...
CDD:153420	322	EUK	Invertebrates:8,Plants:18,Primates:1,Vertebrates:3	cd07920, Pumilio, Pumilio-family RNA binding domain.  Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly ...
CDD:153077	232	PRK	Bacteria:50	cd07930, bacterial_phosphagen_kinase, Phosphagen (guanidino) kinases found in bacteria.  Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, such as phosphocreatine (PCr) or phosphoarginine, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. This subfamily is specific to bacteria and lacks an N-terminal domain, which otherwise forms part of the substrate binding site. ...
CDD:153078	338	EUKprk	Bacteria:2,Invertebrates:12,Plants:1,Primates:1,nodiv:1	cd07931, eukaryotic_phosphagen_kinases, Phosphagen (guanidino) kinases mostly found in eukaryotes.  Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The ...
CDD:153079	350	EUK	Invertebrates:13,Plants:1	cd07932, arginine_kinase_like, Phosphagen (guanidino) kinases such as arginine kinase and similar enzymes.  Eukaryotic arginine kinase-like phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphoarginine in the case of arginine kinase (AK), which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft ...
CDD:153421	85	EUK	Mammals:4,Primates:2,Rodents:1,Vertebrates:4	cd07936, SCAN, SCAN oligomerization domain.  The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, ...
CDD:163675	275	miss	miss	cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain.  This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit.  Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions ...
CDD:163676	274	miss	miss	cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain.  3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues.  Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ...
CDD:163677	259	miss	miss	cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain.  FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase.  The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic.  This protein is also required for assembly ...
CDD:163678	268	EUK	Plants:1	cd07940, DRE_TIM_IPMS, 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain.  2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis.  This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein.  This family also includes a group ...
CDD:163679	273	miss	miss	cd07941, DRE_TIM_LeuA3, Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain.  Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown.  Members of this family have an N-terminal TIM barrel domain that belongs to the DRE-TIM metallolyase superfamily.  DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase ...
CDD:163680	284	miss	miss	cd07942, DRE_TIM_LeuA, Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain.  Alpha-isopropylmalate synthase (LeuA), a key enzyme in leucine biosynthesis, catalyzes the first committed step in the pathway, converting acetyl-CoA and alpha-ketoisovalerate to alpha-isopropyl malate and CoA.  Although the reaction catalyzed by LeuA is similar to that of the Arabidopsis thaliana IPMS1 protein, the two fall into phylogenetically ...
CDD:163681	263	miss	miss	cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain.  4-hydroxy 2-ketovalerate aldolase  (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol.  This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG ...
CDD:163682	266	miss	miss	cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain.  This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown.  This family includes the Bacteroides vulgatus Bvu_2661 protein and belongs to the DRE-TIM metallolyase superfamily.  DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), ...
CDD:163684	279	miss	miss	cd07947, DRE_TIM_Re_CS, Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain.  Re-citrate synthase (Re-CS) is a Clostridium kluyveri enzyme that converts acetyl-CoA and oxaloacetate to citrate.  In most organisms, this reaction is catalyzed by Si-citrate synthase which is Si-face stereospecific with respect to C-2 of oxaloacetate, and phylogenetically unrelated to Re-citrate synthase.  Re-citrate synthase is also found in a few other ...
CDD:163685	262	miss	miss	cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase and related proteins, catalytic TIM barrel domain.  Homocitrate synthase (HCS) catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, the first step in the lysine biosynthesis pathway.  This family includes the Yarrowia lipolytica LYS1 protein as well as the Saccharomyces cerevisiae LYS20 and LYS21 proteins.  This family belongs to the DRE-TIM metallolyase superfamily.  ...
CDD:153388	256	PRK	Bacteria:28	cd07951, ED_3B_N_AMMECR1, The N-terminal domain, an extradiol dioxygenase class III subunit B-like domain, of unknown proteins containing a C-terminal AMMECR1 domain.  This subfamily is composed of uncharacterized proteins containing an N-terminal domain with similarity to the catalytic B subunit of class III extradiol dioxygenases and a C-terminal AMMECR1-like domain. This model represents the N-terminal domain. Class III extradiol dioxygenases use a non-heme ...
CDD:153389	256	EUKprk	Bacteria:12,Invertebrates:1,Plants:1	cd07952, ED_3B_like, Uncharacterized class III extradiol dioxygenases.  This subfamily is composed of proteins of unknown function with similarity to the catalytic B subunit of class III extradiol dioxygenases. Class III extradiol dioxygenases use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. They play key roles in the degradation of aromatic compounds.
CDD:271157	245	EUK	Plants:1,Primates:1,Rodents:2	cd07954, AP_MHD_Cterm, C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD).  This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an ...
CDD:153410	156	EUKprk	Bacteria:15,Invertebrates:3,Plants:4	cd07956, Anticodon_Ia_Arg, Anticodon-binding domain of arginyl tRNA synthetases.  This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA.
CDD:153411	129	EUKprk	Bacteria:133,Environmental:5,Invertebrates:17,Plants:31,Primates:1,Vertebrates:3,nodiv:1	cd07957, Anticodon_Ia_Met, Anticodon-binding domain of methionyl tRNA synthetases.  This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA.
CDD:153412	117	EUKprk	Bacteria:113,Environmental:3,Invertebrates:3,Plants:5,Primates:1,Vertebrates:3,nodiv:1	cd07958, Anticodon_Ia_Leu_BEm, Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases.  This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with ...
CDD:153413	117	EUKprk	Bacteria:9,Environmental:2,Invertebrates:4,Plants:7,Primates:1,Vertebrates:3	cd07959, Anticodon_Ia_Leu_AEc, Anticodon-binding domain of archaeal and eukaryotic cytoplasmic leucyl tRNA synthetases.  This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with exceptions ...
CDD:153414	180	EUKprk	Bacteria:78,Environmental:2,Invertebrates:17,Plants:25,Rodents:1,Vertebrates:2,nodiv:1	cd07960, Anticodon_Ia_Ile_BEm, Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases.  This domain is found in isoleucyl tRNA synthetases (IleRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. This family includes bacterial and ...
CDD:153415	183	EUKprk	Bacteria:50,Environmental:3,Invertebrates:20,Plants:9,Vertebrates:3	cd07961, Anticodon_Ia_Ile_ABEc, Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases.  This domain is found in isoleucyl tRNA synthetases (IleRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. This family includes bacterial, archaeal, and ...
CDD:153416	135	EUKprk	Bacteria:90,Environmental:3,Invertebrates:18,Plants:13,Rodents:1,Vertebrates:2,nodiv:1	cd07962, Anticodon_Ia_Val, Anticodon-binding domain of valyl tRNA synthetases.  This domain is found in valyl tRNA synthetases (ValRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ValRS catalyzes the transfer of valine to the 3'-end of its tRNA.
CDD:153417	156	PRK	Bacteria:25,nodiv:1	cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl tRNA synthetases.  This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA.
CDD:176481	103	PRK	Bacteria:1,Phages:5,Viruses:3	cd07964, RBP-H, Head domain of virus receptor-binding proteins (RBP).  Virus receptor-binding proteins (RBPs) are found in lactococcal bacteriophages, as well as in adenoviruses and reoviruses, which invade mammalian cells. Lactococcus lactis is widely used in dairy fermentations and infection of L. lactis by phages greatly impairs the fermentation process. Adenovirus typically infects respiratory tracts with symptoms ranging from the common cold ...
CDD:153437	140	EUK	Invertebrates:2,Plants:4	cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA ...
CDD:153438	144	EUK	Invertebrates:8,Plants:10,Vertebrates:1	cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes ...
CDD:153439	122	PRK	Bacteria:5	cd07970, OBF_DNA_ligase_LigC, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, ...
CDD:153440	115	PRK	Bacteria:23	cd07971, OBF_DNA_ligase_LigD, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, ...
CDD:153441	122	PRK	Bacteria:4	cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes ...
CDD:153422	98	EUK	Invertebrates:16,Plants:12,Rodents:1,Vertebrates:3,nodiv:1	cd07973, Spt4, Transcription elongation factor Spt4.  Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important ...
CDD:199899	102	EUK	Invertebrates:23,Plants:45,Primates:1,Vertebrates:5,nodiv:1	cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA alpha and beta subunits and similar proteins.  Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription ...
CDD:153423	75	EUK	Invertebrates:13,Plants:13,Primates:1,Vertebrates:3,nodiv:1	cd07977, TFIIE_beta_winged_helix, TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity.  Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is ...
CDD:173962	92	EUK	Invertebrates:12,Plants:28,Primates:1,Vertebrates:3	cd07978, TAF13, The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is  involved  in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, ...
CDD:173963	117	EUK	Invertebrates:18,Plants:19,Primates:1,Vertebrates:3	cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that ...
CDD:259828	123	EUK	Invertebrates:20,Mammals:1,Plants:53,Primates:1,Vertebrates:4	cd07980, TFIIF_beta, Transcription initiation factor IIF, beta subunit.  The TFIIF-beta subunit, also called RNA Polymerase II-associating Protein 30 (RAP30), forms a heteromeric complex of RAP30/74 (TFIIF, beta/gamma) that is involved in both initiation and elongation of RNA chains by RNA polymerase II. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA ...
CDD:173964	72	EUK	Invertebrates:15,Plants:17,Primates:1,Vertebrates:3,nodiv:1	cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, ...
CDD:187739	108	EUK	Invertebrates:12,Plants:17,Primates:1,Vertebrates:3	cd07982, TAF10, The TATA Binding Protein (TBP) Associated Factor 10.  The TATA Binding Protein (TBP) Associated Factor 10 (TAF 10) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of the seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II ...
CDD:153245	189	PRK	Bacteria:54	cd07983, LPLAT_DUF374-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or ...
CDD:153246	192	PRK	Bacteria:121	cd07984, LPLAT_LABLAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or ...
CDD:153248	210	PRK	Bacteria:19,Environmental:1	cd07986, LPLAT_ACT14924-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone ...
CDD:153249	212	EUKprk	Bacteria:11,Invertebrates:11,Plants:7,Primates:1,Vertebrates:3	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol ...
CDD:153250	163	PRK	Bacteria:21	cd07988, LPLAT_ABO13168-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or ...
CDD:153251	184	EUKprk	Bacteria:188,Environmental:4,Invertebrates:16,Plants:14,Primates:1,Vertebrates:3,nodiv:1	cd07989, LPLAT_AGPAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into ...
CDD:153252	193	EUKprk	Bacteria:5,Invertebrates:15,Plants:10,Primates:1,Vertebrates:4,nodiv:1	cd07990, LPLAT_LCLAT1-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as ...
CDD:153253	211	EUK	Invertebrates:19,Plants:5,Primates:1,Vertebrates:3	cd07991, LPLAT_LPCAT1-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LPCAT1-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, ...
CDD:153254	203	EUKprk	Bacteria:9,Invertebrates:3,Plants:4	cd07992, LPLAT_AAK14816-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown AAK14816-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, ...
CDD:153255	205	EUKprk	Bacteria:7,Invertebrates:10,Plants:4,Primates:1,Vertebrates:4	cd07993, LPLAT_DHAPAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like.  Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol ...
CDD:153431	208	EUKprk	Bacteria:205,Environmental:1,Invertebrates:20,Plants:21,Rodents:1,Vertebrates:3,nodiv:2	cd07995, TPK, Thiamine pyrophosphokinase.  Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The ...
CDD:153425	74	PRK	Bacteria:79,nodiv:1	cd07996, WGR_MMR_like, WGR domain of molybdate metabolism regulator and related proteins.  The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together ...
CDD:153426	102	EUK	Invertebrates:13,Plants:9,Primates:1	cd07997, WGR_PARP, WGR domain of poly(ADP-ribose) polymerases.  The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent ...
CDD:153427	77	PRK	Bacteria:7	cd07998, WGR_DNA_ligase, WGR domain of bacterial DNA ligases.  The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.
CDD:153432	386	EUK	Invertebrates:3,Plants:8	cd07999, GH7_CBH_EG, Glycosyl hydrolase family 7.  Glycosyl hydrolase family 7 contains eukaryotic endoglucanases (EGs) and cellobiohydrolases (CBHs) that hydrolyze glycosidic bonds using a double-displacement mechanism. This leads to a net retention of the conformation at the anomeric carbon. Both enzymes work synergistically in the degradation of cellulose,which is the main component of plant cell wall, and is composed of beta-1,4 linked glycosyl ...
CDD:193574	99	EUKprk	Bacteria:18,Plants:1,Primates:1,nodiv:1	cd08000, NGN, N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily.  The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN ...
CDD:153428	104	EUK	Invertebrates:17,Plants:4,Vertebrates:2,nodiv:1	cd08001, WGR_PARP1_like, WGR domain of poly(ADP-ribose) polymerase 1 and similar proteins.  The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding ...
CDD:153430	103	EUK	Invertebrates:11,Vertebrates:3	cd08003, WGR_PARP2_like, WGR domain of poly(ADP-ribose) polymerases.  The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent ...
CDD:153433	245	PRK	Bacteria:47	cd08010, yceG_like, proteins similar to Escherichia coli yceG.  The gene product of Escherichia coli yceG has been erroneously annotated as an aminodeoxychorismate lyase. Its overexpression has been reported to cause abnormal biofilm architecture, and it has been reported to be part of a putative five-gene operon. It might function as a periplasmic solute-binding protein. The family also includes Streptomyces caeruleus NovB, an uncharacterized member of the ...
CDD:193559	390	PRK	Bacteria:4	cd08011, M20_ArgE_DapE_like6, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned peptidases. ...
CDD:193561	377	EUKprk	Bacteria:6,Plants:5	cd08013, M20_ArgE_DapE_like3, M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases.  Peptidase M20 family, Uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned ...
CDD:193562	372	PRK	Bacteria:25	cd08014, M20_Acy1_like4, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of uncharacterized bacterial proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be ...
CDD:193563	275	PRK	Bacteria:8	cd08015, M28_like_4, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions.
CDD:193564	377	EUK	Plants:8	cd08017, M20_IAA_Hyd, M20 Peptidase Indole-3-acetic acid amino acid hydrolase.  Peptidase M20 family, Plant Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase (IAA-Asp hydrolase; IAAspH; IAAH; IAA amidohydrolase; EC 3.5.1.-) subfamily. IAAspH hydrolyzes indole-3-acetyl-N-aspartic acid (IAA or auxin) to indole-3-acetic acid. Genes encoding IAA-amidohydrolases were first cloned from Arabidopsis; ILR1, IAR3, ILL1 and ILL2 encode active IAA- amino acid hydrolases, ...
CDD:193565	365	PRK	Bacteria:12	cd08018, M20_Acy1_amhX_like, M20 Peptidase Aminoacylase 1 amhX_like subfamily.  Peptidase M20 family, Uncharacterized subfamily of uncharacterized proteins predicted as putative amidohydrolases, including the amhX gene product from Bacillus subtilis. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and ...
CDD:193566	372	PRK	Bacteria:25	cd08019, M20_Acy1_subfamily5, M20 Peptidase Aminoacylase 1 subfamily.  Peptidase M20 family, Uncharacterized subfamily of bacterial proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be ...
CDD:193567	277	PRK	Bacteria:18	cd08021, M28_like_5, M28 Zn-Peptidase IAP aminopeptidase may contain PA domain insert.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized ...
CDD:193568	286	EUKprk	Bacteria:5,Invertebrates:3,Plants:14,Primates:1	cd08022, M28_PSMA_like, M28 Zn-peptidase prostate-specific membrane antigen.  Peptidase M28 family; prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase II or GCP-II)-like subfamily. PSMA is a homodimeric type II transmembrane protein containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion ...
CDD:185693	235	EUKprk	Bacteria:103,Invertebrates:7,Plants:3	cd08023, GH16_laminarinase_like, Laminarinase, member of the glycosyl hydrolase family 16.  Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.
CDD:185694	330	EUK	Invertebrates:20,Plants:7,nodiv:1	cd08024, GH16_CCF, Coelomic cytolytic factor, member of glycosyl hydrolase family 16.  Subgroup of glucanases of unknown function that are related to beta-GRP (beta-1,3-glucan recognition protein), but contain active site residues. Beta-GRPs are one group of pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation ...
CDD:153090	400	PRK	Bacteria:8	cd08025, RNR_PFL_like_DUF711, Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase.  This subfamily contains Streptococcus pneumoniae Sp0239 and similar uncharacterized proteins. Sp0239 is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which are believed to have diverged from a common ancestor. RNR and PFL possess a ten-stranded alpha-beta barrel domain that hosts the active site, ...
CDD:153434	102	PRK	Bacteria:83	cd08026, DUF326, Cysteine-rich 4 helical bundle widely conserved in bacteria.  This functionally uncharacterized protein forms a 4-helical bundle with a bromodomain-like topology. It is present in major bacterial lineages and contains highly conserved cysteines in a repeated pattern, whose sidechains appear buried. Some family members have been (mis)annotated as putative ferredoxins.
CDD:153397	82	EUK	Invertebrates:10,Vertebrates:3	cd08028, LARP_3, La RNA-binding domain of La-related protein 3.  This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La ...
CDD:153398	76	EUK	Plants:14	cd08029, LA_like_fungal, La-motif domain of fungal proteins similar to the La autoantigen.  This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
CDD:153402	77	EUK	Invertebrates:6,Plants:6,Vertebrates:3	cd08033, LARP_6, La RNA-binding domain of La-related protein 6.  This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
CDD:153443	77	EUKprk	Bacteria:8,Invertebrates:3,Plants:4	cd08041, OBF_kDNA_ligase_like, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit.  ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the ...
CDD:176269	133	EUK	Invertebrates:23,Plants:25,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd08044, TAF5_NTD2, TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID).  The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at ...
CDD:173965	212	EUK	Invertebrates:18,Plants:24,Primates:1,Vertebrates:4	cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, ...
CDD:173966	162	EUK	Invertebrates:30,Plants:27,Primates:1,Vertebrates:3,nodiv:1	cd08047, TAF7, TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, ...
CDD:173967	85	EUK	Invertebrates:11,Plants:29,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd08048, TAF11, TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) ...
CDD:176263	54	EUK	Invertebrates:14,Plants:22,Rodents:1,Vertebrates:3	cd08049, TAF8, TATA Binding Protein (TBP) Associated Factor 8.  The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. ...
CDD:173968	343	EUK	Invertebrates:16,Plants:18,Primates:1,Rodents:1,Vertebrates:3	cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex.  The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, ...
CDD:153445	121	PRK	Bacteria:26	cd08053, Yqbg, Putative Head-Tail Connector Protein Yqbg from Bacillus subtilis and similar proteins.  The uncharacterized Bacillus subtilis Yqbg protein, whose gene is part of the unusual genetic element called skin, shows a similar structure to the connector proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. gp6 and gp15 are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail ...
CDD:153446	91	EUKprk	Bacteria:212,Phages:1,Plants:1	cd08054, gp6, Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins.  The bacteriophage HK97 gp6 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the ...
CDD:153447	95	PRK	Bacteria:18,Phages:1	cd08055, gp15, Head-Tail Connector Protein gp15 of Bacteriophage SPP1 and similar proteins.  The bacteriophage SPP1 gp15 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal ...
CDD:163687	252	EUK	Invertebrates:22,Plants:18,Primates:1,Vertebrates:3	cd08056, MPN_PRP8, Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8.  Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of ...
CDD:163688	157	EUK	Invertebrates:5,Plants:12,Primates:1	cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic.  This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants  lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins ...
CDD:163691	182	EUK	Invertebrates:22,Plants:11,Primates:1,Vertebrates:3,nodiv:1	cd08060, MPN_UPF0172, Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p).  This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members ...
CDD:163692	274	EUK	Invertebrates:19,Plants:15,Primates:1,Vertebrates:2	cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain.  Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with ...
CDD:163693	280	EUK	Invertebrates:19,Plants:12,Vertebrates:3	cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8.  This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by ...
CDD:163694	288	EUK	Invertebrates:13,Plants:19,Vertebrates:2	cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6.  CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, ...
CDD:163695	265	EUK	Invertebrates:18,Plants:16,Vertebrates:3	cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f.  Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and ...
CDD:163696	266	EUK	Invertebrates:18,Plants:17,Vertebrates:3,nodiv:1	cd08065, MPN_eIF3h, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h.  Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, ...
CDD:163697	173	EUK	Invertebrates:11,Plants:13,Primates:1,Vertebrates:3,nodiv:1	cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family.  AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating ...
CDD:163698	187	EUK	Invertebrates:15,Plants:3,Primates:1,Vertebrates:3	cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase.  This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb ...
CDD:163699	244	EUK	Invertebrates:10,Plants:3,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex.  BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs),  possibly with ...
CDD:163700	268	EUK	Invertebrates:21,Plants:22,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5.  This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; ...
CDD:163701	128	PRK	Bacteria:105	cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding).  This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated ...
CDD:163702	113	EUKprk	Bacteria:281,Environmental:3,Plants:1,nodiv:2	cd08071, MPN_DUF2466, Mov34/MPN/PAD-1 family.  Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
CDD:163703	117	PRK	Bacteria:11,Environmental:3	cd08072, MPN_archaeal, Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme.  This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having ...
CDD:163704	108	PRK	Bacteria:30	cd08073, MPN_NLPC_P60, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains.  This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides ...
CDD:163707	328	EUKprk	Bacteria:3,Invertebrates:1,Plants:2	cd08151, AOS, Allene oxide synthase.  Allene oxide synthase converts a fatty acid hydroperoxide to an allene oxide, which is an unstable epoxide. In corals, the enzyme is part of a eiconaosid synthesis pathway that is initiated by a lipoxygenase, which generates the fatty acid hydroperoxides in the first step. The structure of allene oxide synthase closely resembles that of catalase, but allene oxide synthase does not have catalase activity.
CDD:163708	305	EUKprk	Bacteria:31,Plants:2	cd08152, y4iL_like, Catalase-like heme-binding proteins similar to the uncharacterized y4iL.  Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity.  This ...
CDD:163709	295	EUKprk	Bacteria:42,Plants:1	cd08153, srpA_like, Catalase-like heme-binding proteins similar to the uncharacterized srpA.  Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity.  This ...
CDD:163710	469	EUKprk	Bacteria:12,Plants:4	cd08154, catalase_clade_1, Clade 1 of the heme-binding enzyme catalase.  Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 1 catalases are found in bacteria, algae, ...
CDD:163712	429	EUKprk	Bacteria:33,Invertebrates:10,Plants:3,Primates:1,Vertebrates:3	cd08156, catalase_clade_3, Clade 3 of the heme-binding enzyme catalase.  Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 3 ...
CDD:163713	451	EUK	Plants:12	cd08157, catalase_fungal, Fungal catalases similar to yeast catalases A and T.  Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. This family of fungal catalases has a relatively small ...
CDD:163669	313	EUKprk	Bacteria:12,Plants:1	cd08162, MPP_PhoA_N, Synechococcus sp. strain PCC 7942  PhoA and related proteins, N-terminal metallophosphatase domain.  Synechococcus sp. strain PCC 7942 PhoA is a large atypical alkaline phosphatase.  It is known to be transported across the inner cytoplasmic membrane and into the periplasmic space.  In vivo inactivation of the gene encoding PhoA leads to a loss of extracellular, phosphate-regulated phosphatase activity, but does not appear to affect ...
CDD:163670	257	EUK	Plants:6	cd08163, MPP_Cdc1, Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain.  Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen.  In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization.  Cdc1 mutant cells accumulate an unidentified phospholipid, ...
CDD:163672	156	EUK	Invertebrates:6,Plants:2,Primates:1,Vertebrates:3	cd08165, MPP_MPPE1, human MPPE1 and related proteins, metallophosphatase domain.  MPPE1 is a functionally uncharacterized metallophosphatase domain-containing protein. The MPPE1 gene is located on chromosome 18 and is a candidate susceptibility gene for Bipolar disorder.  MPPE1 belongs to the metallophosphatase (MPP) superfamily.  MPPs are functionally diverse, but all share a conserved domain with an active site consisting of ...
CDD:163673	195	EUK	Invertebrates:8	cd08166, MPP_Cdc1_like_1, uncharacterized subgroup related to Saccharomyces cerevisiae CDC1, metallophosphatase domain.  A functionally uncharacterized subgroup related to the metallophosphatase domain of Saccharomyces cerevisiae Cdc1, S. cerevisiae Ted1 and human MPPE1. Cdc1 is an endoplasmic reticulum-localized transmembrane lipid phosphatase and is a subunit of DNA polymerase delta. TED1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), acts ...
CDD:173979	85	PRK	Bacteria:37,Environmental:2	cd08168, Cytochrom_C3, Heme-binding domain of the class III cytochrome C family and related proteins.  This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains ...
CDD:173929	351	EUKprk	Bacteria:34,Invertebrates:2,Plants:1	cd08170, GlyDH, Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation.  Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the ...
CDD:173930	345	PRK	Bacteria:20	cd08171, GlyDH-like2, Glycerol dehydrogenase-like.  Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of ...
CDD:173931	347	PRK	Bacteria:33	cd08172, GlyDH-like1, Glycerol dehydrogenases-like.  Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of ...
CDD:173932	339	PRK	Bacteria:10,Environmental:1	cd08173, Gro1PDH, Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme.  Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. It catalyzes the ...
CDD:173933	331	PRK	Bacteria:12	cd08174, G1PDH-like, Glycerol-1-phosphate dehydrogenase-like.  Glycerol-1-phosphate dehydrogenase-like. The proteins of this family have not been characterized. The protein sequences have high similarity with that of glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a ...
CDD:173934	348	PRK	Bacteria:27	cd08175, G1PDH, Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner.  Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity ...
CDD:173935	377	EUKprk	Bacteria:22,Invertebrates:2,Plants:4	cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria.  Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is ...
CDD:173936	337	EUKprk	Bacteria:39,Plants:9	cd08177, MAR, Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes.  Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds  in aerobic microbes. In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, ...
CDD:173937	398	EUKprk	Bacteria:11,Invertebrates:3	cd08178, AAD_C, C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD).  Alcohol dehydrogenase domain located on the C-terminal of a bifunctional two-domain protein. The N-terminal of the protein contains an acetaldehyde-CoA dehydrogenase domain. This protein is involved in pyruvate metabolism. Pyruvate is converted to acetyl-CoA and formate by pyruvate formate-lysase ...
CDD:173938	375	EUKprk	Bacteria:20,Invertebrates:1	cd08179, NADPH_BDH, NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria.  NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria. The fermentation process is characterized by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as ...
CDD:173939	332	PRK	Bacteria:32	cd08180, PDD, 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism.  1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation ...
CDD:173940	357	PRK	Bacteria:18	cd08181, PPD-like, 1,3-propanediol dehydrogenase-like (PPD).  1,3-propanediol dehydrogenase-like (PPD). This family is a member of the iron-containing alcohol dehydrogenase superfamily, and exhibits a dehydroquinate synthase-like fold.  Protein sequence similarity search and other biochemical evidences suggest that they are close to the iron-containing 1,3-propanediol dehydrogenase (EC 1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the oxidation of ...
CDD:173941	367	PRK	Bacteria:23	cd08182, HEPD, Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP).  Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin ...
CDD:173942	374	EUKprk	Bacteria:30,Plants:1	cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.  Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains ...
CDD:173944	380	PRK	Bacteria:28	cd08185, Fe-ADH1, Iron-containing alcohol dehydrogenases-like.  Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein ...
CDD:173945	383	EUKprk	Bacteria:10,Invertebrates:1	cd08186, Fe-ADH8, Iron-containing alcohol dehydrogenase.  Type III Iron-containing alcohol dehydrogenases (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. ...
CDD:173946	382	EUKprk	Bacteria:86,Invertebrates:3	cd08187, BDH, Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process.  The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold ...
CDD:173947	377	PRK	Bacteria:23	cd08188, Fe-ADH4, Iron-containing alcohol dehydrogenases-like.  Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains.  ...
CDD:173948	374	EUKprk	Bacteria:26,Invertebrates:1	cd08189, Fe-ADH5, Iron-containing alcohol dehydrogenases-like.  Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contains different protein ...
CDD:173949	414	EUKprk	Bacteria:7,Invertebrates:7,Plants:4,Primates:2,Rodents:1,Vertebrates:3	cd08190, HOT, Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism.  Hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate ...
CDD:173950	386	PRK	Bacteria:12	cd08191, HHD, 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.  6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental ...
CDD:173951	370	PRK	Bacteria:26,Environmental:1	cd08192, Fe-ADH7, Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway.  NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to ...
CDD:173952	376	PRK	Bacteria:38	cd08193, HVD, 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor.  5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some ...
CDD:173953	375	PRK	Bacteria:16	cd08194, Fe-ADH6, Iron-containing alcohol dehydrogenases-like.  Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains.  Alcohol dehydrogenase catalyzes the reduction of ...
CDD:173954	345	EUKprk	Bacteria:133,Environmental:4,Invertebrates:2,Plants:10,nodiv:1	cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis.  Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway, which involves seven sequential enzymatic steps in the conversion of erythrose ...
CDD:173955	346	PRK	Bacteria:8	cd08196, DHQS-like1, Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis.  Dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose ...
CDD:173956	355	EUKprk	Bacteria:9,Invertebrates:1	cd08197, DOIS, 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics.  2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine ...
CDD:173957	369	PRK	Bacteria:7	cd08198, DHQS-like2, Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis.  Dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose ...
CDD:173958	354	EUKprk	Bacteria:12,Plants:3	cd08199, EEVS, 2-epi-5-epi-valiolone synthase (EEVS).  2-epi-5-epi-valiolone synthases catalyze the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product, 2-epi-5-epi-valiolone ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,5-tetrol), is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as ...
CDD:173828	297	EUKprk	Bacteria:8,Environmental:1,Plants:2	cd08200, catalase_peroxidase_2, C-terminal non-catalytic domain of catalase-peroxidases.  This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen ...
CDD:188876	67	EUK	Invertebrates:10,Primates:1,Rodents:1	cd08203, SAM_PNT, Sterile alpha motif (SAM)/Pointed domain.  Sterile alpha motif (SAM)/Pointed domain is found in about 40% of transcriptional regulators of ETS family (initially named for Erythroblastosis virus, E26-E Twenty Six).  SAM Pointed domain containing proteins of this family additionally have a C-terminal ETS DNA-binding domain. In a few cases, SAM Pointed domain appears as a single domain protein.  Members of this group are ...
CDD:173970	367	EUKprk	Bacteria:49,Plants:1	cd08205, RuBisCO_IV_RLP, Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV.  Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads ...
CDD:173971	414	EUKprk	Bacteria:21,Plants:10	cd08206, RuBisCO_large_I_II_III, Ribulose bisphosphate carboxylase large chain, Form I,II,III.  Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and ...
CDD:173972	406	miss	miss	cd08207, RLP_NonPhot, Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria.  Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the ...
CDD:173974	391	miss	miss	cd08209, RLP_DK-MTP-1-P-enolase, 2,3-diketo-5-methylthiopentyl-1-phosphate enolase.  Ribulose bisphosphate carboxylase like proteins (RLPs) similar to B. subtilis YkrW protein, have been identified as 2,3-diketo-5-methylthiopentyl-1-phosphate enolases. They catalyze the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P). This is an important step in the methionine salvage pathway in which 5-methylthio-D-ribose (MTR) derived from ...
CDD:173975	364	miss	miss	cd08210, RLP_RrRLP, Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP.  RLP from Rhodospirillum rubrum plays a role in an uncharacterized sulfur salvage pathway and has been shown to catalyze a novel isomerization reaction that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate.
CDD:270855	258	EUK	Invertebrates:30,Plants:8,Primates:1,Vertebrates:2	cd08215, STKc_Nek, Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek family is composed of 11 different mammalian members (Nek1-11) with similarity to the catalytic domain of Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was ...
CDD:270856	315	EUK	Invertebrates:10,Primates:1	cd08216, PK_STRAD, Pseudokinase domain of STE20-related kinase adapter protein.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. STRAD forms a complex with the scaffolding protein MO25, and the serine/threonine kinase (STK), LKB1, resulting in the activation of the kinase. In the complex, LKB1 phosphorylates and activates adenosine monophosphate-activated protein kinases (AMPKs), which ...
CDD:270857	265	EUK	Invertebrates:16,Plants:13,Primates:1,Vertebrates:3	cd08217, STKc_Nek2, Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 2.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek2 subfamily includes Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was identified in a screen for cell cycle mutants prevented from entering mitosis. ...
CDD:270863	262	EUK	Invertebrates:13,Plants:4,Primates:1	cd08224, STKc_Nek6_7, Catalytic domain of the Serine/Threonine Kinases, Never In Mitosis gene A (NIMA)-related kinase 6 and 7.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek6 and Nek7 are the shortest Neks, consisting only of the catalytic domain and a very short N-terminal extension. They show distinct expression patterns and both appear to be downstream substrates ...
CDD:176192	355	PRK	Bacteria:20	cd08230, glucose_DH, Glucose dehydrogenase.  Glucose dehydrogenase (GlcDH), a member of the medium chain dehydrogenase/zinc-dependent alcohol dehydrogenase-like family, catalyzes the NADP(+)-dependent oxidation of glucose to gluconate, the first step in the Entner-Doudoroff pathway, an alternative to or substitute for glycolysis or the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which ...
CDD:176193	361	EUKprk	Bacteria:21,Invertebrates:1,Plants:3	cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the zinc-dependent alcohol dehydrogenases (ADH).  This group contains the hypothetical TM0436 alcohol dehydrogenase from Thermotoga maritima,  proteins annotated as 5-exo-alcohol dehydrogenase, and other members of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  MDR, which contains the zinc-dependent alcohol dehydrogenase ...
CDD:176194	339	PRK	Bacteria:25	cd08232, idonate-5-DH, L-idonate 5-dehydrogenase.  L-idonate 5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion of L-lodonate to 5-ketogluconate in the metabolism of L-Idonate to  6-P-gluconate. In E. coli, this GntII pathway is a subsidiary pathway to the canonical GntI system, which also phosphorylates and transports gluconate.  L-ido 5-DH is found in an operon with a regulator indR, transporter idnT, 5-keto-D-gluconate 5-reductase, and Gnt kinase. L-ido 5-DH ...
CDD:176195	351	EUKprk	Bacteria:25,Plants:16,nodiv:1	cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.  (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent medium chain alcohol dehydrogenase, catalyzes the NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and meso-butanediol to acetoin. BDH functions as a homodimer.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.  The medium chain alcohol dehydrogenase ...
CDD:176196	334	EUKprk	Bacteria:75,Plants:28,nodiv:1	cd08234, threonine_DH_like, L-threonine dehydrogenase.  L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine, via NAD(H)-dependent oxidation.  THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs  have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in ...
CDD:176197	343	PRK	Bacteria:22,Environmental:2	cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase.  Putative L-iditol 2-dehydrogenase based on annotation of some members in this subgroup.  L-iditol 2-dehydrogenase catalyzes the NAD+-dependent conversion of L-iditol to L-sorbose in fructose and mannose metabolism. This enzyme is related to sorbitol dehydrogenase, alcohol dehydrogenase, and other medium chain dehydrogenase/reductases. The zinc-dependent alcohol dehydrogenase (ADH-Zn)-like family ...
CDD:176198	343	PRK	Bacteria:28,Environmental:1	cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases.  This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and ...
CDD:176201	339	PRK	Bacteria:13	cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.  MDR/AHD-like proteins, including a protein annotated as a threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones.  Zinc-dependent ADHs are medium chain ...
CDD:176202	350	EUKprk	Bacteria:12,Environmental:2,Invertebrates:3	cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate dehydrogenase.  6-hydroxyhexanoate dehydrogenase, an enzyme of the zinc-dependent alcohol dehydrogenase-like family of medium chain dehydrogenases/reductases catalyzes the conversion of 6-hydroxyhexanoate and NAD(+) to 6-oxohexanoate + NADH and H+.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.  Alcohol ...
CDD:176203	323	EUKprk	Bacteria:46,Environmental:1,Invertebrates:5,Mammals:2,Plants:9,Vertebrates:1	cd08241, QOR1, Quinone oxidoreductase (QOR).  QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. ...
CDD:176204	319	EUKprk	Bacteria:18,Environmental:1,Plants:1	cd08242, MDR_like, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family, including threonine dehydrogenase. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) ...
CDD:176205	320	EUKprk	Bacteria:16,Plants:6	cd08243, quinone_oxidoreductase_like_1, Quinone oxidoreductase (QOR).  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.  The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or ...
CDD:176206	324	PRK	Bacteria:10	cd08244, MDR_enoyl_red, Possible enoyl reductase.  Member identified as possible enoyl reductase of the MDR family. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part ...
CDD:176207	330	EUKprk	Bacteria:7,Plants:1,nodiv:1	cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related proteins.  Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The ...
CDD:176209	352	EUK	Plants:14	cd08247, AST1_like, AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast.  This group contains members identified in targeting of yeast membrane proteins ATPase. AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast, identified as a multicopy suppressor of pma1 mutants which cause temperature sensitive growth arrest due to the inability of ATPase to target to the cell surface. This family is homologous to the ...
CDD:176210	350	EUK	Invertebrates:17,Vertebrates:3,nodiv:1	cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1.  Human Reticulon 4 Interacting Protein 1 is a member of the medium chain dehydrogenase/ reductase (MDR) family. Riticulons are endoplasmic reticulum associated proteins involved in membrane trafficking  and neuroendocrine secretion. The MDR/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a ...
CDD:176211	339	EUKprk	Bacteria:4,Plants:59	cd08249, enoyl_reductase_like, enoyl_reductase_like.  Member identified as possible enoyl reductase of the MDR family. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in  Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR ...
CDD:176212	329	EUKprk	Bacteria:1,Invertebrates:7,Plants:3,Primates:1,Vertebrates:3	cd08250, Mgc45594_like, Mgc45594 gene product and other MDR family members.  Includes Human Mgc45594 gene product of undetermined function. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ...
CDD:176214	336	EUKprk	Bacteria:42,Environmental:1,Invertebrates:1,Plants:3	cd08252, AL_MDR, Arginate lyase and other MDR family members.  This group contains a structure identified as an arginate lyase. Other members are identified quinone reductases, alginate lyases, and other proteins related to the zinc-dependent dehydrogenases/reductases. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived from aromatic compounds. Membrane ...
CDD:176215	325	EUKprk	Bacteria:22,Invertebrates:5,Vertebrates:3	cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent quinone reductase activity (QOR).  Zeta-crystallin is a eye lens protein with NADP-dependent quinone reductase activity (QOR). It has been cited as a structural component in mammalian eyes, but also has homology to quinone reductases in unrelated species. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived ...
CDD:176216	338	EUKprk	Bacteria:18,Environmental:1,Plants:14	cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, and other MDR family members.  This group contains enzymes of the zinc-dependent alcohol dehydrogenase family, including members (aka MDR) identified as 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and N-benzyl-3-pyrrolidinol dehydrogenase. 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase catalyzes the ...
CDD:176217	277	EUKprk	Bacteria:57,Environmental:2,Plants:2	cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like, 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members.  This subgroup of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family has members identified as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase and alcohol dehydrogenases. The medium chain dehydrogenases/reductase ...
CDD:176219	306	PRK	Bacteria:11	cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family.  This group shares the zinc coordination sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of ...
CDD:176220	332	EUKprk	Bacteria:5,Plants:1	cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. This group contains proteins that share the characteristic catalytic and structural zinc-binding sites of the zinc-dependent alcohol dehydrogenase family.  Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other ...
CDD:176221	345	EUKprk	Bacteria:21,Plants:1	cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. This group has the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases.  Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the ...
CDD:176222	337	PRK	Bacteria:33	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family.  This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  ...
CDD:176223	341	PRK	Bacteria:14	cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family.  The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids ...
CDD:176224	367	EUKprk	Bacteria:5,Plants:2	cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.   Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation.  ADH is a member of the medium chain alcohol dehydrogenase ...
CDD:176225	325	PRK	Bacteria:6	cd08264, Zn_ADH_like2, Alcohol dehydrogenases of the MDR family.  This group resembles the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase family. However, this subgroup does not contain the characteristic catalytic zinc site. Also, it contains an atypical structural zinc-binding pattern: DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.   Alcohol ...
CDD:176227	342	PRK	Bacteria:14,Environmental:1	cd08266, Zn_ADH_like1, Alcohol dehydrogenases of the MDR family.  This group contains proteins related to the zinc-dependent  alcohol dehydrogenases. However, while the group has structural zinc site characteristic of these enzymes, it lacks the consensus site for a catalytic zinc. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.   Alcohol dehydrogenase in the liver converts ...
CDD:176228	319	EUKprk	Bacteria:44,Invertebrates:1,Plants:31	cd08267, MDR1, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the ...
CDD:176229	328	EUKprk	Bacteria:27,Invertebrates:1,Plants:1	cd08268, MDR2, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the ...
CDD:176230	312	EUKprk	Bacteria:10,Invertebrates:1	cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family.  The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ ...
CDD:176231	305	PRK	Bacteria:9	cd08270, MDR4, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase ...
CDD:176232	325	EUKprk	Bacteria:14,Invertebrates:3	cd08271, MDR5, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent ...
CDD:176233	326	EUKprk	Bacteria:36,Invertebrates:1,nodiv:1	cd08272, MDR6, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the ...
CDD:176234	331	EUKprk	Bacteria:8,Plants:7	cd08273, MDR8, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol ...
CDD:176235	350	EUKprk	Bacteria:15,Plants:1	cd08274, MDR9, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol ...
CDD:176236	337	EUKprk	Bacteria:8,Invertebrates:7,Plants:3,Primates:1,Vertebrates:5,nodiv:1	cd08275, MDR3, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like ...
CDD:176237	336	EUKprk	Bacteria:54,Invertebrates:2,Plants:24	cd08276, MDR7, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family.  This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the ...
CDD:176238	365	EUKprk	Bacteria:1,Mammals:1,Plants:4,Vertebrates:1	cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones.  Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation.  There are 7 vertebrate ADH 7 classes, ...
CDD:176239	365	EUKprk	Bacteria:44,Plants:15,nodiv:1	cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase.  Benzyl alcohol dehydrogenase is similar to liver alcohol dehydrogenase, but has some amino acid substitutions  near  the active site, which may determine the enzyme's specificity of oxidizing aromatic substrates.  Also known as aryl-alcohol dehydrogenases, they catalyze the conversion of an aromatic alcohol + NAD+ to an aromatic aldehyde + NADH + H+.  NAD(P)(H)-dependent oxidoreductases ...
CDD:176240	363	PRK	Bacteria:37	cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.  Glutathione-dependent formaldehyde dehydrogenases (FDHs, Class III ADH) are members of the zinc-dependent/medium chain alcohol dehydrogenase family.  FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the ...
CDD:176242	375	EUKprk	Bacteria:16,Plants:9,nodiv:1	cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH).  Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family.  Unlike typical FDH, Pseudomonas putida aldehyde-dismutating FDH (PFDH) is glutathione-independent.  PFDH converts 2 molecules of aldehydes to corresponding carboxylic acid and alcohol.  MDH family uses NAD(H) as a cofactor in the ...
CDD:176243	386	EUKprk	Bacteria:25,Plants:11	cd08283, FDH_like_1, Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1.  Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc-dependent/medium chain alcohol dehydrogenase family.  FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed ...
CDD:176244	344	EUKprk	Bacteria:8,Plants:9	cd08284, FDH_like_2, Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2.  Glutathione-dependent formaldehyde dehydrogenases (FDHs) are members of the zinc-dependent/medium chain alcohol dehydrogenase family. Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family.  FDH converts formaldehyde and NAD to formate and NADH. The initial step in this process the spontaneous formation ...
CDD:176245	351	EUKprk	Bacteria:13,Environmental:1,Invertebrates:2,Plants:1	cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases.  This group is predominated by atypical alcohol dehydrogenases; they exist as tetramers and exhibit specificity for NADP(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones.  Like other zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), tetrameric ADHs have a catalytic zinc that ...
CDD:176246	345	EUKprk	Bacteria:11,Plants:11	cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.  This group is related to formaldehyde dehydrogenase (FDH), which  is a member of the zinc-dependent/medium chain alcohol dehydrogenase family.  This family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Another member is identified as a dihydroxyacetone reductase. Like the zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol ...
CDD:176247	345	PRK	Bacteria:14	cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.  This group contains proteins identified as alcohol dehydrogenases and glutathione-dependant formaldehyde dehydrogenases (FDH) of the zinc-dependent/medium chain alcohol dehydrogenase family.  The MDR family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones.  FDH converts formaldehyde and NAD to formate and NADH. The initial step in this process the spontaneous ...
CDD:176248	324	EUKprk	Bacteria:36,Invertebrates:1,Vertebrates:1	cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases.  Yhdh putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in ...
CDD:176250	341	EUKprk	Bacteria:3,Invertebrates:14,Plants:25,Primates:1,Vertebrates:3	cd08290, ETR, 2-enoyl thioester reductase (ETR).  2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in  Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain ...
CDD:176251	324	EUKprk	Bacteria:16,Invertebrates:2	cd08291, ETR_like_1, 2-enoyl thioester reductase (ETR) like proteins, child 1.  2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the ...
CDD:176252	324	EUKprk	Bacteria:10,Vertebrates:1	cd08292, ETR_like_2, 2-enoyl thioester reductase (ETR) like proteins, child 2.  2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the ...
CDD:176254	329	EUK	Invertebrates:11,Rodents:1,Vertebrates:3,nodiv:1	cd08294, leukotriene_B4_DH_like, 13-PGR is a bifunctional enzyme with delta-13 15-prostaglandin reductase and leukotriene B4 12 hydroxydehydrogenase activity.  Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin ...
CDD:176255	338	EUK	Plants:7	cd08295, double_bond_reductase_like, Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase.  This group includes proteins identified as the Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase.  The Arabidopsis enzyme, a member of the medium chain dehydrogenase/reductase family, catalyzes the reduction of 7-8-double bond of phenylpropanal substrates as a plant defense mechanism.  Prostaglandins and related ...
CDD:176256	333	EUKprk	Bacteria:11,Invertebrates:1,Plants:6	cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD).  Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium ...
CDD:176257	341	EUKprk	Bacteria:17,Invertebrates:1,Plants:26	cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD).  These alcohol dehydrogenases are related to the cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Cinnamyl alcohol dehydrogenases (CAD) reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal ...
CDD:176258	329	PRK	Bacteria:30,Environmental:1	cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD).  These alcohol dehydrogenases are related to the cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Cinnamyl alcohol dehydrogenases (CAD) reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in ...
CDD:176259	373	EUK	Mammals:2,Primates:5,Rodents:6,Vertebrates:9	cd08299, alcohol_DH_class_I_II_IV, class I, II, IV alcohol dehydrogenases.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones.  This group includes alcohol dehydrogenases corresponding to mammalian classes I, II, IV. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the ...
CDD:176260	368	EUKprk	Bacteria:9,Invertebrates:12,Mammals:3,Plants:15,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.  Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family.  FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from ...
CDD:176261	369	EUK	Plants:15	cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.  NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones.  Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation.  There are 7 vertebrate ADH 7 classes, 6 of which have been identified in humans. ...
CDD:260019	73	EUK	Primates:1,Rodents:2	cd08305, Pyrin, Pyrin: a protein-protein interaction domain.  The Pyrin domain (or PYD), also called DAPIN or PAAD, is a subfamily of the Death Domain (DD) superfamily and it functions in several signaling pathways. The Pyrin domain is found at the N-terminus of a variety of proteins and serves as a linker that recruits other domains into signaling complexes. Pyrin-containing proteins include NALPs, ASC (Apoptosis-associated speck-like protein containing a ...
CDD:260020	85	EUK	Invertebrates:4,Mammals:2,Primates:1,Rodents:1,Vertebrates:6	cd08306, Death_FADD, Fas-associated Death Domain protein-protein interaction domain.  Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune ...
CDD:260021	97	EUK	Invertebrates:14	cd08307, Death_Pelle, Death domain of the protein kinase Pelle.  Death domain (DD) of the protein kinase Pelle from Drosophila melanogaster and similar proteins. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and in mediating innate immune responses to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the ...
CDD:260022	128	EUK	Invertebrates:16	cd08308, Death_Tube, Death domain of Tube.  Death domains (DDs) similar to the DD in the protein Tube from Drosophila melanogaster. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in mediating innate immune response to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Some members ...
CDD:260023	88	EUK	Invertebrates:2,Primates:1	cd08309, Death_IRAK, Death domain of Interleukin-1 Receptor-Associated Kinases.  Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein ...
CDD:260024	72	EUK	Invertebrates:15,Primates:1	cd08310, Death_NFkB-like, Death domain of Nuclear Factor-KappaB precursor proteins.  Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and ...
CDD:260025	80	EUK	Invertebrates:5,Rodents:1,Vertebrates:2	cd08311, Death_p75NR, Death domain of p75 Neurotrophin Receptor.  Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR ...
CDD:260026	79	EUK	Invertebrates:12,Primates:1,Vertebrates:6	cd08312, Death_MyD88, Death domain of Myeloid Differentation primary response protein MyD88.  Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a ...
CDD:260027	88	EUK	Mammals:3,Primates:1,Rodents:2,Vertebrates:6	cd08315, Death_TRAILR_DR4_DR5, Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors.  Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling ...
CDD:260028	94	EUK	Mammals:1,Primates:1,Rodents:2,Vertebrates:9	cd08316, Death_FAS_TNFRSF6, Death domain of FAS or TNF receptor superfamily member 6.  Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction ...
CDD:260029	84	EUK	Invertebrates:17,Primates:1,Vertebrates:1	cd08317, Death_ank, Death domain associated with Ankyrins.  Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium ...
CDD:260031	83	EUK	Invertebrates:1,Primates:1,Vertebrates:4	cd08319, Death_RAIDD, Death domain of RIP-associated ICH-1 homologous protein with a death domain.  Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating ...
CDD:260032	84	EUK	Mammals:6,Primates:1,Rodents:3	cd08320, Pyrin_NALPs, Pyrin death domain found in NALP proteins.  Pyrin Death Domain found in NALP (NACHT, LRR and PYD domains) proteins including NALP1 (CARD7, NLRP1), NALP3 (NLRP3, Cryopyrin, CIAS1), and NALP12 (NLRP12, Monarch-1), among others. Mammals contains at least 14 NALP proteins, named NALP1-14 (or NLRP1-14). NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR ...
CDD:260033	82	EUK	Mammals:3,Primates:1,Rodents:1,Vertebrates:11	cd08321, Pyrin_ASC-like, Pyrin Death Domain found in ASC.  Pyrin Death Domain found in ASC (Apoptosis-associated speck-like protein containing a CARD) and similar proteins. ASC is an adaptor molecule that functions in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. ASC contains two domains from the Death Domain (DD) superfamily, an ...
CDD:260036	83	EUK	Mammals:7,Primates:2,Rodents:3,Vertebrates:5	cd08325, CARD_CASP1-like, Caspase activation and recruitment domain found in Caspase-1 and related proteins.  Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) ...
CDD:260039	81	EUK	Mammals:1,Rodents:1,Vertebrates:8	cd08330, CARD_ASC_NALP1, Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins.  Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein ...
CDD:260042	83	EUK	Invertebrates:3,Mammals:1,Primates:1,Vertebrates:10	cd08334, DED_Caspase_8_10_r2, Death effector domain, repeat 2, of initator caspases 8 and 10.  Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor ...
CDD:260043	82	EUK	Invertebrates:5,Primates:1,Vertebrates:4,nodiv:1	cd08336, DED_FADD, Death Effector Domain found in Fas-Associated via Death Domain.  Death Effector Domain (DED) found in Fas-Associated via Death Domain (FADD). DEDs comprise a subfamily of the Death Domain (DD) superfamily. FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such ...
CDD:176690	136	EUKprk	Bacteria:35,Invertebrates:4,Plants:3,Vertebrates:1,nodiv:2	cd08342, HPPD_N_like, N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS).  HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of HPP to homogentisate (2,5-dihydroxyphenylacetic acid, HG). HmaS ...
CDD:211355	131	PRK	Bacteria:12	cd08343, ED_TypeI_classII_C, C-terminal domain of type I, class II extradiol dioxygenases; catalytic domain.  This family contains the C-terminal, catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; ...
CDD:211356	126	EUKprk	Bacteria:43,Plants:1	cd08346, PcpA_N_like, N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins.  The N-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to ...
CDD:176695	157	PRK	Bacteria:47	cd08347, PcpA_C_like, C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins.  The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to ...
CDD:176696	134	EUKprk	Bacteria:21,Plants:4	cd08348, BphC2-C3-RGP6_C_like, The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6,  and similar proteins.  This subfamily contains Rhodococcus globerulus P6 BphC2-RGP6 and BphC3-RGP6, and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, yielding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. This is the third step in the ...
CDD:211357	112	EUKprk	Bacteria:78,Environmental:1,Plants:2,nodiv:1	cd08349, BLMA_like, Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm.  BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by ...
CDD:176698	120	PRK	Bacteria:12	cd08350, BLMT_like, BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins.  BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMT has strong ...
CDD:176699	123	PRK	Bacteria:10	cd08351, ChaP_like, ChaP, an enzyme involved in the biosynthesis of the antitumor agent chartreusin (cha); and similar proteins.  ChaP is an enzyme involved in the biosynthesis of the potent antitumor agent chartreusin (cha). Cha is an aromatic polyketide glycoside produced by Streptomyces chartreusis. ChaP may play a role as a meta-cleavage dioxygenase in the oxidative rearrangement of the anthracyclic polyketide. ChaP belongs to a conserved domain superfamily ...
CDD:211359	142	PRK	Bacteria:11	cd08353, Glo_EDI_BRP_like_7, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members ...
CDD:176702	122	EUKprk	Bacteria:18,Plants:1,nodiv:1	cd08354, Glo_EDI_BRP_like_13, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein ...
CDD:176703	122	PRK	Bacteria:28	cd08355, Glo_EDI_BRP_like_14, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:176704	113	PRK	Bacteria:10	cd08356, Glo_EDI_BRP_like_17, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:176705	125	EUKprk	Bacteria:16,Invertebrates:1,Plants:4	cd08357, Glo_EDI_BRP_like_18, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for ...
CDD:176706	127	EUK	Invertebrates:6,Primates:1,Vertebrates:2	cd08358, Glo_EDI_BRP_like_21, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for ...
CDD:176707	119	PRK	Bacteria:26	cd08359, Glo_EDI_BRP_like_22, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the ...
CDD:176708	134	PRK	Bacteria:13	cd08360, MhqB_like_C, C-terminal domain of Burkholderia sp. NF100 MhqB and similar proteins; MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion.  This subfamily contains the C-terminal, catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation ...
CDD:176710	120	PRK	Bacteria:9	cd08362, BphC5-RrK37_N_like, N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins.  2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting ...
CDD:176484	139	EUK	Invertebrates:23,Plants:24,Primates:1,Vertebrates:3	cd08366, APC10, APC10 subunit of the anaphase-promoting complex (APC) that mediates substrate ubiquitination.  This model represents the single domain protein APC10, a subunit of the anaphase-promoting complex (APC), which is a multi-subunit E3 ubiquitin ligase. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a vital component of the ubiquitin-26S proteasome pathway for selective proteolytic ...
CDD:176262	179	EUK	Invertebrates:19,Primates:1,Rodents:1,Vertebrates:3,nodiv:2	cd08367, P53, P53 DNA-binding domain.  P53 is a tumor suppressor gene product; mutations in p53 or lack of expression are found associated with a large fraction of all human cancers. P53 is activated by DNA damage and acts as a regulator of gene expression that ultimatively blocks progression through the cell cycle. P53 binds to DNA as a tetrameric transcription factor. In its inactive form, p53 is bound to the ring ...
CDD:259829	53	EUK	Invertebrates:44,Mammals:3,Plants:44,Primates:1,Rodents:1,Vertebrates:8,nodiv:3	cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers.  LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric ...
CDD:187712	173	EUKprk	Bacteria:32,Primates:1	cd08369, FMT_core, Formyltransferase, catalytic core domain.  Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide ...
CDD:187727	73	PRK	Bacteria:7	cd08370, FMT_C_like, Carboxy-terminal domain of Formyltransferase and similar domains.  This family represents the C-terminal domain of formyltransferase and similar proteins. This domain is found in a variety of enzymes with formyl transferase and alkyladenine DNA glycosylase activities. The proteins with formyltransferase function include methionyl-tRNA formyltransferase, ArnA, 10-formyltetrahydrofolate dehydrogenase and HypX proteins. Although most proteins with ...
CDD:197306	241	EUKprk	Bacteria:6,Invertebrates:1,Mammals:1,Plants:1,Primates:1	cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily.  This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate ...
CDD:176019	127	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd08373, C2A_Ferlin, C2 domain first repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide range of ...
CDD:176020	133	EUK	Invertebrates:8,Vertebrates:1	cd08374, C2F_Ferlin, C2 domain sixth repeat in Ferlin.  Ferlins are involved in vesicle fusion events.  Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together.  There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6.  Defects in these genes can lead to a wide range of diseases including muscular ...
CDD:176022	116	EUK	Invertebrates:6,Vertebrates:1	cd08376, C2B_MCTP_PRT, C2 domain second repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP).  MCTPs are involved in Ca2+ signaling at the membrane.  MCTP is composed of a variable N-terminal sequence, three C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended ...
CDD:176023	119	EUK	Invertebrates:3,Vertebrates:1	cd08377, C2C_MCTP_PRT, C2 domain third repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP).  MCTPs are involved in Ca2+ signaling at the membrane.  The cds in this family contain multiple C2 domains as well as a C-terminal PRT domain.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only ...
CDD:176024	121	EUK	Plants:4	cd08378, C2B_MCTP_PRT_plant, C2 domain second repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset.  MCTPs are involved in Ca2+ signaling at the membrane.  Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended ...
CDD:176025	126	EUK	Plants:3	cd08379, C2D_MCTP_PRT_plant, C2 domain fourth repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset.  MCTPs are involved in Ca2+ signaling at the membrane.  Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence.  It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended ...
CDD:176026	156	EUK	Invertebrates:15,Primates:1,Vertebrates:2,nodiv:1	cd08380, C2_PI3K_like, C2 domain present in phosphatidylinositol 3-kinases (PI3Ks).  C2 domain present in all classes of PI3Ks.  PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility.  PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 ...
CDD:176027	122	EUK	Invertebrates:3,Primates:1,Vertebrates:2	cd08381, C2B_PI3K_class_II, C2 domain second repeat present in class II phosphatidylinositol 3-kinases (PI3Ks).  There are 3 classes of PI3Ks based on structure, regulation, and specificity.  All classes contain a N-terminal C2 domain, a PIK domain, and a kinase catalytic domain. Unlike class I and class III, class II PI3Ks have additionally a PX domain and a C-terminal C2 domain containing a nuclear localization signal both of which ...
CDD:176028	123	EUK	Invertebrates:5,Plants:5,Vertebrates:3	cd08382, C2_Smurf-like, C2 domain present in Smad ubiquitination-related factor (Smurf)-like proteins.  A single C2 domain is found in Smurf proteins, C2-WW-HECT-domain E3s, which play an important role in the downregulation of the TGF-beta signaling pathway.  Smurf proteins also regulate cell shape, motility, and polarity by degrading small guanosine triphosphatases (GTPases). C2 domains fold into an 8-standed beta-sandwich that can ...
CDD:176029	117	EUK	Invertebrates:6,Primates:1,Vertebrates:3	cd08383, C2A_RasGAP, C2 domain (first repeat) of Ras GTPase activating proteins (GAPs).  RasGAPs suppress Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras.  In this way it can control cellular proliferation and differentiation.  The proteins here all contain either a single C2 domain or two tandem C2 domains,  a Ras-GAP domain, and a pleckstrin homology (PH)-like domain. C2 ...
CDD:176031	124	EUK	Invertebrates:12,Primates:1,Rodents:1,Vertebrates:4	cd08385, C2A_Synaptotagmin-1-5-6-9-10, C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 1, a member of class 1 synaptotagmins, is located in the brain and endocranium and localized to the synaptic vesicles and secretory granules.  It functions as a Ca2+ ...
CDD:176035	124	EUK	Invertebrates:6,Primates:1,Vertebrates:5,nodiv:1	cd08389, C2A_Synaptotagmin-14_16, C2A domain first repeat present in Synaptotagmins 14 and 16.  Synaptotagmin 14 and 16 are membrane-trafficking proteins in specific tissues outside the brain.   Both of these contain C-terminal tandem C2 repeats, but only Synaptotagmin 14 has an N-terminal transmembrane domain and a putative fatty-acylation site. Previously all synaptotagmins were thought to be calcium sensors in the regulation ...
CDD:176036	123	EUK	Invertebrates:6,Vertebrates:3,nodiv:1	cd08390, C2A_Synaptotagmin-15-17, C2A domain first repeat present in Synaptotagmins 15 and 17.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. It is thought to be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues and is Ca2+ independent. Human synaptotagmin 15 has 2 alternatively spliced forms that encode ...
CDD:176037	121	EUK	Invertebrates:3,Vertebrates:2	cd08391, C2A_C2C_Synaptotagmin_like, C2 domain first and third repeat in Synaptotagmin-like proteins.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium.  Of the 17 ...
CDD:176042	159	EUK	Invertebrates:10,Plants:22,Primates:1,Vertebrates:2	cd08397, C2_PI3K_class_III, C2 domain present in class III phosphatidylinositol 3-kinases (PI3Ks).  PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility.  PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of ...
CDD:176054	137	EUK	Invertebrates:1	cd08409, C2B_Synaptotagmin-15, C2 domain second repeat present in Synaptotagmin 15.  Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. It is thought to be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues and is Ca2+ independent. Human synaptotagmin 15 has 2 alternatively spliced forms that encode proteins with different C-termini.  ...
CDD:176103	200	EUKprk	Bacteria:73,Plants:1	cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily.  OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family ...
CDD:176104	198	PRK	Bacteria:24	cd08412, PBP2_PAO1_like, The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily.  This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains ...
CDD:176105	198	EUKprk	Bacteria:13,Plants:1	cd08413, PBP2_CysB_like, The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold.  CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with ...
CDD:176106	197	PRK	Bacteria:187,nodiv:1	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold.  This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered ...
CDD:176107	196	PRK	Bacteria:25	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold.  This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as ...
CDD:176109	200	PRK	Bacteria:190,nodiv:1	cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold.  This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. ...
CDD:176110	201	PRK	Bacteria:6	cd08418, PBP2_TdcA, The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold.  TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one ...
CDD:176111	197	PRK	Bacteria:47	cd08419, PBP2_CbbR_RubisCO_like, The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold.  CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB ...
CDD:176112	201	EUKprk	Bacteria:88,Plants:3	cd08420, PBP2_CysL_like, C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold.  CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from ...
CDD:176113	198	PRK	Bacteria:34	cd08421, PBP2_LTTR_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved ...
CDD:176114	197	EUKprk	Bacteria:237,Environmental:1,Plants:1,nodiv:2	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain.  This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide ...
CDD:176115	200	PRK	Bacteria:25	cd08423, PBP2_LTTR_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved ...
CDD:176116	197	PRK	Bacteria:5	cd08425, PBP2_CynR, The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold.  CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function).  CynR negatively regulates its ...
CDD:176117	199	PRK	Bacteria:7	cd08426, PBP2_LTTR_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved ...
CDD:176118	195	PRK	Bacteria:22	cd08427, PBP2_LTTR_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved ...
CDD:176119	195	PRK	Bacteria:5	cd08428, PBP2_IciA_ArgP, The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold.  The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward ...
CDD:176120	204	PRK	Bacteria:11	cd08429, PBP2_NhaR, The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold.  NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, ...
CDD:176121	199	PRK	Bacteria:13	cd08430, PBP2_IlvY, The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold.  In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of ...
CDD:176122	195	PRK	Bacteria:11	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold.  HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA,  is regulated at the transcriptional level by iron and an iron-binding repressor ...
CDD:176123	194	PRK	Bacteria:84	cd08432, PBP2_GcdR_TrpI_HvrB_AmpR_like, The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold.  This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan ...
CDD:176124	198	PRK	Bacteria:23	cd08433, PBP2_Nac, The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold.  The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of ...
CDD:176125	195	PRK	Bacteria:32	cd08434, PBP2_GltC_like, The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold.  GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by ...
CDD:176126	201	PRK	Bacteria:16	cd08435, PBP2_GbpR, The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold.  Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE.   The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction ...
CDD:176127	194	PRK	Bacteria:20	cd08436, PBP2_LTTR_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved ...
CDD:176129	197	miss	miss	cd08438, PBP2_CidR, The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold.  This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, ...
CDD:176130	185	PRK	Bacteria:8	cd08439, PBP2_LrhA_like, The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold.  This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR.  LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of ...
CDD:176131	197	EUKprk	Bacteria:50,Plants:1	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.  LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker ...
CDD:176132	198	PRK	Bacteria:28	cd08441, PBP2_MetR, The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold.  MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine ...
CDD:176133	193	PRK	Bacteria:16	cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold.  YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during ...
CDD:176136	203	miss	miss	cd08445, PBP2_BenM_CatM_CatR, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold.  This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to ...
CDD:176137	198	PRK	Bacteria:1	cd08446, PBP2_Chlorocatechol, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold.  This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as ...
CDD:176138	198	miss	miss	cd08447, PBP2_LTTR_aromatics_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes ...
CDD:176139	197	miss	miss	cd08448, PBP2_LTTR_aromatics_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes ...
CDD:176140	197	miss	miss	cd08449, PBP2_XapR, The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold.  In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the ...
CDD:176142	199	miss	miss	cd08451, PBP2_BudR, The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 ...
CDD:176148	201	miss	miss	cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold.  This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such ...
CDD:176149	200	PRK	Bacteria:3	cd08460, PBP2_DntR_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.  This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in ...
CDD:176150	198	PRK	Bacteria:2	cd08461, PBP2_DntR_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.  This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in ...
CDD:176151	200	PRK	Bacteria:1	cd08462, PBP2_NodD, The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold.  The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are ...
CDD:176152	203	PRK	Bacteria:1	cd08463, PBP2_DntR_like_4, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.  This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in ...
CDD:176153	200	miss	miss	cd08464, PBP2_DntR_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.  This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such ...
CDD:176154	200	miss	miss	cd08465, PBP2_ToxR, The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold.  In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the ...
CDD:176155	200	miss	miss	cd08466, PBP2_LeuO, The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of  leucine synthesis operon, contains the type 2 periplasmic binding fold.  LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB ...
CDD:176158	221	miss	miss	cd08469, PBP2_PnbR, The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold.  PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate  reductase, which is responsible for catalyzing the ...
CDD:176159	197	miss	miss	cd08470, PBP2_CrgA_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176160	201	miss	miss	cd08471, PBP2_CrgA_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176161	202	miss	miss	cd08472, PBP2_CrgA_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176162	202	miss	miss	cd08473, PBP2_CrgA_like_4, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176163	202	miss	miss	cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176164	199	miss	miss	cd08475, PBP2_CrgA_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176165	197	miss	miss	cd08476, PBP2_CrgA_like_7, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176166	197	miss	miss	cd08477, PBP2_CrgA_like_8, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176168	198	miss	miss	cd08479, PBP2_CrgA_like_9, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.  This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino ...
CDD:176170	194	miss	miss	cd08481, PBP2_GcdR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold.  GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids.  The structural topology ...
CDD:176172	190	miss	miss	cd08483, PBP2_HvrB, The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold.  The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine ...
CDD:173854	488	PRK	Bacteria:30	cd08489, PBP2_NikA, The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner ...
CDD:173855	470	PRK	Bacteria:46,nodiv:1	cd08490, PBP2_NikA_DppA_OppA_like_3, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity ...
CDD:173856	473	PRK	Bacteria:5	cd08491, PBP2_NikA_DppA_OppA_like_12, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173857	484	PRK	Bacteria:35	cd08492, PBP2_NikA_DppA_OppA_like_15, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173858	482	PRK	Bacteria:64,Environmental:1	cd08493, PBP2_DppA_like, The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold.  This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a ...
CDD:173859	448	PRK	Bacteria:24	cd08494, PBP2_NikA_DppA_OppA_like_6, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173860	482	EUKprk	Bacteria:16,Plants:1	cd08495, PBP2_NikA_DppA_OppA_like_8, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence ...
CDD:173861	454	PRK	Bacteria:10	cd08496, PBP2_NikA_DppA_OppA_like_9, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173862	491	PRK	Bacteria:87	cd08497, PBP2_NikA_DppA_OppA_like_14, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173863	481	PRK	Bacteria:48,Environmental:1,nodiv:1	cd08498, PBP2_NikA_DppA_OppA_like_2, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant ...
CDD:173864	474	PRK	Bacteria:19	cd08499, PBP2_Ylib_like, The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding ...
CDD:173865	499	PRK	Bacteria:38,Environmental:1,nodiv:1	cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant ...
CDD:173866	486	PRK	Bacteria:39	cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold.  LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs).  Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature ...
CDD:173867	472	PRK	Bacteria:37,nodiv:1	cd08502, PBP2_NikA_DppA_OppA_like_16, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity ...
CDD:173868	460	PRK	Bacteria:60	cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173869	498	PRK	Bacteria:164,Environmental:1,nodiv:1	cd08504, PBP2_OppA, The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous ...
CDD:173870	528	PRK	Bacteria:20,nodiv:1	cd08505, PBP2_NikA_DppA_OppA_like_18, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity ...
CDD:173871	466	PRK	Bacteria:22	cd08506, PBP2_clavulanate_OppA2, The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold.  Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the ...
CDD:173872	448	PRK	Bacteria:23	cd08507, PBP2_SgrR_like, The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold.  A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type ...
CDD:173873	470	PRK	Bacteria:8	cd08508, PBP2_NikA_DppA_OppA_like_1, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173874	509	PRK	Bacteria:52	cd08509, PBP2_TmCBP_oligosaccharides_like, The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold.  This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) ...
CDD:173875	516	PRK	Bacteria:21	cd08510, PBP2_Lactococcal_OppA_like, The substrate binding component of an ABC-type lactococcal OppA-like transport system contains.  This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at ...
CDD:173876	467	PRK	Bacteria:14	cd08511, PBP2_NikA_DppA_OppA_like_5, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to ...
CDD:173877	476	PRK	Bacteria:62,nodiv:1	cd08512, PBP2_NikA_DppA_OppA_like_7, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity ...
CDD:173878	482	PRK	Bacteria:46,nodiv:1	cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold.  This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from ...
CDD:173879	483	PRK	Bacteria:28	cd08514, PBP2_AppA_like, The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold.  This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two ...
CDD:173880	460	PRK	Bacteria:20	cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173881	457	PRK	Bacteria:14	cd08516, PBP2_NikA_DppA_OppA_like_11, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173882	480	PRK	Bacteria:29,nodiv:1	cd08517, PBP2_NikA_DppA_OppA_like_13, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity ...
CDD:173883	464	PRK	Bacteria:36	cd08518, PBP2_NikA_DppA_OppA_like_19, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173884	469	PRK	Bacteria:24	cd08519, PBP2_NikA_DppA_OppA_like_20, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, ...
CDD:173885	468	PRK	Bacteria:11,Environmental:1	cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.  This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence ...
CDD:176056	123	EUK	Invertebrates:4,Vertebrates:3	cd08521, C2A_SLP, C2 domain first repeat present in Synaptotagmin-like proteins.  All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length.  Slp1/JFC1 and Slp2/exophilin 4 promote granule docking to the plasma membrane.  Additionally, their C2A domains are both Ca2+ ...
CDD:197342	161	EUK	Primates:1,Rodents:1,Vertebrates:2	cd08525, Reelin_subrepeat_1, N-terminal subrepeat in the tandem repeat unit of reelin and related proteins.  Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and ...
CDD:197343	152	EUK	Invertebrates:3,Vertebrates:2	cd08526, Reelin_subrepeat_2, C-terminal subrepeat in the tandem repeat unit of reelin and related proteins.  Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the ...
CDD:188878	81	EUK	Invertebrates:9,Vertebrates:3	cd08532, SAM_PNT-PDEF-like, Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor.  SAM Pointed domain of PDEF-like (Prostate-Derived ETS Factor) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. In human males this activator is highly expressed in the prostate gland and enhances androgen-mediated activation of the PSA promoter though interaction with the DNA binding domain of androgen ...
CDD:176084	89	EUK	Invertebrates:8,Vertebrates:3	cd08534, SAM_PNT-GABP-alpha, Sterile alpha motif (SAM)/Pointed domain of GA-binding protein (GABP) alpha chain.  SAM Pointed domain of GA-binding protein (GABP) alpha subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. This type of transcriptional regulators forms heterotetramers containing two alpha and two beta subunits.  It interacts with GA repeats (purine rich repeats). GABP transcriptional factors ...
CDD:176086	66	EUK	Invertebrates:6	cd08536, SAM_PNT-Mae, Sterile alpha motif (SAM)/Pointed domain of Mae protein homolog.  Mae (Modulator of the Activity of ETS) subfamily represents a group of SAM Pointed monodomain proteins. SAM Pointed domain is a protein-protein interaction domain. It can interact with other SAM pointed domains forming head-to-tail heterodimers and also provides a kinase docking site. For example, in Drosophila Mae is required for facilitating phosphorylation of the Yan ...
CDD:260081	135	EUKprk	Bacteria:3,Invertebrates:29,Mammals:1,Plants:1,Primates:1,Rodents:2,Vertebrates:4	cd08544, Reeler, Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins.  This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, ...
CDD:260082	152	EUKprk	Bacteria:64,Plants:1	cd08545, YcnI_like, Reeler-like domain of YcnI and similar proteins.  YcnI is a copper-responsive gene of Bacillus subtilis. It is homologous to an uncharacterized protein from Nocardia farcinica, which shares a conserved three-dimensional structure with cohesins and the reeler domain. Some members in this YcnI_like family have C-terminal domains (DUF461) that may bind copper.
CDD:260084	136	EUKprk	Bacteria:46,Environmental:2,Invertebrates:1	cd08547, Type_II_cohesin, Type II cohesin domain, interaction partner of dockerin.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module ...
CDD:260085	135	PRK	Bacteria:20	cd08548, Type_I_cohesin_like, Type I cohesin domain, interaction partner of dockerin.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent ...
CDD:173961	370	PRK	Bacteria:2	cd08551, Fe-ADH, iron-containing alcohol dehydrogenases (Fe-ADH)-like.  Large metal-containing  alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol ...
CDD:176489	131	EUK	Invertebrates:17,Plants:5,Primates:1,Rodents:1	cd08554, Cyt_b561, Eukaryotic cytochrome b(561).  Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous.
CDD:176498	179	EUKprk	Bacteria:9,Invertebrates:1,nodiv:1	cd08555, PI-PLCc_GDPD_SF, Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily.  The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), ...
CDD:176499	189	EUKprk	Bacteria:107,Environmental:1,Invertebrates:2,Plants:6,Primates:1,nodiv:2	cd08556, GDPD, Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins.  The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which ...
CDD:176500	271	EUKprk	Bacteria:78,Invertebrates:26,Mammals:1,Plants:35,Primates:1,Rodents:1,Vertebrates:5,nodiv:1	cd08557, PI-PLCc_bacteria_like, Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins.  This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, ...
CDD:176501	226	EUK	Invertebrates:17,Mammals:1,Plants:14,Primates:1,Rodents:1,Vertebrates:8	cd08558, PI-PLCc_eukaryota, Catalytic domain of eukaryotic phosphoinositide-specific phospholipase C and similar proteins.  This family corresponds to the catalytic domain present in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) and similar proteins. The higher eukaryotic PI-PLCs play a critical role in most signal transduction pathways, controlling numerous cellular events ...
CDD:176502	296	EUKprk	Bacteria:22,Invertebrates:4,Plants:5	cd08559, GDPD_periplasmic_GlpQ_like, Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the ...
CDD:176504	249	EUKprk	Bacteria:23,Invertebrates:2	cd08561, GDPD_cytoplasmic_ScUgpQ2_like, Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded ...
CDD:176505	229	PRK	Bacteria:20	cd08562, GDPD_EcUgpQ_like, Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes ...
CDD:176506	230	PRK	Bacteria:24	cd08563, GDPD_TtGDE_like, Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the ...
CDD:176508	235	PRK	Bacteria:7	cd08565, GDPD_pAtGDE_like, Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to ...
CDD:176509	240	EUKprk	Bacteria:46,Invertebrates:1,Plants:1,nodiv:1	cd08566, GDPD_AtGDE_like, Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (AtGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homolgoues. Members in this family shows high sequence similarity to Escherichia coli ...
CDD:176510	263	EUKprk	Bacteria:15,Plants:1	cd08567, GDPD_SpGDE_like, Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter ...
CDD:176511	226	PRK	Bacteria:13	cd08568, GDPD_TmGDE_like, Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized  homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of ...
CDD:176512	234	EUK	Plants:22	cd08570, GDPD_YPL206cp_fungi, Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL206cp and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL206cp and uncharacterized hypothetical homologs existing in fungi. The product of S. cerevisiae ORF YPL206c (PGC1), YPL206cp (Pgc1p), displays homology to bacterial and mammalian glycerophosphodiester ...
CDD:176513	302	EUK	Plants:7	cd08571, GDPD_SHV3_plant, Glycerophosphodiester phosphodiesterase domain of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase (GDPD) domain present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play an important role in cell wall organization. The prototype of this family is a ...
CDD:176514	293	EUK	Invertebrates:10,Plants:14	cd08572, GDPD_GDE5_like, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins. GDE5 is widely expressed in mammalian tissues, with highest expression in spinal chord. Although its biological function remains unclear, ...
CDD:176515	258	EUK	Invertebrates:9,Vertebrates:3,nodiv:1	cd08573, GDPD_GDE1, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE1 (also known as MIR16, membrane interacting protein of RGS16) and their metazoan homologs. GDE1 is widely expressed in mammalian tissues, including the heart, brain, liver, and ...
CDD:176516	252	EUK	Invertebrates:3,Mammals:1,Primates:1,Vertebrates:4	cd08574, GDPD_GDE_2_3_6, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian ...
CDD:176517	264	EUKprk	Bacteria:18,Invertebrates:13,Primates:1,Vertebrates:4,nodiv:2	cd08575, GDPD_GDE4_like, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein ...
CDD:176518	265	EUKprk	Bacteria:2,Invertebrates:7,Plants:6	cd08576, GDPD_like_SMaseD_PLD, Glycerophosphodiester phosphodiesterase-like domain of spider venom sphingomyelinases D, bacterial phospholipase D, and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase-like domain (GDPD-like) present in sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.4) from spider venom, the Corynebacterium pseudotuberculosis Phospholipase D (PLD)-like ...
CDD:176519	228	EUKprk	Bacteria:12,Plants:9	cd08577, PI-PLCc_GDPD_SF_unchar3, Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases.  This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) ...
CDD:176520	300	EUK	Plants:13	cd08578, GDPD_NUC-2_fungi, Putative glycerophosphodiester phosphodiesterase domain of ankyrin repeat protein NUC-2 and similar proteins.  This subfamily corresponds to a putative glycerophosphodiester phosphodiesterase domain (GDPD) present in Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81. Some uncharacterized NUC-2 sequence homologs are also included in this family. ...
CDD:176521	220	PRK	Bacteria:34	cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial glycerophosphodiester phosphodiesterases. In addition to a C-terminal GDPD domain, most members in this family have an N-terminus that functions as a membrane anchor.
CDD:176522	263	miss	miss	cd08580, GDPD_Rv2277c_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial protein Rv2277c and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial protein Rv2277c and similar proteins. Members in this subfamily are bacterial homologous of mammalian GDE4, a transmembrane protein whose cellular function has not yet been elucidated.
CDD:176523	229	PRK	Bacteria:10	cd08581, GDPD_like_1, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of ...
CDD:176524	233	PRK	Bacteria:15	cd08582, GDPD_like_2, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of ...
CDD:176525	237	PRK	Bacteria:12	cd08583, PI-PLCc_GDPD_SF_unchar1, Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases.  This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar ...
CDD:176526	192	PRK	Bacteria:10	cd08584, PI-PLCc_GDPD_SF_unchar2, Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases.  This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar ...
CDD:176527	237	PRK	Bacteria:8	cd08585, GDPD_like_3, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity with Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation ...
CDD:176528	279	miss	miss	cd08586, PI-PLCc_BcPLC_like, Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins.  This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce ...
CDD:176529	288	miss	miss	cd08587, PI-PLCXDc_like, Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins.  This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase ...
CDD:176530	270	miss	miss	cd08588, PI-PLCc_At5g67130_like, Catalytic domain of Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs.  This subfamily corresponds to the catalytic domain present in Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs. Members in this family show high sequence similarity to bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), which participates in ...
CDD:176531	324	miss	miss	cd08589, PI-PLCc_SaPLC1_like, Catalytic domain of Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1-like proteins.  This subfamily corresponds to the catalytic domain present in Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1 (SaPLC1) and similar proteins. The typical bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) catalyzes Ca2+-independent hydrolysis of the membrane lipid phosphatidylinositol ...
CDD:176532	267	miss	miss	cd08590, PI-PLCc_Rv2075c_like, Catalytic domain of uncharacterized Mycobacterium tuberculosis Rv2075c-like proteins.  This subfamily corresponds to the catalytic domain present in uncharacterized Mycobacterium tuberculosis Rv2075c and its homologs. Members in this family are more closely related to the Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1(SaPLC1)-like proteins rather than the typical bacterial phosphatidylinositol-specific ...
CDD:176533	257	miss	miss	cd08591, PI-PLCc_beta, Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta.  This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2)  to generate two important second messengers in eukaryotic signal transduction cascades,  Inositol ...
CDD:176535	257	miss	miss	cd08593, PI-PLCc_delta, Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta.  This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-delta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2)  to generate two important second messengers in eukaryotic signal transduction cascades,  Inositol ...
CDD:176540	231	miss	miss	cd08598, PI-PLC1c_yeast, Catalytic domain of putative yeast phosphatidylinositide-specific phospholipases C.  This family corresponds to the catalytic domain present in a group of putative phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) encoded by PLC1 genes from yeasts, which are homologs of the delta isoforms of mammalian PI-PLC in terms of overall sequence similarity and domain organization. Mammalian PI-PLC is a signaling enzyme that hydrolyzes the ...
CDD:176543	256	miss	miss	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase ...
CDD:176544	309	miss	miss	cd08602, GDPD_ScGlpQ1_like, Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present  in a group of putative bacterial and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ, as well as plant glycerophosphodiester phosphodiesterases (GP-PDEs), ...
CDD:176546	300	miss	miss	cd08604, GDPD_SHV3_repeat_2, Glycerophosphodiester phosphodiesterase domain repeat 2 of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) repeat 2 present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play important an role in cell wall organization. The prototype of this family is a ...
CDD:176549	290	miss	miss	cd08607, GDPD_GDE5, Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative mammalian GDE5 and similar proteins. Mammalian GDE5 is widely expressed in mammalian tissues, with highest expression in the spinal chord. Although its biological function remains unclear, mammalian GDE5 shows ...
CDD:176553	300	miss	miss	cd08612, GDPD_GDE4, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins.  This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function has not yet been elucidated. It ...
CDD:176555	290	miss	miss	cd08616, PI-PLCXD1c, Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1.  This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific ...
CDD:176557	281	miss	miss	cd08620, PI-PLCXDc_like_1, Catalytic domain of uncharacterized hypothetical proteins similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins.  This subfamily corresponds to the catalytic domain present in a group of uncharacterized hypothetical proteins found in bacteria and fungi, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic ...
CDD:176558	300	miss	miss	cd08621, PI-PLCXDc_like_2, Catalytic domain of uncharacterized hypothetical proteins similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins.  This subfamily corresponds to the catalytic domain present in a group of uncharacterized hypothetical proteins found in bacteria and fungi, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic ...
CDD:176559	276	miss	miss	cd08622, PI-PLCXDc_CG14945_like, Catalytic domain of Drosophila melanogaster CG14945-like proteins similar to phosphatidylinositol-specific phospholipase C, X domain containing.  This subfamily corresponds to the catalytic domain present in uncharacterized metazoan Drosophila melanogaster CG14945-like proteins, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic ...
CDD:176474	377	PRK	Bacteria:73,Environmental:2	cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication.  Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli ...
CDD:176475	373	EUK	Invertebrates:18,Plants:8,Primates:1,Vertebrates:2,nodiv:1	cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation.  DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), ...
CDD:176476	324	EUKprk	Bacteria:7,Invertebrates:4	cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol A is different from Escherichia coli  Pol A by three signature sequences.  Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class ...
CDD:176477	371	EUK	Invertebrates:2,Plants:3	cd08640, DNA_pol_A_plastid_like, DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication.  DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. ...
CDD:176478	425	EUK	Invertebrates:6,Plants:6,Vertebrates:2,nodiv:1	cd08641, DNA_pol_gammaA, Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria.  DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. ...
CDD:176479	378	PRK	Bacteria:26	cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication.  Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III ...
CDD:187714	183	EUKprk	Bacteria:126,Environmental:5,Invertebrates:7,Plants:9,Primates:1,Vertebrates:1,nodiv:1	cd08645, FMT_core_GART, Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART).  Phosphoribosylglycinamide formyltransferase, also known as GAR transformylase or GART, is an essential enzyme that catalyzes the third step in de novo purine biosynthesis. This enzyme uses formyl tetrahydrofolate as a formyl group donor to produce 5'-phosphoribosyl-N-formylglycinamide. In ...
CDD:187715	204	EUKprk	Bacteria:142,Environmental:3,Invertebrates:9,Plants:24,Vertebrates:1	cd08646, FMT_core_Met-tRNA-FMT_N, Methionyl-tRNA formyltransferase, N-terminal hydrolase domain.  Methionyl-tRNA formyltransferase (Met-tRNA-FMT), N-terminal formyltransferase domain.  Met-tRNA-FMT transfers a formyl group from N-10 formyltetrahydrofolate to the amino terminal end of a methionyl-aminoacyl-tRNA acyl moiety, yielding formyl-Met-tRNA. Formyl-Met-tRNA plays essential role in protein ...
CDD:187717	196	EUKprk	Bacteria:18,Plants:6	cd08648, FMT_core_Formyl-FH4-Hydrolase_C, Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain.  Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formate is the substrate of phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase has been proposed to regulate the balance of FH4 and C1-FH4 in the cell.  ...
CDD:187718	166	PRK	Bacteria:14	cd08649, FMT_core_NRPS_like, N-terminal formyl transferase catalytic core domain of NRPS_like proteins, one of the proteins involved in the synthesis of Oxazolomycin.  This family represents the N-terminal formyl transferase catalytic core domain present in a subgroup of non-ribosomal peptide synthetases. In Streptomyces albus a member of this family has been shown to be involved in the synthesis of oxazolomycin (OZM). OZM is a hybrid peptide-polyketide antibiotic ...
CDD:187719	151	EUKprk	Bacteria:12,Invertebrates:1,Plants:1,nodiv:1	cd08650, FMT_core_HypX_N, HypX protein, N-terminal hydrolase domain.  The family represents the N-terminal hydrolase domain of HypX protein.  HypX is involved in the maturation process of active [NiFe] hydrogenase. [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions. [NiFe] hydrogenases consist of a large ...
CDD:187720	180	PRK	Bacteria:16	cd08651, FMT_core_like_4, Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group.  This domain contains a Rossmann fold and it is the catalytic domain of the enzyme.
CDD:187721	152	EUKprk	Bacteria:27,Plants:1,nodiv:1	cd08653, FMT_core_like_3, Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group.  This domain contains a Rossmann fold and it is the catalytic domain of the enzyme.
CDD:193569	281	PRK	Bacteria:20	cd08656, M28_like_6, M28 Zn-Peptidases.  Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions.
CDD:193570	365	EUKprk	Bacteria:57,Invertebrates:1,Plants:3	cd08659, M20_ArgE_DapE_like, Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like.  Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) like family of enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine ...
CDD:189000	611	EUKprk	Bacteria:140,Invertebrates:31,Mammals:1,Plants:5,Primates:1,Vertebrates:6,nodiv:2	cd08662, M13, Peptidase family M13 includes neprilysin, endothelin-converting enzyme I.  M13 family of metallopeptidases includes neprilysin (neutral endopeptidase, NEP, enkephalinase, CD10, CALLA, EC 3.4.24.11), endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), erythrocyte surface antigen KELL (ECE-3), phosphate-regulating gene on the X chromosome (PHEX), soluble secreted endopeptidase ...
CDD:176450	266	PRK	Bacteria:38	cd08663, DAP_dppA_1, Peptidase M55, D-aminopeptidase dipeptide-binding protein family.  M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early ...
CDD:176571	185	EUK	Invertebrates:16,Plants:9,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd08674, Cdt1_m, The middle winged helix fold of replication licensing factor Cdt1 binds geminin to inhibit binding of the MCM complex to origins of replication and DNA.  Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the origin recognition complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and ...
CDD:176057	137	EUK	Primates:1	cd08675, C2B_RasGAP, C2 domain second repeat of Ras GTPase activating proteins (GAPs).  RasGAPs suppress Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras.  In this way it can control cellular proliferation and differentiation.  The proteins here all contain two tandem C2 domains,  a Ras-GAP domain, and a pleckstrin homology (PH)-like domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 ...
CDD:176058	153	EUK	Invertebrates:2,Rodents:1	cd08676, C2A_Munc13-like, C2 domain first repeat in Munc13 (mammalian uncoordinated)-like proteins.  C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner.  Mutations in Unc13 results ...
CDD:176060	126	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd08678, C2_C21orf25-like, C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein.  The members in this cd are named after the Human C21orf25 which contains a single C2 domain.  Several other members contain a C1 domain downstream of the C2 domain.  No other information on this protein is currently known. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can ...
CDD:176061	178	EUK	Invertebrates:12,Plants:15,Primates:1,Vertebrates:2	cd08679, C2_DOCK180_related, C2 domains found in Dedicator Of CytoKinesis 1 (DOCK 180) and related proteins.  Dock180 was first identified as an 180kd proto-oncogene product c-Crk-interacting protein involved in actin cytoskeletal changes.  It is now known that it has Rac-specific GEF activity, but lacks the conventional Dbl homology (DH) domain. There are 10 additional related proteins that can be divided into four classes ...
CDD:176062	124	EUK	Invertebrates:9,Primates:1,Vertebrates:5,nodiv:1	cd08680, C2_Kibra, C2 domain found in Human protein Kibra.  Kibra is thought to be a regulator of the Salvador (Sav)/Warts (Wts)/Hippo (Hpo) (SWH) signaling network, which limits tissue growth by inhibiting cell proliferation and promoting apoptosis. The core of the pathway consists of a MST and LATS family kinase cascade that ultimately phosphorylates and inactivates the YAP/Yorkie (Yki) transcription coactivator. The FERM ...
CDD:176063	118	EUK	Plants:16	cd08681, C2_fungal_Inn1p-like, C2 domain found in fungal Ingression 1 (Inn1) proteins.  Saccharomyces cerevisiae Inn1 associates with the contractile actomyosin ring at the end of mitosis and is needed for cytokinesis. The C2 domain of Inn1, located at the N-terminus, is required for ingression of the plasma membrane. The C-terminus is relatively unstructured and contains eight PXXP motifs that are thought to mediate interaction of Inn1 with other proteins with SH3 ...
CDD:176070	110	EUK	Invertebrates:13,Plants:1,Vertebrates:3	cd08688, C2_KIAA0528-like, C2 domain found in the Human KIAA0528 cDNA clone.  The members of this CD are named after the Human KIAA0528 cDNA clone.  All members here contain a single C2 repeat.  No other information on this protein is currently known. The C2 domain was first identified in PKC.  C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular ...
CDD:176071	109	EUK	Plants:9	cd08689, C2_fungal_Pkc1p, C2 domain found in protein kinase C (Pkc1p) in Saccharomyces cerevisiae.  This family is named after the protein kinase C in Saccharomyces cerevisiae, Pkc1p. Protein kinase C is a member of a family of Ser/Thr phosphotransferases that are involved in many cellular signaling pathways. PKC has two antiparallel coiled-coiled regions (ACC finger domain) (AKA PKC homology region 1 (HR1)/ Rho binding domain) upstream of the C2 domain and two C1 ...
CDD:176072	155	EUK	Invertebrates:7,Rodents:1,Vertebrates:4,nodiv:1	cd08690, C2_Freud-1, C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1).  Freud-1 is a novel calcium-regulated repressor that negatively regulates basal 5-HT1A receptor expression in neurons.  It may also play a role in the altered regulation of 5-HT1A receptors associated with anxiety or major depression. Freud-1 contains two DM-14 basic repeats, a helix-loop-helix DNA binding domain, and a ...
CDD:176075	173	EUK	Invertebrates:10,Primates:1,Rodents:1,Vertebrates:3	cd08693, C2_PI3K_class_I_beta_delta, C2 domain present in class I beta and delta phosphatidylinositol 3-kinases (PI3Ks).  PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility.  PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl ...
CDD:176078	179	EUK	Invertebrates:10,Primates:1,Vertebrates:3	cd08696, C2_Dock-C, C2 domains found in Dedicator Of CytoKinesis (Dock) class C proteins.  Dock-C is one of 4 classes of Dock family proteins.  The members here include: Dock6/Zir1, Dock7/Zir2, and Dock8/Zir3.  Dock-C members are GEFs for both Rac and Cdc42. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related ...
CDD:176079	185	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd08697, C2_Dock-D, C2 domains found in Dedicator Of CytoKinesis (Dock) class C proteins.  Dock-D is one of 4 classes of Dock family proteins.  The members here include: Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2/ACG (activated Cdc42-associated GEF).  Dock-D are Cdc42-specific GEFs. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA ...
CDD:187728	100	PRK	Bacteria:16	cd08700, FMT_C_OzmH_like, C-terminal subdomain of the Formyltransferase-like domain found in OzmH-like proteins.  Domain found in OzmH-like proteins with similarity to the C-terminal domain of Formyltransferase. OzmH is one of the proteins involved in the synthesis of Oxazolomycin (OZM), which is a hybrid peptide-polyketide antibiotic that exhibits potent antitumor and antiviral activities. OzmH is a multi-domain protein consisting of a formyl transferase domain, a ...
CDD:187729	96	EUKprk	Bacteria:10,Invertebrates:1,Plants:1	cd08701, FMT_C_HypX, C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins.  Domain found in HypX-like proteins with similarity to the C-terminal domain of Formyltransferase. HypX is involved in the maturation process of active [NiFe] hydrogenase. [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalents under aerobic and ...
CDD:187730	92	EUKprk	Bacteria:14,Plants:2	cd08702, Arna_FMT_C, C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose.  Domain found in ArnA with similarity to the C-terminal domain of Formyltransferase. ArnA is a bifunctional enzyme required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. The ...
CDD:187731	100	EUK	Invertebrates:11,Primates:1,Vertebrates:3	cd08703, FDH_Hydrolase_C, The C-terminal subdomain of the hydrolase domain on the bi-functional protein 10-formyltetrahydrofolate dehydrogenase.  The family represents the C-terminal subdomain of the hydrolase domain on the bi-functional protein, 10-formyltetrahydrofolate dehydrogenase (FDH). FDH catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. The protein comprises ...
CDD:187732	87	EUKprk	Bacteria:288,Environmental:3,Invertebrates:6,Plants:1,nodiv:3	cd08704, Met_tRNA_FMT_C, C-terminal domain of Formyltransferase and other enzymes.  C-terminal domain of formyl transferase and other proteins with diverse enzymatic activities. Proteins found in this family include methionyl-tRNA formyltransferase, ArnA, and 10-formyltetrahydrofolate dehydrogenase. Methionyl-tRNA formyltransferases constitute the majority of the family and also demonstrate greater sequence ...
CDD:188660	121	EUK	Invertebrates:8,Mammals:1,Primates:3,Rodents:1,Vertebrates:5	cd08705, RGS_R7-like, Regulator of G protein signaling (RGS) domain found in the R7 subfamily of proteins.  The RGS (Regulator of G-protein Signaling) domain is an essential part of the R7 (Neuronal RGS) protein subfamily of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS ...
CDD:188661	113	EUK	Invertebrates:4,Primates:1,Vertebrates:5	cd08706, RGS_R12-like, Regulator of G protein signaling (RGS) domain found in the R12 subfamily of proteins.  The RGS (Regulator of G-protein Signaling) domain is an essential part of the R12 (Neuronal RGS) protein subfamily of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play a critical regulatory role as ...
CDD:188663	148	EUK	Plants:9	cd08708, RGS_FLBA, Regulator of G protein signaling (RGS) domain found in the FLBA (Fluffy Low BrlA) protein.  The RGS (Regulator of G-protein Signaling) domain is an essential part of the FLBA (Fluffy Low BrlA) protein. FLBA is a member of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are ...
CDD:188676	121	EUK	Invertebrates:8	cd08721, RGS_AKAP2_2, Regulator of G protein signaling (RGS) domain 2 found in the A-kinase anchoring protein, D-AKAP2.  The RGS (Regulator of G-protein Signaling) domain is an essential part of the D-AKAP2 (A-kinase anchoring protein), a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic ...
CDD:188677	127	EUK	Invertebrates:4,Primates:1	cd08722, RGS_SNX14, Regulator of G protein signaling (RGS) domain found in the Sorting Nexin14 (SNX14) protein.  The RGS (Regulator of G-protein Signaling) domain is an essential part of the SNX14 (Sorting Nexin14) protein, a member of  the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic ...
CDD:188679	114	EUK	Invertebrates:9,Mammals:1,Primates:1,Vertebrates:4	cd08724, RGS_GRK-like, Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase (GRK).  The RGS domain is found in G protein-coupled receptor kinases (GRKs).  These proteins play a key role in phosphorylation-dependent desensitization/resensitization of GPCRs (G protein-coupled receptors), intracellular trafficking, endocytosis, as well as in the modulation of important intracellular signaling ...
CDD:188687	139	EUK	Invertebrates:1,Plants:4	cd08732, RGS-like_4, Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 4.  These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory ...
CDD:188688	109	EUKprk	Bacteria:2,Invertebrates:2,Plants:6	cd08734, RGS-like_1, Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 1.  These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play ...
CDD:188690	120	EUK	Invertebrates:6,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd08736, RGS_RhoGEF-like, Regulator of G protein signaling (RGS) domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein.  The RGS domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein subfamily of the RGS domain containing protein family, which is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors ...
CDD:188885	69	EUK	Invertebrates:5,Mammals:1,Vertebrates:1	cd08757, SAM_PNT_ESE, Sterile alpha motif (SAM)/Pointed domain of ESE-like ETS transcriptional regulators.  SAM Pointed domain of ESE-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ETS factors are important for cell differentiation. They can be involved in regulation of ...
CDD:260086	167	PRK	Bacteria:9	cd08759, Type_III_cohesin_like, Cohesin domain, interaction partner of dockerin.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents type III cohesins and closely related domains.
CDD:176490	191	EUKprk	Bacteria:1,Invertebrates:16,Plants:39,Vertebrates:1	cd08760, Cyt_b561_FRRS1_like, Eukaryotic cytochrome b(561), including the FRRS1 gene product.  Cytochrome b(561), as found in eukaryotes, similar to and including the human FRRS1 gene product (ferric-chelate reductase 1), also called SDR-2 (stromal cell-derived receptor 2). This family comprises a variety of domain architectures, many of which contain dopamine beta-monooxygenase (DOMON) domains. The protein might act as a ...
CDD:176491	183	EUK	Invertebrates:13,Plants:22,Primates:1,Vertebrates:2,nodiv:1	cd08761, Cyt_b561_CYB561D2_like, Eukaryotic cytochrome b(561), including the CYB561D2 gene product.  Cytochrome b(561), as found in eukaryotes, similar to and including the human CYB561D2 gene product. CYB561D2 is a candidate tumor suppressor. The protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the ...
CDD:176496	144	EUK	Plants:7	cd08766, Cyt_b561_ACYB-1_like, Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1.  Cytochrome b(561), as found in plants, similar to the Arabidopsis thaliana ACYB-1 gene product, a cytochrome b561 isoform localized to the tonoplast. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), and might be capable of trans-membrane electron transport from intracellular ascorbate to extracellular ferric ...
CDD:176572	126	EUK	Invertebrates:1,Plants:1,Rodents:1,Vertebrates:2	cd08767, Cdt1_c, The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase.  Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region ...
CDD:176573	87	EUKprk	Bacteria:22,Invertebrates:6,Mammals:1,Plants:2,Vertebrates:2	cd08768, Cdc6_C, Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding.  This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome ...
CDD:176451	270	PRK	Bacteria:20	cd08769, DAP_dppA_2, Peptidase M55, D-aminopeptidase dipeptide-binding protein family.  M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early ...
CDD:176452	263	PRK	Bacteria:11	cd08770, DAP_dppA_3, Peptidase M55, D-aminopeptidase dipeptide-binding protein family.  M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early ...
CDD:206738	278	EUK	Invertebrates:17,Plants:24,Primates:1,Vertebrates:4	cd08771, DLP_1, Dynamin_like protein family includes dynamins and Mx proteins.  The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) ...
CDD:185718	286	EUKprk	Bacteria:10,Plants:4	cd08772, GH43_62_32_68, Glycosyl hydrolase families: GH43, GH62, GH32, GH68.  Members of the glycosyl hydrolase families 32, 43, 62 and 68 (GH32, GH43, GH62, GH68) all possess 5-bladed beta-propeller domains and comprise clans F and J, as classified by the carbohydrate-active enzymes database (CAZY).  Clan F consists of families GH43 and GH62. GH43 includes beta-xylosidases, beta-xylanases, alpha-L-arabinases, and alpha-L-arabinofuranosidases, using ...
CDD:176798	117	EUKprk	Bacteria:18,Plants:1,Primates:1,Rodents:1,Viruses:1	cd08773, FpgNei_N, N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases.  DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes ...
CDD:206755	225	EUK	Invertebrates:35,Plants:18,Primates:1,Vertebrates:2,nodiv:1	cd08774, 14-3-3, 14-3-3 domain.  14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, ...
CDD:260049	86	EUK	Invertebrates:4,Primates:1,Vertebrates:2	cd08779, Death_PIDD, Death Domain of p53-induced protein with a death domain.  Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, ...
CDD:260051	83	EUK	Invertebrates:12,Primates:1,Rodents:1,Vertebrates:3	cd08781, Death_UNC5-like, Death domain found in Uncoordinated-5 homolog family.  Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an ...
CDD:260052	82	EUK	Invertebrates:6,Vertebrates:3	cd08782, Death_DAPK1, Death domain found in death-associated protein kinase 1.  Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal-binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and ...
CDD:260059	77	EUK	Invertebrates:2,Vertebrates:1	cd08792, DED_Caspase_8_10_r1, Death effector domain, repeat 1, of initator caspases 8 and 10.  Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 1. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they ...
CDD:260077	92	EUK	Mammals:2,Primates:1,Vertebrates:8	cd08818, CARD_MDA5_r1, Caspase activation and recruitment domain found in MDA5, first repeat.  Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral ...
CDD:260078	92	EUK	Primates:1,Vertebrates:1	cd08819, CARD_MDA5_r2, Caspase activation and recruitment domain found in MDA5, second repeat.  Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon ...
CDD:187723	211	PRK	Bacteria:9	cd08821, FMT_core_like_1, Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalytic core domain found in a group of proteins with unknown functions.  Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group.  This domain contains a Rossmann fold and it is the catalytic domain of the enzyme.
CDD:193585	70	EUK	Invertebrates:8,Plants:5,Primates:1,Rodents:2,Vertebrates:1	cd08824, LOTUS, LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7.  LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary ...
CDD:259807	151	EUKprk	Bacteria:2,Invertebrates:15,Plants:1,Primates:1,Vertebrates:3,nodiv:1	cd08825, MVP_shoulder, Shoulder domain of the major vault protein.  The major vault protein is the major polypeptide component of a large cellular ribonuclear protein complex found in the cytoplasm of eukaryotic cells. Its shoulder domain appears to be a homolog of the SPFH core domain. Vault proteins may be involved in detoxification processes, and have been associated with the multi-drug resistance ...
CDD:259808	178	PRK	Bacteria:41,Environmental:1	cd08826, SPFH_eoslipins_u1, Uncharacterized prokaryotic subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria and archaebacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of ...
CDD:259811	111	EUKprk	Bacteria:103,Environmental:5,Invertebrates:19,Plants:22,Primates:1,Vertebrates:3	cd08829, SPFH_paraslipin, Paraslipin or slipin-2 (SLP-2, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in all three kingdoms of life. The conserved domain common to these families has also been ...
CDD:176870	142	PRK	Bacteria:29	cd08861, OtcD1_ARO-CYC_like, N-terminal and C-terminal aromatase/cyclase domains of Streptomyces rimosus  OtcD1 and related domains.  This family includes the N- and C- terminal aromatase/cyclase (ARO/CYC) domains of Streptomyces rimosus OtcD1 and related domains. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. ARO/CYC ...
CDD:176871	138	PRK	Bacteria:15	cd08862, SRPBCC_Smu440-like, Ligand-binding SRPBCC domain of Streptococcus mutans Smu.440 and related proteins.  This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Streptococcus mutans Smu.440 and related proteins. This domain belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Streptococcus mutans is a dental pathogen, and the leading ...
CDD:176872	141	EUKprk	Bacteria:9,Plants:8	cd08863, SRPBCC_DUF1857, DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily.  Uncharacterized family of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal ...
CDD:176873	208	EUK	Plants:10	cd08864, SRPBCC_DUF3074, DUF3074, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily.  Uncharacterized family of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic ...
CDD:176874	140	PRK	Bacteria:25	cd08865, SRPBCC_10, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the ...
CDD:176875	144	EUKprk	Bacteria:16,Plants:3	cd08866, SRPBCC_11, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.  Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic ...
CDD:176877	208	EUK	Invertebrates:6,Primates:1	cd08868, START_STARD1_3_like, Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD1 (also known as StAR) and STARD3 (also known as metastatic lymph node 64/MLN64). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ...
CDD:176878	197	EUK	Invertebrates:7,Mammals:1,Primates:1,Vertebrates:2,nodiv:1	cd08869, START_RhoGAP, C-terminal lipid-binding START domain of mammalian STARD8, -12, -13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD8 (also known as deleted in liver cancer 3/DLC3, and Arhgap38), STARD12 (also known as DLC-1, Arhgap7, and ...
CDD:176879	209	EUK	Invertebrates:2,Plants:4,Primates:1	cd08870, START_STARD2_7-like, Lipid-binding START domain of mammalian STARD2, -7, and related proteins.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD2 (also known as phosphatidylcholine transfer protein/PC-TP), and STARD7 (also known as gestational trophoblastic tumor 1/GTT1). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) ...
CDD:176880	222	EUK	Invertebrates:14,Vertebrates:3,nodiv:1	cd08871, START_STARD10-like, Lipid-binding START domain of mammalian STARD10 and related proteins.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD10 (also known as CGI-52, PTCP-like, and SDCCAG28). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC ...
CDD:176881	235	EUK	Invertebrates:10,Primates:1,Vertebrates:2,nodiv:1	cd08872, START_STARD11-like, Ceramide-binding START domain of mammalian STARD11 and related domains.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD11 and related domains. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a ...
CDD:176884	229	EUK	Plants:15	cd08875, START_ArGLABRA2_like, C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins.  This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of the Arabidopsis homeobox protein GLABRA 2 and related proteins. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. ...
CDD:176885	195	PRK	Bacteria:26	cd08876, START_1, Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family.  Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the START family ...
CDD:176886	215	EUK	Invertebrates:5,Plants:3	cd08877, START_2, Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family.  Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the ...
CDD:176887	196	PRK	Bacteria:25	cd08878, RHO_alpha_C_DMO-like, C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of Stenotrophomonas maltophilia dicamba O-demethylase (DMO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to ...
CDD:176888	237	PRK	Bacteria:23	cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of anthranilate 1,2-dioxygenase (AntDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize ...
CDD:176889	222	PRK	Bacteria:17	cd08880, RHO_alpha_C_ahdA1c-like, C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins.  C-terminal catalytic domain of the large subunit (ahdA1c) of the AhdA3A4A2cA1c salicylate 1-hydroxylase complex from Sphingomonas sp. strain P2, and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating ...
CDD:176890	206	PRK	Bacteria:34	cd08881, RHO_alpha_C_NDO-like, C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). This domain binds non-heme Fe(II).  RHOs utilize ...
CDD:176891	243	PRK	Bacteria:15	cd08882, RHO_alpha_C_MupW-like, C-terminal catalytic domain of Pseudomonas fluorescens MupW and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas fluorescens MupW and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ...
CDD:176892	175	EUKprk	Bacteria:7,Plants:3	cd08883, RHO_alpha_C_CMO-like, C-terminal catalytic domain of plant choline monooxygenase (CMO) and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of plant choline monooxygenase and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial ...
CDD:176893	205	PRK	Bacteria:22	cd08884, RHO_alpha_C_GbcA-like, C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases.  C-terminal catalytic domain of GbcA  (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze ...
CDD:176894	190	PRK	Bacteria:11,Environmental:1	cd08885, RHO_alpha_C_1, C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme ...
CDD:176896	185	PRK	Bacteria:19	cd08887, RHO_alpha_C_3, C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases.  C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze ...
CDD:176900	149	PRK	Bacteria:19	cd08891, SRPBCC_CalC, Ligand-binding SRPBCC domain of Micromonospora echinospora CalC and related proteins.  This subfamily includes Micromonospora echinospora CalC (MeCalC) and related proteins. These proteins belong to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. MeCalC confers resistance to the enediyne, calicheamicin gamma 1 ...
CDD:176901	126	EUKprk	Bacteria:4,Invertebrates:24,Plants:16,Rodents:1,Vertebrates:3,nodiv:1	cd08892, SRPBCC_Aha1, Putative hydrophobic ligand-binding SRPBCC domain of the Hsp90 co-chaperone Aha1 and related proteins.  This subfamily includes the C-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Aha1, and related domains. Proteins in this group belong to the SRPBCC domain superfamily of proteins which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ...
CDD:176902	136	PRK	Bacteria:30	cd08893, SRPBCC_CalC_Aha1-like_GntR-HTH, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; some contain an N-terminal GntR family winged HTH DNA-binding domain.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers ...
CDD:176903	139	PRK	Bacteria:20,nodiv:1	cd08894, SRPBCC_CalC_Aha1-like_1, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones ...
CDD:176904	146	PRK	Bacteria:21	cd08895, SRPBCC_CalC_Aha1-like_2, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176905	146	PRK	Bacteria:29	cd08896, SRPBCC_CalC_Aha1-like_3, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176906	133	PRK	Bacteria:20	cd08897, SRPBCC_CalC_Aha1-like_4, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176907	145	PRK	Bacteria:24	cd08898, SRPBCC_CalC_Aha1-like_5, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176908	157	PRK	Bacteria:52,nodiv:1	cd08899, SRPBCC_CalC_Aha1-like_6, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones ...
CDD:176909	143	PRK	Bacteria:18	cd08900, SRPBCC_CalC_Aha1-like_7, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176910	136	PRK	Bacteria:17	cd08901, SRPBCC_CalC_Aha1-like_8, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins.  SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which ...
CDD:176920	207	EUK	Invertebrates:10,Vertebrates:2	cd08911, START_STARD7-like, Lipid-binding START domain of mammalian STARD7 and related proteins.  This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD7 (also known as gestational trophoblastic tumor 1/GTT1). It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. ...
CDD:185746	342	EUK	Plants:16,Primates:1	cd08915, V_Alix_like, Protein-interacting V-domain of mammalian Alix and related domains.  This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting ...
CDD:271269	116	EUKprk	Bacteria:170,Environmental:1,Plants:1,nodiv:1	cd08916, TrHb3_P, Truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 3 (P).  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex ...
CDD:271270	118	EUKprk	Bacteria:12,Invertebrates:1,Plants:8	cd08917, TrHb2_O, Truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 2 (O).  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of ...
CDD:271271	155	EUKprk	Bacteria:15,Plants:3	cd08919, PBP_like, Phycobiliproteins (PBPs) and related proteins.  Phycobiliosomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. ...
CDD:271273	140	EUKprk	Bacteria:21,Plants:25	cd08922, FHb-globin, Globin domain of flavohemoglobins (flavoHbs).  FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of ...
CDD:271276	140	EUK	Primates:1,Rodents:1,Vertebrates:17	cd08925, Hb-beta_like, Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits.  Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated ...
CDD:271278	140	EUK	Primates:2,Rodents:1,Vertebrates:22	cd08927, Hb-alpha_like, Hemoglobin alpha, zeta, mu, theta, and related Hb subunits.  Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated ...
CDD:187635	250	PRK	Bacteria:7	cd08930, SDR_c8, classical (c) SDR, subgroup 8.  This subgroup has a fairly well conserved active site tetrad and domain size of the classical SDRs, but has an atypical NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. ...
CDD:212493	223	PRK	Bacteria:7	cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c) SDR.  This subgroup includes Anabaena sp. strain PCC 7120 HetN, a putative oxidoreductase involved in heterocyst differentiation, and related proteins.  SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal ...
CDD:187643	239	EUKprk	Bacteria:5,Invertebrates:5,Plants:11,Primates:1,Vertebrates:2	cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR) and related proteins, classical (c) SDR.  These proteins include members identified as KDSR, ribitol type dehydrogenase, and others. The group shows strong conservation of the active site tetrad and glycine rich NAD-binding motif of the classical SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a ...
CDD:187645	290	EUK	Invertebrates:1,Plants:5,Primates:1,Vertebrates:1	cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.  3-keto steroid reductase (in concert with other enzymes) catalyzes NADP-dependent sterol C-4 demethylation, as part of steroid biosynthesis. 3-keto reductase is a classical SDR, with a well conserved canonical active site tetrad and fairly well conserved characteristic NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a ...
CDD:212494	200	EUKprk	Bacteria:36,Invertebrates:1,Plants:1,Vertebrates:1	cd08946, SDR_e, extended (e) SDRs.  Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically ...
CDD:187652	308	EUKprk	Bacteria:29,Plants:31	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs.  5beta-POR catalyzes the reduction of progesterone to 5beta-pregnane-3,20-dione in Digitalis plants. This subgroup of atypical-extended SDRs, shares the structure of an extended SDR, but has a different glycine-rich nucleotide binding motif  (GXXGXXG) and lacks the YXXXK active site motif of classical and extended SDRs. Tyr-179 and Lys 147 are ...
CDD:187653	259	EUKprk	Bacteria:10,Plants:18	cd08950, KR_fFAS_SDR_c_like, ketoacyl reductase (KR) domain of fungal-type fatty acid synthase (fFAS), classical (c)-like SDRs.  KR domain of fungal-type fatty acid synthase (FAS), type I. Fungal-type FAS is a heterododecameric FAS composed of alpha and beta multifunctional polypeptide chains. The KR, an SDR family member, is located centrally in the alpha chain. KR catalyzes the NADP-dependent reduction of ketoacyl-ACP to hydroxyacyl-ACP. KR shares ...
CDD:187655	480	PRK	Bacteria:67	cd08952, KR_1_SDR_x, ketoreductase (KR), subgroup 1, complex (x) SDRs.  Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding  to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann ...
CDD:187656	436	PRK	Bacteria:18	cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x) SDRs.  Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding  to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann ...
CDD:187657	452	EUK	Invertebrates:3,Mammals:1,Rodents:2	cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.  NADP-dependent KR domain of the multidomain type I FAS, a complex SDR family. This subfamily also includes proteins identified as polyketide synthase (PKS), a protein with related modular protein architecture and similar function. It includes the KR domains of mammalian and chicken FAS, and Dictyostelium discoideum ...
CDD:187658	376	PRK	Bacteria:9	cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x).  Ketoreductase, a module of the multidomain polyketide synthase, has 2 subdomains, each corresponding  to a short-chain dehydrogenases/reductase (SDR) family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. ...
CDD:187659	448	EUKprk	Bacteria:33,Plants:2	cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 3, complex (x).  Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding  to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal ...
CDD:187661	293	EUK	Invertebrates:1,Plants:11	cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.  This subgroup contains FRs of the extended SDR-type and related proteins. These FRs act in the NADP-dependent reduction of  flavonoids, ketone-containing plant secondary metabolites; they have the characteristic active site triad of the SDRs (though not the upstream active site Asn) and a NADP-binding motif that is very similar to the typical extended SDR motif. Extended SDRs are ...
CDD:199206	402	PRK	Bacteria:18,Environmental:1	cd08962, GatD, GatD subunit of archaeal Glu-tRNA amidotransferase.  GatD is involved in the alternative synthesis of Gln-tRNA(Gln) in archaea via the transamidation of incorrectly charged Glu-tRNA(Gln). GatD is active as a dimer, and it provides the amino group required for this reaction. GatD is related to bacterial L-asparaginases (amidohydrolases), which catalyze the hydrolysis of asparagine to aspartic acid and ammonia. This CD spans both the ...
CDD:199207	316	EUKprk	Bacteria:62,Environmental:1,Invertebrates:2,Plants:4	cd08963, L-asparaginase_I, Type I (cytosolic) bacterial L-asparaginase.  Asparaginases (amidohydrolases, E.C. 3.5.1.1) are enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases. This model represents type I L-asparaginases, which are highly specific for asparagine and localized in the cytosol. Type I L-asparaginase acts as a dimer. A ...
CDD:199208	319	EUKprk	Bacteria:162,Plants:7	cd08964, L-asparaginase_II, Type II (periplasmic) bacterial L-asparaginase.  Asparaginases (amidohydrolases, E.C. 3.5.1.1) are enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases. This model represents type II L-asparaginases, which tend to be highly specific for asparagine and localized to the periplasm. They are potent antileukemic agents and have been used in the ...
CDD:176800	120	PRK	Bacteria:151,Environmental:4	cd08966, EcFpg-like_N, N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases.  This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ...
CDD:176803	140	EUK	Invertebrates:1,Mammals:2,Plants:1,Vertebrates:5	cd08969, MeNeil3_N, N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3).  This family contains the N-terminal domain of the Metazoan Neil3. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and ...
CDD:176804	110	PRK	Bacteria:22,Environmental:1	cd08970, AcNei1_N, N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases.  This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or ...
CDD:176805	114	PRK	Bacteria:36,Environmental:1	cd08971, AcNei2_N, N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases.  This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or ...
CDD:176806	137	EUKprk	Bacteria:2,Plants:11	cd08972, PF_Nei_N, N-terminal domain of the plant and fungal Nei and related proteins.  This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and ...
CDD:176807	122	PRK	Bacteria:28,Environmental:1	cd08973, BaFpgNei_N_1, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei  (endonuclease VIII) base-excision repair DNA glycosylases.  This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen ...
CDD:176808	98	PRK	Bacteria:10	cd08974, BaFpgNei_N_2, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei  (endonuclease VIII) base-excision repair DNA glycosylases.  This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They ...
CDD:176809	117	PRK	Bacteria:9	cd08975, BaFpgNei_N_3, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei  (endonuclease VIII) base-excision repair DNA glycosylases.  This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They ...
CDD:176810	117	PRK	Bacteria:7	cd08976, BaFpgNei_N_4, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei  (endonuclease VIII) base-excision repair DNA glycosylases.  This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They ...
CDD:185760	359	PRK	Bacteria:7	cd08977, SusD, starch binding outer membrane protein SusD.  SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, ...
CDD:185719	271	EUKprk	Bacteria:7,Plants:2	cd08978, GH_F, Glycosyl hydrolase families 43 and 62 form CAZY clan GH-F.  This glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) includes family 43 (GH43) and 62 (GH62). GH43 includes enzymes with beta-xylosidase (EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanases (beta-xylanases) and galactan ...
CDD:185720	276	EUKprk	Bacteria:35,Plants:2	cd08979, GH_J, Glycosyl hydrolase families 32 and 68, which for the clan GH-J.  This glycosyl hydrolase family clan J (according to carbohydrate-active enzymes database (CAZY)) includes family 32 (GH32) and 68 (GH68). The overall sequence homology between the two families is low (<15% identity), but common sequence motifs have been identified. GH32 enzymes are invertases that also include other fructofuranosidases such as inulinase (EC 3.2.1.7), ...
CDD:185721	288	EUKprk	Bacteria:35,Invertebrates:1,Plants:8	cd08980, GH43_1, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-xylosidase (EC 3.2.1.37) and alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly bifunctional xylosidase/arabinofuranosidase activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the ...
CDD:185722	291	PRK	Bacteria:14	cd08981, GH43_2, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric ...
CDD:185723	295	PRK	Bacteria:9	cd08982, GH43_3, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric ...
CDD:185724	276	EUKprk	Bacteria:18,Plants:3	cd08983, GH43_4, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of ...
CDD:185725	294	PRK	Bacteria:14	cd08984, GH43_5, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric ...
CDD:185726	265	EUKprk	Bacteria:29,Invertebrates:2,Plants:10	cd08985, GH43_6, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the ...
CDD:185727	269	PRK	Bacteria:7	cd08986, GH43_7, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric ...
CDD:185731	274	EUKprk	Bacteria:42,Environmental:1,Plants:4	cd08990, GH43_AXH_like, Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase.  This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. These are all ...
CDD:185732	294	EUKprk	Bacteria:15,Plants:1	cd08991, GH43_bXyl_2, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized with xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase) activities. These are all inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid ...
CDD:185735	291	EUKprk	Bacteria:16,Invertebrates:1,Plants:2	cd08994, GH43_like_2, Glycosyl hydrolase 43-like family consists of hypothetical proteins.  This subfamily mostly contains uncharacterized proteins similar to glycosyl hydrolase family 43 (GH43) which includes enzymes with beta-xylosidase (EC 3.2.1.37) and alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly bifunctional xylosidase/arabinofuranosidase activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the ...
CDD:185736	280	EUKprk	Bacteria:16,Plants:2	cd08995, GH32_Aec43_like, Glycosyl hydrolase family 32.  This glycosyl hydrolase family 32 (GH32) includes characterized as well as uncharacterized proteins. GH32 enzymes cleave sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). GH32 family also contains other fructofuranosidases such as inulinase (EC ...
CDD:185737	298	EUKprk	Bacteria:161,Environmental:2,Invertebrates:7,Plants:30	cd08996, GH32_B_Fructosidase, Glycosyl hydrolase family 32, beta-fructosidases.  Glycosyl hydrolase family GH32 cleaves sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). This family also contains other fructofuranosidases such as inulinase (EC 3.2.1.7), exo-inulinase ...
CDD:185738	349	PRK	Bacteria:16	cd08997, GH68, Glycosyl hydrolase family 68, includes levansucrase, beta-fructofuranosidase and inulosucrase.  Glycosyl hydrolase family 68 (GH68) consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10), beta-fructofuranosidase (EC 3.2.1.26) and inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Levansucrase, also known as beta-D-fructofuranosyl transferase, catalyzes the transfer of the sucrose ...
CDD:185739	288	EUKprk	Bacteria:43,Environmental:1,Plants:10	cd08998, GH43_ABN_1, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes mostly enzymes with alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and ...
CDD:185740	287	EUKprk	Bacteria:30,Invertebrates:1,Plants:10	cd08999, GH43_ABN_2, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes mostly enzymes with alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and ...
CDD:185741	288	EUKprk	Bacteria:52,Environmental:1,Plants:8	cd09000, GH43_XYL_1, Glycosyl hydrolase family 43, beta-D-xylosidase.  This glycosyl hydrolase family 43 (GH43) includes mostly enzymes that have been characterized to have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds ...
CDD:185742	269	EUKprk	Bacteria:32,Environmental:1,Plants:3	cd09001, GH43_XYL_2, Glycosyl hydrolase family 43, beta-D-xylosidase.  This glycosyl hydrolase family 43 (GH43) includes mostly enzymes that have been characterized to have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds ...
CDD:185744	311	PRK	Bacteria:6	cd09003, GH43_AXH_1, Glycosyl hydrolase family 43.  This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), xylanase (endo-alpha-L-arabinanase) as well as arabinoxylan arabinofuranohydrolase (AXH) activities. These are all inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the ...
CDD:185745	275	EUKprk	Bacteria:12,Plants:2	cd09004, GH43_bXyl, Glycosyl hydrolase family 43, includes mostly 1,4-beta-xylanases.  This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized with xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase) activities. These are all inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a ...
CDD:176713	120	EUKprk	Bacteria:8,Plants:1	cd09011, Glo_EDI_BRP_like_23, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for ...
CDD:176714	124	EUKprk	Bacteria:46,Plants:5	cd09012, Glo_EDI_BRP_like_24, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.  This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities ...
CDD:176715	121	PRK	Bacteria:9	cd09013, BphC-JF8_N_like, N-terminal, non-catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8 and similar proteins.  2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in ...
CDD:176716	166	PRK	Bacteria:3	cd09014, BphC-JF8_C_like, C-terminal, catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8 and similar proteins.  2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its ...
CDD:185696	326	EUKprk	Bacteria:141,Invertebrates:11,Plants:21,Vertebrates:3	cd09019, galactose_mutarotase_like, galactose mutarotase_like.  Galactose mutarotase catalyzes the conversion of beta-D-galactose to alpha-D-galactose. Beta-D-galactose is produced by the degradation of lactose, a disaccharide composed of beta-D-glucose and beta-D-galactose. This epimerization reaction is the first step in the four-step Leloir pathway, which converts galactose into metabolically important glucose. This ...
CDD:185697	269	EUKprk	Bacteria:57,Invertebrates:4,Plants:13	cd09020, D-hex-6-P-epi_like, D-hexose-6-phosphate epimerase-like.  D-Hexose-6-phosphate epimerase Ymr099c from Saccharomyces cerevisiae belongs to the large superfamily of aldose-1-epimerases. Its active site is very similar to the catalytic site of galactose mutarotase, the best studied member of the superfamily. It also contains the conserved glutamate and histidine residues that have been shown in galactose mutarotase to be critical ...
CDD:185698	273	PRK	Bacteria:24	cd09021, Aldose_epim_Ec_YphB, aldose 1-epimerase, similar to Escherichia coli YphB.  Proteins similar to Escherichia coli YphB are uncharacterized members of the aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic ...
CDD:185699	284	PRK	Bacteria:48	cd09022, Aldose_epim_Ec_YihR, Aldose 1-epimerase, similar to Escherichia coli YihR.  Proteins similar to Escherichia coli YihR are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion ...
CDD:185700	284	PRK	Bacteria:43,nodiv:1	cd09023, Aldose_epim_Ec_c4013, Aldose 1-epimerase, similar to Escherichia coli c4013.  Proteins, similar to Escherichia coli c4013, are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific ...
CDD:185701	288	EUKprk	Bacteria:72,Invertebrates:1	cd09024, Aldose_epim_lacX, Aldose 1-epimerase, similar to Lactococcus lactis lacX.  Proteins similar to Lactococcus lactis lacX are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific ...
CDD:185702	271	PRK	Bacteria:18	cd09025, Aldose_epim_Slr1438, Aldose 1-epimerase, similar to Synechocystis Slr1438.  Proteins similar to Synechocystis Slr1438 are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion ...
CDD:193601	82	EUK	Invertebrates:4,Primates:1,Vertebrates:1	cd09027, PET, PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions.  PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups ...
CDD:176923	101	PRK	Bacteria:71	cd09030, DUF1425, Putative periplasmic lipoprotein.  This bacterial family of proteins contains members described as putative lipoproteins, some are also known as YcfL. The function of this family is unknown. Family members have also been annotated as predicted periplasmic lipoproteins (COG5633), and appear to contain an N-terminal membrane lipoprotein lipid attachment side (pfam08139), which is not included in this alignment model.
CDD:185761	345	EUK	Invertebrates:10,Mammals:1,Plants:8,Primates:1,Vertebrates:1	cd09034, BRO1_Alix_like, Protein-interacting Bro1-like domain of mammalian Alix and related domains.  This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces ...
CDD:176924	92	EUKprk	Bacteria:14,Invertebrates:38,Plants:15,Primates:1,Rodents:1,Vertebrates:3	cd09071, FAR_C, C-terminal domain of fatty acyl CoA reductases.  C-terminal domain of fatty acyl CoA reductases, a family of SDR-like proteins. SDRs or short-chain dehydrogenases/reductases are Rossmann-fold NAD(P)H-binding proteins. Many proteins in this FAR_C family may function as fatty acyl-CoA reductases (FARs), acting on medium and long chain fatty acids, and have been reported to be involved in ...
CDD:197307	251	EUKprk	Bacteria:8,Plants:1,Primates:1	cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases.  The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most ...
CDD:197308	299	EUK	Invertebrates:4,Plants:1,Primates:1,Rodents:1	cd09074, INPP5c, Catalytic domain of inositol polyphosphate 5-phosphatases.  Inositol polyphosphate 5-phosphatases (5-phosphatases) are signal-modifying enzymes, which hydrolyze the 5-phosphate from the inositol ring of specific 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), such as PI(4,5)P2, PI(3,4,5)P3, PI(3,5)P2, I(1,4,5)P3, and I(1,3,4,5)P4. These enzymes are Mg2+-dependent, and belong to the ...
CDD:197310	236	EUK	Invertebrates:10,Mammals:1,Plants:5,Primates:1,Rodents:1,Vertebrates:6,nodiv:1	cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains.  This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: ...
CDD:197311	205	EUK	Invertebrates:12,Plants:1	cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons.  This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an ...
CDD:197312	280	EUKprk	Bacteria:24,Invertebrates:13,Plants:1,Rodents:2,Vertebrates:3	cd09078, nSMase, Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine.  Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase ...
CDD:197313	259	EUKprk	Bacteria:21,Invertebrates:1,Plants:5	cd09079, RgfB-like, Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins.  This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus ...
CDD:197314	248	EUKprk	Bacteria:7,Invertebrates:15,Plants:15,Vertebrates:3	cd09080, TDP2, Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains.  Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a ...
CDD:197315	247	PRK	Bacteria:7,Phages:2	cd09081, CdtB, CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein.  CDT is a secreted protein toxin produced by a number of Gram-negative disease-causing bacteria. CDT causes cell cycle arrest and eventual cell death in eukaryotic cells, as a result of chromosomal DNA damage caused by the catalytic, DNase I-like, CdtB subunit. Bacterial CDTs are generally comprised of three subunits, CdtA, -B and -C. CdtB is translocated  ...
CDD:197317	252	EUKprk	Bacteria:63,Invertebrates:2,Plants:13	cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1.  This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases ...
CDD:197318	246	PRK	Bacteria:42,Environmental:1	cd09084, EEP-2, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2.  This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), ...
CDD:197319	252	PRK	Bacteria:15,Environmental:1	cd09085, Mth212-like_AP-endo, Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases.  This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains ...
CDD:197320	254	EUKprk	Bacteria:57,Invertebrates:1	cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases.  This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes ...
CDD:197321	253	EUKprk	Bacteria:14,Invertebrates:22,Plants:6,Primates:1,Vertebrates:3,nodiv:1	cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases.  This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse ...
CDD:197322	309	EUK	Invertebrates:5,Plants:8,Rodents:1,Vertebrates:2	cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases.  This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common ...
CDD:197324	291	EUK	Plants:7	cd09090, INPP5c_ScInp51p-like, Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of Saccharomyces cerevisiae Inp51p, Inp52p, and Inp53p, and related proteins.  This subfamily contains the INPP5c domain of three Saccharomyces cerevisiae synaptojanin-like inositol polyphosphate 5-phosphatases (INP51, INP52, and INP53), Schizosaccharomyces pombe synaptojanin (SPsynaptojanin), and related proteins. It belongs to a family of Mg2+-dependent inositol ...
CDD:197327	292	EUK	Invertebrates:7,Plants:2,Primates:1,Vertebrates:3,nodiv:1	cd09093, INPP5c_INPP5B, Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of Type II inositol polyphosphate 5-phosphatase I, Oculocerebrorenal syndrome of Lowe 1, and related proteins.  This subfamily contains the INPP5c domain of type II inositol polyphosphate 5-phosphatase I (INPP5B), Oculocerebrorenal syndrome of Lowe 1 (OCRL-1), and related proteins. It belongs to a family of Mg2+-dependent inositol ...
CDD:197328	300	EUK	Invertebrates:5,Vertebrates:3	cd09094, INPP5c_INPP5J-like, Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of inositol polyphosphate 5-phosphatase J and related proteins.  INPP5c domain of Inositol polyphosphate-5-phosphatase J (INPP5J), also known as PIB5PA or PIPP, and related proteins. This subfamily belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position ...
CDD:197331	329	EUK	Invertebrates:6,Plants:8,Primates:1	cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4 and related domains.  This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving ...
CDD:197202	184	EUKprk	Bacteria:3,Vertebrates:1	cd09103, PLDc_CDP-OH_P_transf_II_2, Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members.  Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members, which mainly include gram-negative bacterial phosphatidylserine synthases (PSS; CDP-diacylglycerol--serine O-phosphatidyltransferase, EC 2.7.8.8), yeast phosphatidylglycerophosphate synthase (PGP synthase; ...
CDD:197203	147	EUKprk	Bacteria:14,Invertebrates:2,Plants:2	cd09104, PLDc_vPLD1_2_like_1, Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins.  Catalytic domain, repeat 1, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester ...
CDD:197204	146	PRK	Bacteria:10	cd09105, PLDc_vPLD1_2_like_2, Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins.  Catalytic domain, repeat 2, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids ...
CDD:197205	153	EUKprk	Bacteria:3,Invertebrates:16,Mammals:1,Plants:3,Primates:1,Viruses:8,nodiv:1	cd09106, PLDc_vPLD3_4_5_like_1, Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins.  Putative catalytic domain, repeat 1, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two ...
CDD:197206	175	EUKprk	Bacteria:3,Invertebrates:2,Viruses:1	cd09107, PLDc_vPLD3_4_5_like_2, Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins.  Putative catalytic domain, repeat 2, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, ...
CDD:197207	210	EUKprk	Bacteria:6,Plants:2,nodiv:1	cd09108, PLDc_PMFPLD_like_1, Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins.  Catalytic domain, repeat 1, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and ...
CDD:197209	154	EUKprk	Bacteria:121,Invertebrates:9,Plants:1	cd09110, PLDc_CLS_1, Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins.  Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. ...
CDD:197210	162	PRK	Bacteria:57	cd09111, PLDc_ymdC_like_1, Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins.  Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized ...
CDD:197211	174	PRK	Bacteria:38	cd09112, PLDc_CLS_2, catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins.  This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of ...
CDD:197212	218	PRK	Bacteria:52	cd09113, PLDc_ymdC_like_2, Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins.  Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized ...
CDD:197215	138	EUKprk	Bacteria:22,Primates:1	cd09116, PLDc_Nuc_like, Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins.  Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), and similar proteins. Nuc is an endonuclease from Salmonella typhimurium and the smallest known member of the PLD superfamily. It cleaves both single- and double-stranded DNA. PLD6 selectively hydrolyzes the terminal phosphodiester ...
CDD:197216	117	PRK	Bacteria:59,nodiv:1	cd09117, PLDc_Bfil_DEXD_like, Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain.  Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif ...
CDD:197217	144	PRK	Bacteria:11	cd09118, PLDc_yjhR_C_like, C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins.  C-terminal domain of Escherichia coli uncharacterized protein yjhR, encoded by the o338 gene, and similar proteins.  Although the biological function of yjhR remains unknown, it shows sequence similarity to the C-terminal portions of superfamily I DNA and RNA helicases, which are ubiquitous enzymes mediating ATP-dependent unwinding of DNA and RNA ...
CDD:197218	269	EUK	Primates:1,Rodents:1,Vertebrates:1	cd09119, PLDc_FAM83_N, N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83.  N-terminal phospholipase D (PLD)-like domain of vetebrate proteins from the Family with sequence similarity 83 (FAM83), which is comprised of 8 members, designated FAM83A through FAM83H. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally ...
CDD:197219	141	EUKprk	Bacteria:1,Invertebrates:22,Plants:1,Primates:1,Vertebrates:1,nodiv:1	cd09120, PLDc_DNaseII_1, Catalytic domain, repeat 1, of Deoxyribonuclease II and similar proteins.  Catalytic domain, repeat 1, of Deoxyribonuclease II (DNase II, EC 3.1.22.1), an endodeoxyribonuclease with ubiquitous tissue distribution. It is essential for accessory apoptotic DNA fragmentation and DNA clearance during development, as well as in tissue regeneration in higher eukaryotes. Unlike the ...
CDD:197220	139	EUKprk	Bacteria:1,Invertebrates:11,Rodents:1	cd09121, PLDc_DNaseII_2, Catalytic domain, repeat 2, of Deoxyribonuclease II and similar proteins.  Catalytic domain, repeat 2, of Deoxyribonuclease II (DNase II, EC 3.1.22.1), an endodeoxyribonuclease with ubiquitous tissue distribution. It is essential for accessory apoptotic DNA fragmentation and DNA clearance during development, as well as in tissue regeneration in higher eukaryotes. Unlike the majority of nucleases, DNase II ...
CDD:197221	145	EUK	Invertebrates:10,Plants:17	cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-), which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that ...
CDD:197222	182	EUK	Invertebrates:1,Plants:12	cd09123, PLDc_Tdp1_2, Catalytic domain, repeat 2, of tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 2, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-), which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that ...
CDD:197223	126	EUKprk	Bacteria:48,Invertebrates:1	cd09124, PLDc_like_TrmB_middle, Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins.  Middle phospholipase D (PLD)-like domain of the transcriptional regulator TrmB and similar proteins. TrmB acts as a bifunctional sugar-sensing transcriptional regulator which controls two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus fruiosus. It  functions as a dimer. Full length ...
CDD:197224	126	PRK	Bacteria:26	cd09126, PLDc_C_DEXD_like, C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases.  C-terminal putative phospholipase D (PLD)-like domain of uncharacterized prokaryotic HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. In addition to the helicase-like region, members of this family also contain a PLD-like domain in the ...
CDD:197225	141	PRK	Bacteria:16	cd09127, PLDc_unchar1_1, Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins.  Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs ...
CDD:197226	142	EUKprk	Bacteria:14,Plants:1	cd09128, PLDc_unchar1_2, Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins.  Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD ...
CDD:197227	196	PRK	Bacteria:18	cd09129, PLDc_unchar2_1, Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins.  Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs ...
CDD:197228	157	PRK	Bacteria:3	cd09130, PLDc_unchar2_2, Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins.  Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs ...
CDD:197229	143	PRK	Bacteria:8	cd09131, PLDc_unchar3, Putative catalytic domain of uncharacterized phospholipase D-like proteins.  Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.
CDD:197230	122	PRK	Bacteria:18	cd09132, PLDc_unchar4, Putative catalytic domain of uncharacterized phospholipase D-like proteins.  Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.
CDD:197231	127	PRK	Bacteria:15	cd09133, PLDc_unchar5, Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif.  Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this ...
CDD:197232	173	PRK	Bacteria:3	cd09134, PLDc_PSS_G_neg_1, Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria.  Catalytic domain, repeat 1, of phosphatidylserine synthases (PSSs) from gram-negative bacteria. There are two subclasses of PSS enzymes in bacteria: subclass I of gram-negative bacteria and subclass II of gram-positive bacteria. It is common that PSSs in gram-positive bacteria and yeast are tight membrane-associated enzymes. By contrast, the ...
CDD:197233	170	EUK	Invertebrates:21,Plants:15,Primates:1,Vertebrates:2	cd09135, PLDc_PGS1_euk_1, Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases.  Catalytic domain, repeat 1, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the ...
CDD:197234	215	miss	miss	cd09136, PLDc_PSS_G_neg_2, Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria.  Catalytic domain, repeat 2, of phosphatidylserine synthases (PSSs) from gram-negative bacteria. There are two subclasses of PSS enzymes in bacteria: subclass I of gram-negative bacteria and subclass II of gram-positive bacteria. It is common that PSSs in gram-positive bacteria and yeast are tight membrane-associated enzymes. By contrast, the gram-negative ...
CDD:197235	186	EUK	Invertebrates:3,Plants:4,Vertebrates:1	cd09137, PLDc_PGS1_euk_2, Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases.  Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of ...
CDD:197236	146	EUK	Invertebrates:7,Plants:8,Primates:1,nodiv:1	cd09138, PLDc_vPLD1_2_yPLD_like_1, Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins.  Catalytic domain, repeat 1, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond ...
CDD:197238	146	PRK	Bacteria:46	cd09140, PLDc_vPLD1_2_like_bac_1, Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2.  Catalytic domain, repeat 1, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of ...
CDD:197239	183	EUKprk	Bacteria:4,Invertebrates:8,Plants:3	cd09141, PLDc_vPLD1_2_yPLD_like_2, Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins.  Catalytic domain, repeat 2, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of ...
CDD:197241	142	PRK	Bacteria:15	cd09143, PLDc_vPLD1_2_like_bac_2, Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2.  Catalytic domain, repeat 2, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of ...
CDD:197250	163	PRK	Bacteria:26	cd09152, PLDc_EcCLS_like_1, Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins.  Catalytic domain, repeat 1, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin ...
CDD:197251	155	PRK	Bacteria:32	cd09154, PLDc_SMU_988_like_1, Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins.  Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible ...
CDD:197252	156	PRK	Bacteria:9	cd09155, PLDc_PaCLS_like_1, Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins.  Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer ...
CDD:197253	154	PRK	Bacteria:13	cd09156, PLDc_CLS_unchar1_1, Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase.  Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any ...
CDD:197254	155	PRK	Bacteria:28,Environmental:1	cd09157, PLDc_CLS_unchar2_1, Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase.  Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x ...
CDD:197255	174	PRK	Bacteria:4	cd09158, PLDc_EcCLS_like_2, Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins.  Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin ...
CDD:197256	170	EUKprk	Bacteria:18,Invertebrates:1	cd09159, PLDc_ybhO_like_2, Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins.  Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase ybhO and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli CL synthase. The prototype of this subfamily is Escherichia coli CL synthase ybhO ...
CDD:197257	176	PRK	Bacteria:14	cd09160, PLDc_SMU_988_like_2, Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins.  Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible ...
CDD:197258	176	PRK	Bacteria:1	cd09161, PLDc_PaCLS_like_2, Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins.  Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer ...
CDD:197259	172	PRK	Bacteria:2	cd09162, PLDc_CLS_unchar1_2, Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase.  Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino ...
CDD:197260	176	PRK	Bacteria:10	cd09163, PLDc_CLS_unchar2_2, Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase.  Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any ...
CDD:197261	162	PRK	Bacteria:15,Environmental:1	cd09164, PLDc_EcPPK1_C1_like, Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins.  Catalytic C-terminal domain, first repeat (C1 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for ...
CDD:197262	164	EUKprk	Bacteria:25,Invertebrates:1,Plants:3	cd09165, PLDc_PaPPK1_C1_like, Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins.  Catalytic C-terminal domain, first repeat (C1 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress ...
CDD:197264	165	PRK	Bacteria:10	cd09167, PLDc_EcPPK1_C2_like, Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins.  Catalytic C-terminal domain, second repeat (C2 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis ...
CDD:197265	163	PRK	Bacteria:36	cd09168, PLDc_PaPPK1_C2_like, Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins.  Catalytic C-terminal domain, second repeat (C2 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and ...
CDD:197266	162	PRK	Bacteria:19	cd09169, PLDc_PPK1_C2_unchar, Catalytic C-terminal domain, second repeat, of uncharacterized prokaryotic polyphosphate kinases.  Catalytic C-terminal domain, second repeat (C2 domain), of a group of uncharacterized prokaryotic polyphosphate kinases (Poly P kinase 1 or PPK1, EC 2.7.4.1). Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P ...
CDD:197267	142	PRK	Bacteria:51	cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins.  Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of ...
CDD:197268	136	EUKprk	Bacteria:5,Invertebrates:10,Plants:3,Vertebrates:2	cd09171, PLDc_vPLD6_like, Catalytic domain of vertebrate phospholipase D6 and similar proteins.  Catalytic domain of vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), a homolog of the EDTA-resistant nuclease Nuc from Salmonella typhimurium, and similar proteins. PLD6 can selectively hydrolyze the terminal phosphodiester bond of phosphatidylcholine (PC) with the formation of phosphatidic acid and alcohols. Phosphatidic acid is ...
CDD:197269	144	EUKprk	Bacteria:19,Plants:1	cd09172, PLDc_Nuc_like_unchar1_1, Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium.  Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short ...
CDD:197270	159	PRK	Bacteria:4	cd09173, PLDc_Nuc_like_unchar1_2, Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium.  Putative catalytic domain, repeat 2,  of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence ...
CDD:197271	136	EUKprk	Bacteria:11,Invertebrates:1	cd09174, PLDc_Nuc_like_unchar2, Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , an endonuclease from Salmonella typhimurium.  Putative catalytic domain of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved ...
CDD:197273	114	PRK	Bacteria:60	cd09176, PLDc_unchar6, Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif.  Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this ...
CDD:197275	134	PRK	Bacteria:49,Environmental:1	cd09178, PLDc_N_Snf2_like, N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family.  N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they ...
CDD:197276	190	PRK	Bacteria:51,Environmental:1	cd09179, PLDc_N_DEXD_a, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( ...
CDD:197277	142	PRK	Bacteria:5	cd09180, PLDc_N_DEXD_b, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a ...
CDD:197289	169	EUK	Invertebrates:12,Primates:1,Vertebrates:3	cd09193, PLDc_mTdp1_1, Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-). Human Tdp1 (hTdp1) acts as an important DNA repair enzyme with a preference for single-stranded or blunt-ended duplex oligonucleotides. It can remove stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a ...
CDD:197290	166	EUK	Plants:11	cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase (yTdp1, EC 3.1.4.-). yTdp1 is involved in the repair of topoisomerase I DNA lesions by  hydrolyzing the topoisomerase from the 3'-end of the DNA during double-strand break repair. Unlike human Tdp1 whose substrate-binding pocket can accommodate a fairly large topoisomerase I peptide fragment, yTdp1 has a ...
CDD:197291	191	EUK	Invertebrates:7,Vertebrates:1	cd09195, PLDc_mTdp1_2, Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-). Human Tdp1 (hTdp1) acts as an important DNA repair enzyme with a preference for single-stranded or blunt-ended duplex oligonucleotides. It can remove stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side ...
CDD:197292	200	EUK	Plants:4	cd09196, PLDc_yTdp1_2, Catalytic domain, repeat 2, of yeast tyrosyl-DNA phosphodiesterase.  Catalytic domain, repeat 2, of yeast tyrosyl-DNA phosphodiesterase (yTdp1, EC 3.1.4.-). yTdp1 is involved in the repair of topoisomerase I DNA lesions by  hydrolyzing the topoisomerase from the 3'-end of the DNA during double-strand break repair. Unlike human Tdp1 whose substrate-binding pocket can accommodate a fairly large topoisomerase I peptide fragment, yTdp1 has a ...
CDD:197297	143	PRK	Bacteria:21	cd09203, PLDc_N_DEXD_b1, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a ...
CDD:197298	139	PRK	Bacteria:34,Environmental:1,nodiv:2	cd09204, PLDc_N_DEXD_b2, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain ...
CDD:197299	143	PRK	Bacteria:18	cd09205, PLDc_N_DEXD_b3, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a ...
CDD:187742	133	EUKprk	Bacteria:102,Environmental:3,Invertebrates:3,Plants:19	cd09209, Lumazine_synthase-I, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I.  Type-I LS, also known as RibH1, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyse the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of ...
CDD:187744	131	PRK	Bacteria:7,Environmental:1	cd09211, Lumazine_synthase_archaeal, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2).  Archaeal LS is an important enzyme in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors ...
CDD:198416	96	EUK	Invertebrates:32,Plants:18,Primates:1,Rodents:1	cd09212, PUB, PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins.  The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as ...
CDD:188873	312	EUK	Invertebrates:4,Plants:7,Rodents:1	cd09213, Luminal_IRE1_like, The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins.  The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3  (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic ...
CDD:185753	319	PRK	Bacteria:18,nodiv:1	cd09214, GH64-like, glycosyl hydrolase 64 family.  This family is represented by the laminaripentaose-producing, beta-1,3-glucanase (LPHase) of Streptomyces matensis and related bacterial and ascomycete proteins. LPHase is a member of glycoside hydrolase family 64 (GH64), it is an inverting enzyme involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. LPHase is a two-domain crescent fold structure: ...
CDD:185756	151	EUK	Plants:12	cd09217, TLP-P, thaumatin and allergenic/antifungal thaumatin-like proteins: plant homologs.  This subfamily is represented by the sweet-tasting protein thaumatin from the African berry Thaumatococcus daniellii, allergenic/antifungal Thaumatin-like proteins (TLPs), and related plant proteins. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Plant TLPs are classified as pathogenesis-related (PR) protein ...
CDD:185757	219	EUK	Invertebrates:6,Plants:17	cd09218, TLP-PA, allergenic/antifungal thaumatin-like proteins: plant and animal homologs.  This subfamily is represented by the thaumatin-like proteins (TLPs), Cherry Allergen Pru Av 2 TLP, Peach PpAZ44 TLP (a propylene-induced TLP in abscission), the Caenorhabditis elegans thaumatin family member (thn-6), and other plant and animal homologs. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. ...
CDD:185759	369	EUKprk	Bacteria:4,Plants:9	cd09220, GH64-GluB-like, glycoside hydrolase family 64: beta-1,3-glucanase B (GluB)-like.  This subfamily is represented by GluB, beta-1,3-glucanase B , from Lysobacter enzymogenes Strain N4-7 and related bacterial and ascomycete proteins. GluB is a member of the glycoside hydrolase family 64 (GH64) involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. Among bacteria, many beta-1,3-glucanases are ...
CDD:198423	300	PRK	Bacteria:23	cd09224, CytoC_RC, Cytochrome C subunit of the bacterial photosynthetic reaction center.  Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction center (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidized electron donor. The electron transfer reactions of photosynthesis are performed by the following three components: the photosynthetic reaction ...
CDD:185717	186	EUK	Invertebrates:23,Plants:8,Primates:1,Vertebrates:3	cd09232, Snurportin-1_C, C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1.  Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also ...
CDD:187750	314	EUK	Invertebrates:11,Plants:33,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd09233, ACE1-Sec16-like, Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16.  COPII coat complex plays an important role in vesicular traffic of newly synthezised proteins from the endoplasmatic reticulum (ER) to the Golgi apparatus by mediating the formation of transport vesicles. COPII consists of an outer coat, made up of the scaffold proteins Sec31 and Sec13, and the cargo ...
CDD:185747	337	EUK	Invertebrates:10,Vertebrates:2	cd09234, V_HD-PTP_like, Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains.  This family contains the V-shaped (V) domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23) and related domains. It belongs to the V_Alix_like superfamily which includes the V domains of  Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian ...
CDD:185748	339	EUK	Invertebrates:15,Primates:1,Vertebrates:2,nodiv:1	cd09235, V_Alix, Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules.  This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 ...
CDD:185749	353	EUK	Plants:10	cd09236, V_AnPalA_UmRIM20_like, Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins.  This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas ...
CDD:185750	356	EUK	Plants:20	cd09237, V_ScBro1_like, Protein-interacting V-domain of Saccharomyces cerevisiae Bro1 and related domains.  This family contains the V-shaped (V) domain of Saccharomyces cerevisiae Bro1, and related domains. It belongs to the V_Alix_like superfamily which also includes the V-domain of Saccharomyces cerevisiae Rim20 (also known as PalA), mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known ...
CDD:185763	346	EUK	Invertebrates:3,Primates:1	cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains.  This family contains the N-terminal, Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), also called apoptosis-linked gene-2 interacting protein 1 (AIP1). It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also ...
CDD:185764	355	EUK	Plants:5	cd09241, BRO1_ScRim20-like, Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 and related proteins.  This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 (also known as PalA) and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase ...
CDD:185765	348	EUK	Plants:4	cd09242, BRO1_ScBro1_like, Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins.  This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as ...
CDD:185766	353	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of human Brox1 and related proteins.  This family contains the Bro1-like domain of a single-domain protein, human Brox, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), ...
CDD:185767	350	EUK	Invertebrates:9,Primates:1	cd09244, BRO1_Rhophilin, Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin and related domains.  This family contains the Bro1-like domain of RhoA-binding proteins, Rhophilin-1 and -2, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as ...
CDD:185768	413	EUK	Plants:11	cd09245, BRO1_UmRIM23-like, Protein-interacting, Bro1-like domain of Ustilago maydis Rim23 (PalC), and related domains.  This family contains the Bro1-like domain of Ustilago maydis Rim23 (also known as PalC), and related proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), ...
CDD:185769	353	EUK	Invertebrates:2,Plants:8	cd09246, BRO1_Alix_like_1, Protein-interacting, N-terminal, Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily.  This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins ...
CDD:185770	346	EUK	Invertebrates:3,Plants:8	cd09247, BRO1_Alix_like_2, Protein-interacting Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily.  This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 ...
CDD:271158	272	EUK	Invertebrates:10,Plants:21,Primates:1	cd09250, AP-1_Mu1_Cterm, C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1.  AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex ...
CDD:271159	263	EUK	Invertebrates:15,Plants:21,Rodents:1,Vertebrates:3	cd09251, AP-2_Mu2_Cterm, C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2.  AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, -2, -3, and -4, described in various eukaryotic ...
CDD:271160	251	EUK	Invertebrates:14,Plants:25,Primates:1,Rodents:1,Vertebrates:2	cd09252, AP-3_Mu3_Cterm, C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3.  AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP ...
CDD:271161	271	EUK	Invertebrates:13,Plants:11,Vertebrates:3	cd09253, AP-4_Mu4_Cterm, C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4.  AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four ...
CDD:271162	237	EUK	Invertebrates:22,Plants:32,Vertebrates:3	cd09254, AP_delta-COPI_MHD, Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit.  COPI complex-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. COPI complex-coated vesicles consist of a small GTPase, ADP-ribosylation factor 1 (ARF1) and a heteroheptameric coatomer composed of two subcomplexes, F-COPI and ...
CDD:271164	276	EUK	Invertebrates:7,Plants:2,Vertebrates:2	cd09256, AP_MuD_MHD, Mu-homology domain (MHD) of a adaptor protein (AP) encoded by mu-2 related death-inducing gene, MuD (also known as MUDENG).  This family corresponds to the MHD found in a protein encoded by MuD (also known as Adapter-related protein complex 5 subunit mu-1), which is distantly related to the C-terminal domain of the mu2 subunit of AP complexes that participates in clathrin-mediated endocytosis. MuD is evolutionary ...
CDD:271165	244	EUK	Plants:8,Primates:1	cd09257, AP_muniscins_like_MHD, Mu-homology domain (MHD) of muniscins adaptor proteins (AP) and similar proteins.  This family corresponds to the MHD found in muniscins, a novel family of endocytic adaptor proteins. The term, muniscins, has been assigned to name the MHD of proteins with both EFC/F-BAR domain and MHD. These two domains are responsible for the membrane-tubulation activity associated with transmembrane cargo proteins. Members in this family ...
CDD:271170	257	EUK	Plants:13	cd09264, AP_Syp1_MHD, mu-homology domain (MHD) of adaptor protein (AP), Syp1, and related proteins.  This family corresponds to the MHD found in a novel endocytic adaptor Syp1 and related proteins. Syp1 is a poorly characterized yeast protein with multiple biological functions. It was originally identified as a suppressor of a yeast profiling deletion and later as a suppressor of arf3delta (Arf3 is the yeast homologue of Arf6, a mammalian regulator of endocytosis). ...
CDD:185703	293	PRK	Bacteria:17	cd09269, deoxyribose_mutarotase, deoxyribose mutarotase_like.  Salmonella enterica serovar Typhi DeoM (earlier named as DeoX) is a mutarotase with high specificity for deoxyribose.  It is encoded by one of four genes beonging to the deoK operon. This operon has also been found in  Escherichia coli where it is more common in pathogenic than in commensal strains and is associated with pathogenicity. It has been found on a pathogenicity island from a human blood ...
CDD:187751	211	EUK	Invertebrates:7,Plants:19,Rodents:1,Vertebrates:2	cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids.  Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase ...
CDD:187752	93	EUK	Invertebrates:6,Plants:25,Rodents:1,Vertebrates:2	cd09271, RNase_H2-C, Ribonuclease H2-C is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids.  Ribonuclease H2C is one of the three protein of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase ...
CDD:260004	140	EUKprk	Bacteria:1,Invertebrates:12,Plants:91,Vertebrates:1	cd09272, RNase_HI_RT_Ty1, Ty1/Copia family of RNase HI in long-term repeat retroelements.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in ...
CDD:260005	131	EUK	Invertebrates:1,Mammals:4,Primates:2,Rodents:2,Vertebrates:1	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present ...
CDD:260006	121	EUKprk	Bacteria:1,Invertebrates:33,Plants:71,Vertebrates:3,nodiv:1	cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNase HI in long-term repeat retroelements.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely ...
CDD:260007	120	EUKprk	Bacteria:2,Invertebrates:7,Plants:2,Vertebrates:1	cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase HI in long-term repeat retroelements.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in ...
CDD:260008	131	EUKprk	Bacteria:2,Invertebrates:13,Plants:30	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases.  Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in ...
CDD:260009	133	PRK	Bacteria:79,Environmental:1	cd09277, RNase_HI_bacteria_like, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus.  Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA ...
CDD:260010	139	EUKprk	Bacteria:203,Environmental:1,Invertebrates:4,Plants:2,nodiv:1	cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes.  Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. ...
CDD:260011	128	EUKprk	Bacteria:152,Environmental:5,Invertebrates:6,Plants:24	cd09279, RNase_HI_like, RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI.  Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
CDD:260012	145	EUKprk	Bacteria:1,Invertebrates:25,Plants:40,Vertebrates:2,nodiv:1	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts.  Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a ...
CDD:187753	124	EUKprk	Bacteria:132,Environmental:2,Invertebrates:4,Plants:6,Primates:1,Rodents:1	cd09281, UPF0066, Escherichia coli YaeB and related proteins.  Uncharacterized protein family UPF0066.  This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR.  Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown.
CDD:185681	225	EUK	Invertebrates:4,Plants:4,Primates:1,Vertebrates:4	cd09286, NMNAT_Eukarya, Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic.  Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT).  NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide.  It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide ...
CDD:187754	226	EUK	Plants:9,Primates:1,Vertebrates:3	cd09293, AMN1, Antagonist of mitotic exit network protein 1.  Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase ...
CDD:187755	116	PRK	Bacteria:169,Environmental:2	cd09294, SmpB, Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs.  Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Trans-translation system is composed of a ribonucleoprotein complex of ...
CDD:187756	326	EUKprk	Bacteria:9,Plants:6	cd09299, TDT, The Tellurite-resistance/Dicarboxylate Transporter (TDT) family.  The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux ...
CDD:212512	279	EUKprk	Bacteria:4,Primates:1	cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and related proteins.  The HDAC/HDAC-like family includes Zn-dependent histone deacetylase classes I, II and IV (class III HDACs, also called sirtuins, are NAD-dependent and structurally unrelated, and therefore not part of this family). Histone deacetylases catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98), as opposed to ...
CDD:187706	128	EUKprk	Bacteria:7,Plants:2,Primates:1,Vertebrates:2	cd09302, Jacalin_like, Jacalin-like lectin domain.  Jacalin-like lectins are sugar-binding protein domains mostly found in plants. They adopt a beta-prism topology consistent with a circularly permuted three-fold repeat of a structural motif. Proteins containing this domain may bind mono- or oligosaccharides with high specificity. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures ...
CDD:187757	330	EUK	Plants:13	cd09317, TDT_Mae1_like, C4-dicarboxylate transporter/malic acid transport protein family includes Mae1.  This family contains eukaryotic homologs of C4-dicarboxylate transporter/malic acid transport proteins which are part of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family. This includes the MAE1 gene in Schizosaccharomyces pombe gene that encodes malate permease, Mae1, which functions by proton symport and transports C4-dicarboxylates (malate, ...
CDD:187758	341	EUKprk	Bacteria:11,Plants:20	cd09318, TDT_SSU1, Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes sulfite sensitivity protein (sulfite efflux pump; SSU1).  This family contains the sulfite sensitivity protein (sulfite efflux pump; SSU1) and belongs to the tellurite-resistance/dicarboxylate transporter (TDT) family. The SSU1 gene encodes the sulfite pump required for efficient sulfite efflux. Mutations in the SSU1 gene cause sensitivity to sulfite while ...
CDD:187759	317	PRK	Bacteria:26	cd09319, TDT_like_1, The Tellurite-resistance/Dicarboxylate Transporter (TDT) family.  The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump ...
CDD:187760	327	PRK	Bacteria:22	cd09320, TDT_like_2, The Tellurite-resistance/Dicarboxylate Transporter (TDT) family.  The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump ...
CDD:187761	327	PRK	Bacteria:11	cd09321, TDT_like_3, The Tellurite-resistance/Dicarboxylate Transporter (TDT) family.  The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump ...
CDD:187762	289	EUKprk	Bacteria:95,Plants:5	cd09322, TDT_TehA_like, The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes TehA proteins.  The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other ...
CDD:187763	297	miss	miss	cd09323, TDT_SLAC1_like, Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1).  SLAC1 (Slow Anion Channel-Associated 1) is a plasma membrane protein, preferentially expressed in guard cells, which encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. It is essential for stomatal closure in response to carbon dioxide, abscisic acid, ozone, light/dark transitions, humidity ...
CDD:187764	301	miss	miss	cd09324, TDT_TehA, Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes TehA protein.  This subfamily includes Tellurite resistance protein TehA that belongs to the C4-dicarboxylate transporter/malic acid transport (TDT) protein family and is a homolog of plant Slow Anion Channel-Associated 1 (SLAC1). The tehA gene encodes an integral membrane protein that has been shown to have efflux activity of quaternary ammonium compounds. TehA protein of Escherichia ...
CDD:187765	293	miss	miss	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family.  This subfamily contains bacterial C4-dicarboxylate transporters, which is part of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family. It includes Tellurite resistance protein tehA; the tehA gene encodes an integral membrane protein that has been shown to have efflux activity of quaternary ammonium compounds. TehA protein of ...
CDD:188712	53	EUK	Invertebrates:15,Plants:4,Vertebrates:3,nodiv:1	cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family.  The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact ...
CDD:188713	52	EUK	Invertebrates:12,Primates:1,Vertebrates:4	cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins.  The first LIM domain of actin binding LIM (abLIM) proteins:  Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. ...
CDD:188714	56	EUK	Invertebrates:2,Rodents:1,Vertebrates:1,nodiv:1	cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM (abLIM) proteins.  The second LIM domain of actin binding LIM (abLIM) proteins:  Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding ...
CDD:188715	52	EUK	Invertebrates:4,Primates:1	cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins.  The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, ...
CDD:188717	59	EUK	Invertebrates:11,Primates:2,Vertebrates:2,nodiv:1	cd09331, LIM1_PINCH, The first LIM domain of protein PINCH.  The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the ...
CDD:188718	52	EUK	Invertebrates:5,Mammals:1,Vertebrates:3	cd09332, LIM2_PINCH, The second LIM domain of protein PINCH.  The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other ...
CDD:188720	54	EUK	Invertebrates:1,Primates:1	cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH.  The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction ...
CDD:188721	54	EUK	Invertebrates:1,Mammals:1,Rodents:1,Vertebrates:1	cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH.  The fifth LIM domain of protein PINCH:  PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and ...
CDD:188724	53	EUK	Invertebrates:6,Rodents:1,Vertebrates:2,nodiv:1	cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family.  The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region.  Members of this family are adaptor proteins to recruit key components of ...
CDD:188725	52	EUK	Invertebrates:3,Mammals:2,Primates:1,Rodents:1,Vertebrates:2	cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family.  The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region.  Members of this family are adaptor proteins to recruit key components ...
CDD:188726	58	EUK	Invertebrates:14,Mammals:4,Primates:1,Rodents:2,Vertebrates:1	cd09340, LIM1_Testin_like, The first LIM domain of Testin-like family.  The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain.  Testin ...
CDD:188727	56	EUK	Invertebrates:5,nodiv:1	cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family.  The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain.  Testin is a cytoskeleton associated focal ...
CDD:188728	57	EUK	Invertebrates:1,Vertebrates:2,nodiv:1	cd09342, LIM3_Testin_like, The third LIM domain of Testin-like family.  The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton ...
CDD:188731	54	EUK	Invertebrates:3,Plants:1,Primates:1,Vertebrates:3	cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM domains protein (FHL).  The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the ...
CDD:188732	52	EUK	Mammals:1,Primates:2,Vertebrates:4	cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL).  The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a ...
CDD:188733	56	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:1	cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM domains protein (FHL).  The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to ...
CDD:188744	53	EUK	Invertebrates:18,Mammals:2,Plants:4,Primates:1,Vertebrates:1,nodiv:1	cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family.  The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes  LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function ...
CDD:188755	54	EUK	Invertebrates:11,Vertebrates:1	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family.  The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of ...
CDD:188763	59	EUK	Invertebrates:10,Vertebrates:1	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family.  The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development ...
CDD:188777	57	EUK	Plants:15	cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein.  The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of ...
CDD:188778	53	EUK	Invertebrates:1,Plants:3	cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein.  The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the ...
CDD:188779	56	EUK	Plants:9	cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein.  The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of ...
CDD:188780	55	EUK	Plants:9	cd09394, LIM1_Rga, The first LIM domain of  Rga GTPase-Activating Proteins.  The first LIM domain of  Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is  CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger ...
CDD:188782	53	EUK	Invertebrates:2,Plants:8	cd09396, LIM_DA1, The Lim domain of DA1.  The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which ...
CDD:188783	58	EUK	Plants:8	cd09397, LIM1_UF1, LIM domain in proteins of unknown function.  The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as ...
CDD:188784	61	EUK	Invertebrates:9	cd09400, LIM_like_1, LIM domain in proteins of unknown function.  LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions ...
CDD:188785	53	EUK	Invertebrates:13,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd09401, LIM_TLP_like, The  LIM domains of thymus LIM protein (TLP).  The LIM domain of thymus LIM protein (TLP) like proteins:  This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs.  Like CRP1, CRP2 and CRP3/MLP, TLP has two ...
CDD:188799	59	EUK	Invertebrates:10,Mammals:1,Rodents:1,Vertebrates:5	cd09415, LIM1_Prickle, The first LIM domain of Prickle.  The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain.  Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP).  PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and ...
CDD:188823	55	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:4	cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting with CasL).  The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA)  receptor and is required for Semapho-rin 1a ...
CDD:188827	55	EUK	Invertebrates:5,Plants:1	cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1).  The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal  Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has  putative function in muscle development. The mouse with ky mutant exhibits combined ...
CDD:188831	53	EUK	Invertebrates:10,Primates:1,Vertebrates:4,nodiv:1	cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).  The LIM domain of LIM and SH3 Protein (LASP):  LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ ...
CDD:188886	56	EUKprk	Bacteria:2,Invertebrates:9,Plants:13,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	cd09487, SAM_superfamily, SAM (Sterile alpha motif ).  SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and ...
CDD:188887	61	EUK	Invertebrates:8,Primates:1,Rodents:2,Vertebrates:4	cd09488, SAM_EPH-R, SAM domain of EPH family of tyrosine kinase receptors.  SAM (sterile alpha motif) domain of EPH (erythropoietin-producing hepatocyte) family of receptor tyrosine kinases is a C-terminal signal transduction module located in the cytoplasmic region of these receptors. SAM appears to mediate cell-cell initiated signal transduction via binding proteins to a conserved tyrosine that is phosphorylated. In some ...
CDD:188889	63	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:2	cd09490, SAM_Arap1,2,3, SAM domain of Arap1,2,3 (angiotensin receptor-associated protein).  SAM (sterile alpha motif) domain of Arap1,2,3 subfamily proteins (angiotensin receptor-associated) is a protein-protein interaction domain. Arap1,2,3 proteins are phosphatidylinositol-3,4,5-trisphosphate-dependent GTPase-activating proteins. They are involved in phosphatidylinositol-3 kinase (PI3K) signaling pathways. In ...
CDD:188896	66	EUK	Invertebrates:10,Vertebrates:3,nodiv:1	cd09497, SAM_caskin1,2_repeat1, SAM domain of caskin protein repeat 1.  SAM (sterile alpha motif) domain repeat 1 of caskin1,2 proteins is a protein-protein interaction domain. Caskin has two tandem SAM domains. Caskin protein is known to interact with membrane-associated guanylate kinase CASK, and apparently may play a role in neural development, synaptic protein targeting, and regulation of gene expression.
CDD:188897	71	EUK	Invertebrates:2,Vertebrates:3	cd09498, SAM_caskin1,2_repeat2, SAM domain of caskin protein repeat 2.  SAM (sterile alpha motif) domain repeat 2 of caskin1,2 proteins is a protein-protein interaction domain. Caskin has two tandem SAM domains. Caskin protein is known to interact with membrane-associated guanylate kinase CASK, and may play a role in neural development, synaptic protein targeting, and regulation of gene expression.
CDD:188898	67	EUK	Invertebrates:2,Vertebrates:3	cd09499, SAM_AIDA1AB-like_repeat1, SAM domain of AIDA1AB-like proteins, repeat 1.  SAM (sterile alpha motif) domain repeat 1 of AIDA1AB-like proteins is a protein-protein interaction domain. AIDA1AB-like proteins have two tandem SAM domains. They may form an intramolecular head-to-tail homodimer. One of two basic motifs of the nuclear localization signal (NLS) is located within helix 5 of SAM2 (motif HKRK). This signal plays a role in decoupling of ...
CDD:188899	65	EUK	Invertebrates:1	cd09500, SAM_AIDA1AB-like_repeat2, SAM domain of AIDA1AB-like proteins, repeat 2.  SAM (sterile alpha motif) domain repeat 2 of AIDA1AB-like proteins is a protein-protein interaction domain. AIDA1AB-like proteins have two tandem SAM domains. They may form an intramolecular head-to-tail homodimer. One of two basic motifs of the nuclear localization signal (NLS) is located within helix 5 of the SAM2 (motif HKRK). This signal plays a role in decoupling of SAM2 from ...
CDD:188900	69	EUK	Invertebrates:6,Primates:1,Vertebrates:2	cd09501, SAM_SARM1-like_repeat1, SAM domain ot SARM1-like proteins, repeat 1.  SAM (sterile alpha motif) domain repeat 1 of SARM1-like adaptor proteins is a protein-protein interaction domain. SARM1-like proteins contain two tandem SAM domains. SARM1-like proteins are involved in TLR (Toll-like receptor) signaling. They are responsible for targeted localization of the whole protein to post-synaptic regions of axons. In humans SARM1 ...
CDD:188901	70	EUK	Invertebrates:5	cd09502, SAM_SARM1-like_repeat2, SAM domain of SARM1-like, repeat 2.  SAM (sterile alpha motif) domain repeat 2 of SARM1-like adaptor proteins is a protein-protein interaction domain. SARM1-like proteins contain two tandem SAM domains. SARM1-like proteins are involved in TLR (Toll-like receptor) signaling. They are responsible for targeted localization of the whole protein to post-synaptic regions of axons. In humans SARM1 expression is detected in kidney and liver.
CDD:188902	65	EUK	Invertebrates:7	cd09503, SAM_tumor-p63,p73, SAM domain of tumor-p63,p73 proteins.  SAM (sterile alpha motif) domain of p63, p73 transcriptional factors is a putative protein-protein interaction domain and lipid-binding domain. p63 and p73 are homologs to the tumor suppressor p53. They have a C-terminal SAM domain in their longest spliced alpha forms, while p53 doesn't have it. p63 or p73 knockout mice show significant developmental abnormalities but no increased cancer ...
CDD:188903	74	EUK	Invertebrates:8,Primates:1	cd09504, SAM_STIM-1,2-like, SAM domain of STIM-1,2-like proteins.  SAM (sterile alpha motif) domain of STIM-1,2-like (Stromal interaction molecule) proteins is a putative protein-protein interaction domain. STIM1 and STIM2 human proteins are type I transmembrane proteins. The N-terminal part of them includes "hidden" EF-hand and SAM domains. This region is responsible for sensing changes in store-operated and basal cytoplasmic Ca2+ levels and ...
CDD:188904	72	EUK	Invertebrates:5,Vertebrates:4,nodiv:1	cd09505, SAM_WDSUB1, SAM domain of WDSUB1 proteins.  SAM (sterile alpha motif) domain of WDSUB1 subfamily proteins is a putative protein-protein interaction domain. Proteins of this group contain multiple domains: SAM, one or more WD40 repeats and U-box (derived version of the RING-finger domain). Apparently the WDSUB1 subfamily proteins participate in protein degradation through ubiquitination, since U-box domain are known as a member of ...
CDD:188905	66	EUK	Invertebrates:5,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd09506, SAM_Shank1,2,3, SAM domain of Shank1,2,3 family proteins.  SAM (sterile alpha motif) domain of Shank1,2,3 family proteins is a protein-protein interaction domain. Shank1,2,3 proteins are scaffold proteins that are known to interact with a variety of cytoplasmic and membrane proteins. SAM domains of the Shank1,2,3 family are prone to homooligomerization. They are highly enriched in the postsynaptic density, ...
CDD:188907	70	EUK	Invertebrates:2,Mammals:1,Rodents:1,Vertebrates:4	cd09508, SAM_HD, SAM domain of HD-phosphohydrolase.  SAM (sterile alpha motif) domain of SAM_HD subfamily proteins is a putative protein-protein interaction domain. Proteins of this group, additionally to the SAM domain, contain a HD hydrolase domain. Human SAM-HD1 is a nuclear protein involved in innate immune response and may act as a negative regulator of the cell-intrinsic antiviral response. Mutations in this gene lead to ...
CDD:188908	64	EUK	Invertebrates:17,Primates:2,Rodents:1,Vertebrates:5	cd09509, SAM_Polycomb, SAM domain of Polycomb group.  SAM (sterile alpha motif) domain of Polycomb group is a protein-protein interaction domain. The Polycomb group includes transcriptional repressors which are involved in the regulation of some key regulatory genes during development in many organisms. They are best known for silencing Hox (Homeobox) genes. Polycomb proteins work together in large multimeric and ...
CDD:188909	75	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd09510, SAM_aveugle-like, SAM domain of aveugle-like subfamily.  SAM (sterile alpha motif) domain of SAM_aveugle-like subfamily is a protein-protein interaction domain. In Drosophila, the aveugle (AVE) protein (also known as HYP (Hyphen)) is involved in normal photoreceptor differentiation, and required for epidermal growth factor receptor (EGFR) signaling between ras and raf genes during eye development and wing vein formation. SAM ...
CDD:188910	69	EUK	Invertebrates:4,Primates:1,Vertebrates:4	cd09511, SAM_CNK1,2,3-suppressor, SAM domain of CNK1,2,3-suppressor subfamily.  SAM (sterile alpha motif) domain of CNK (connector enhancer of kinase suppressor of ras (Ksr)) subfamily is a protein-protein interaction domain. CNK proteins are multidomain scaffold proteins containing a few protein-protein interaction domains and are required for connecting Rho and Ras signaling pathways. In Drosophila, the SAM domain of CNK is known to ...
CDD:188911	70	EUK	Invertebrates:11,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	cd09512, SAM_Neurabin-like, SAM domain of SAM_Neurabin-like subfamily.  SAM (sterile alpha motif) domain of Neurabin-like (Neural actin-binding) subfamily is a putative protein-protein interaction domain. This group currently includes the SAM domains of neurobin-I, SAMD14 and neurobin-I/SAMD14-like proteins.  Most are multidomain proteins and in addition to SAM domain they contain other protein-binding domains such ...
CDD:188914	70	EUK	Invertebrates:10,Primates:1,Vertebrates:3,nodiv:1	cd09515, SAM_SGMS1-like, SAM domain of sphingomyelin synthase related subfamily.  SAM (sterile alpha motif) domain of SGMS-like (sphingomyelin synthase) subfamily is a potential protein-protein interaction domain. This group of proteins is related to sphingomyelin synthase 1, and contains an N-terminal SAM domain. The function of SGMS1-like proteins is unknown; they may play a role in sphingolipid metabolism.
CDD:188919	65	EUK	Invertebrates:9,Vertebrates:3	cd09520, SAM_BICC1, SAM domain of BICC1 (bicaudal) subfamily.  SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia ...
CDD:188922	65	EUK	Invertebrates:5,Primates:1,Vertebrates:3	cd09523, SAM_TAL, SAM domain of TAL subfamily.  SAM (sterile alpha motif) domain of TAL (Tsg101-associated ligase) proteins, also known as LRSAM1 (Leucine-rich repeat and sterile alpha motif-containing) proteins, is a putative protein-protein interaction domain. Proteins of this subfamily participate in the regulation of retrovirus budding and receptor endocytosis. They show E3 ubiquitin ligase activity. Human TAL protein interacts with ...
CDD:188929	67	EUK	Invertebrates:7,Vertebrates:1,nodiv:1	cd09530, SAM_Samd14, SAM domain of Samd14 subfamily.  SAM (sterile alpha motif) domain of SamD14 (or FAM15A) subfamily is a putative protein-protein interaction domain. SAM is widespread domain in proteins involved in signal transduction and regulation. In many cases SAM mediates homodimerization/oligomerization. The exact function of proteins belonging to this subfamily is unknown.
CDD:188930	65	EUK	Invertebrates:10,Vertebrates:2	cd09531, SAM_CS047, SAM domain of CS047 subfamily.  SAM (sterile alpha motif) domain of CS047 subfamily is a putative protein-protein interaction domain. Proteins of this subfamily have a SAM domain at the N-terminus. SAM is a widespread domain in signaling and regulatory proteins. In many cases SAM mediates homodimerization/oligomerization. The exact function of proteins belonging to this group is unknown.
CDD:188933	62	EUK	Plants:19	cd09534, SAM_Ste11_fungal, SAM domain of Ste11_fungal subfamily.  SAM (sterile alpha motif) domain of Ste11 subfamily is a protein-protein interaction domain. Proteins of this subfamily have SAM domain at the N-terminus and protein kinase domain at the C-terminus. They participate in regulation of mating pheromone response, invasive growth and high osmolarity growth response. MAP triple kinase Ste11 from S.cerevisia is known to interact with Ste20 kinase and Ste50 ...
CDD:188934	65	EUK	Plants:21	cd09535, SAM_BOI-like_fungal, SAM domain of BOI-like fungal subfamily.  SAM (sterile alpha motif) domain of BOI-like fungal subfamily is a potential protein-protein interaction domain. Proteins of this subfamily are apparently scaffold proteins, since most contain SH3 and PH domains, which are also protein-protein interaction domains, in addition to SAM domain.  BOI-like proteins participate in cell cycle regulation.  In particular BOI1 and BOI2 proteins of budding ...
CDD:188938	62	EUK	Invertebrates:11,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd09539, SAM_TNK-like, SAM domain of TNK(ACK)-like non-receptor tyrosine-protein kinases.  SAM (sterile alpha motif) domain of TNK-like subfamily is a putative protein-protein interaction domain.  This subfamily includes TNK1 and TNK2 (also known as ACK1) non-receptor tyrosine-protein kinases. They contain a SAM domain at the N-terminus followed by a catalytic domain and a few other domains. Members of this group are ...
CDD:188939	66	EUK	Invertebrates:2,Primates:1,Vertebrates:3	cd09540, SAM_EPS8-like, SAM domain of EPS8-like subfamily.  SAM (sterile alpha motif) domain of EPS8-like subfamily is a putative protein-protein interaction domain. This subfamily includes epidermal growth factor receptor kinase substrate 8 proteins (EPS8) and epidermal growth factor receptor kinase substrate 8-like (EPSL8) 1, 2, 3 proteins with the SAM domain located in the C-terminal effector region. This region is responsible for ...
CDD:188940	60	EUK	Invertebrates:6,Plants:4,Vertebrates:2	cd09541, SAM_KIF24-like, SAM domain of KIF24-like subfamily.  SAM (sterile alpha motif) domain of KIF24 subfamily is a putative protein-protein interaction domain. This subfamily includes proteins related to human kinesin-like protein KIF24. SAM domain is located at the N-terminus followed by kinesin motor domain. Kinesins are proteins involved in a number of different cell processes including microtubule dynamics and axonal transport. ...
CDD:188955	69	EUK	Plants:13	cd09556, SAM_VTS1_fungal, SAM domain of VTS1 RNA-binding proteins.  SAM (sterile alpha motif) domain of VTS1 subfamily proteins is RNA binding domain located in the C-terminal region. SAM interacts with stem-loop structures of mRNA. Proteins of this subfamily participate in regulation of transcript stability and degradation, and also may be involved in vacuolar protein transport regulation. VTS1 protein of S.cerevisiae induces mRNA degradation via the major ...
CDD:188956	63	EUK	Invertebrates:10,Primates:1,Vertebrates:3,nodiv:1	cd09557, SAM_Smaug, SAM domain of Smaug subfamily.  SAM (sterile alpha motif) domain of Smaug proteins is an RNA recognition domain. It binds a specific RNA motif known as Smaug recognition element (SRE). Among members of this group are invertebrate Smaug (Smg) proteins and vertebrate Smaug1 and Smaug2 proteins. They are involved in post-transcriptional control during early embryogenesis in animals. In Drosophila, Smaug protein ...
CDD:188962	64	EUK	Invertebrates:15,Primates:1,Vertebrates:4,nodiv:1	cd09563, SAM_liprin-beta1,2_repeat1, SAM domain of liprin-beta1,2 proteins repeat 1.  SAM (sterile alpha motif) domain repeat 1 of liprin-beta1,2 proteins is a protein-protein interaction domain. Liprin-beta protein contain three copies (repeats) of SAM domain. They may form heterodimers with liprins-alpha through their SAM domains. It was suggested based on bioinformatic approaches that the second SAM domain of liprin-beta is ...
CDD:188965	63	EUK	Vertebrates:1	cd09566, SAM_liprin-beta1,2_repeat2, SAM domain of liprin-beta1,2 proteins repeat 2.  SAM (sterile alpha motif) domain repeat 2 of liprin-beta1,2 proteins is a protein-protein interaction domain. Liprin-beta proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-alpha proteins through their SAM domains. It was suggested based on bioinformatic approaches that the second SAM domain of liprin-beta potentially is able to form ...
CDD:188981	66	miss	miss	cd09582, SAM_Scm-like-3MBT3,4, SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group.  SAM (sterile alpha motif) domain of Scm-like-3MBT3,4 (Sex comb on midleg, Malignant brain tumor) subfamily proteins (also known as L3mbtl3,4 proteins)  is a putative protein-protein interaction domain.  Proteins of this subfamily are predicted transcriptional regulators belonging to Polycomb group. The majority of them are multidomain proteins: in addition to the C-terminal SAM ...
CDD:188982	69	miss	miss	cd09583, SAM_Atherin-like, SAM domain of Atherin/Atherin-like subfamily.  SAM (sterile alpha motif) domain of SAM_Atherin and Atherin-like subfamily proteins is a putative protein-protein and/or protein-lipid interaction domain.  In addition to the C-terminal SAM domain, the majority of proteins belonging to this group also have PHD (or Zn finger) domain. As potential members of the polycomb group, these proteins may be involved in regulation of some key regulatory genes ...
CDD:198424	125	EUKprk	Bacteria:15,Primates:1,Vertebrates:1,Viruses:1	cd09593, UDG_like, Uracil-DNA glycosylases (UDG) and related enzymes.  Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. ...
CDD:189001	125	EUKprk	Bacteria:1,Plants:1,Primates:1	cd09594, GluZincin, Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins).  Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single ...
CDD:189002	407	EUKprk	Bacteria:6,Primates:1,Vertebrates:1	cd09595, M1, Peptidase M1 family contains aminopeptidase N and leukotriene A4 hydrolase.  M1 Peptidase family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis.  APN consists of a small N-terminal cytoplasmic ...
CDD:189003	271	EUKprk	Bacteria:26,Plants:5	cd09596, M36, Peptidase M36 family also known as fungalysin family.  Peptidase M36 protease family, also known as fungalysin (elastinolytic metalloproteinase) family, includes endopeptidases from pathogenic fungi. Fungalysin can hydrolyze extracellular matrix proteins such as elastin and keratin, with a preference for cleavage on the amino side of hydrophobic residues with bulky side-chains. This family is similar to the M4 (thermolysin) family due to ...
CDD:189004	280	miss	miss	cd09597, M4_neutral_protease, Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease.  This peptidase M4 family includes several endopeptidases such as thermolysin (EC 3.4.24.27), aureolysin (the extracellular metalloproteinase from Staphylococcus aureus), neutral protease from Bacillus cereus and protealysin. These enzymes have a two-domain structure with the active site between the domains. The N-terminal domain contains the HEXXH ...
CDD:189005	261	miss	miss	cd09598, M4_uncharacterized, Peptidase M4 family containing mostly uncharacterized proteins.  This family of uncharacterized bacterial proteins are homologs of the M4 peptidase family that is also known as the thermolysin-like peptidase (TLP) family. Typically, the M4 peptidases consist of a presequence (signal sequence), a propeptide sequence and a peptidase unit. The presequence is cleaved off during export while the propeptide has inhibitory and chaperone functions ...
CDD:189006	442	EUKprk	Bacteria:10,Invertebrates:15,Plants:23,Primates:1,Vertebrates:4,nodiv:1	cd09599, M1_LTA4H, Peptidase M1 family contains leukotriene A4 hydrolase.  This family includes leukotriene A4 hydrolase (LTA4H; E.C. 3.3.2.6) and the close homolog cold-active aminopeptidase (Colwellia psychrerythraea-type peptidase; ColAP), both members of the aminopeptidase M1 family. LTA4H, is a bifunctional enzyme possessing an aminopeptidase as well as an epoxide hydrolase activity.  The two ...
CDD:189007	861	EUKprk	Bacteria:5,Invertebrates:3,Plants:5	cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.  This family contains aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral membrane protease belonging to the M1 gluzincin family. It includes bacterial-type alanyl aminopeptidases as well as PfA-M1 aminopeptidase (Plasmodium falciparum-type). APN consists of a small N-terminal cytoplasmic domain, a single transmembrane domain and a large ...
CDD:189008	446	EUKprk	Bacteria:21,Environmental:1,Invertebrates:36,Plants:11,Primates:1,Vertebrates:5,nodiv:2	cd09601, M1_APN_2, Peptidase M1 Aminopeptidase N family incudes tricorn interacting factor F3, Endoplasmic reticulum aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ).  This M1 peptidase family includes eukaryotic and bacterial members: aminopeptidase N (APN), aminopeptidase Q (APQ, laeverin), endoplasmic reticulum aminopeptidase 1 (ERAP1) as well as tricorn interacting factor F3. ...
CDD:189009	438	EUKprk	Bacteria:18,Invertebrates:2,nodiv:1	cd09602, M1_APN_3, Peptidase M1 family containing Aminopeptidase N.  This family contains bacterial and eukaryotic aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral membrane protease belonging to the M1 gluzincin family. APN consists of a small N-terminal cytoplasmic domain, a single transmembrane domain and a large extracellular ectodomain that contains the active site.  It preferentially cleaves ...
CDD:189010	415	PRK	Bacteria:72,Environmental:1,nodiv:1	cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N.  This family contains mostly bacterial and some archaeal aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral membrane protease belonging to the M1 gluzincin family. APN consists of a small N-terminal cytoplasmic domain, a single transmembrane domain and a large extracellular ectodomain that contains the active site. It preferentially cleaves neutral ...
CDD:189011	435	PRK	Bacteria:41	cd09604, M1_APN_5, Peptidase M1 family containing bacterial Aminopeptidase N.  This family contains bacterial aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral membrane protease belonging to the M1 gluzincin family. APN consists of a small N-terminal cytoplasmic domain, a single transmembrane domain and a large extracellular ectodomain that contains the active site.  It preferentially cleaves neutral amino acids from the ...
CDD:189012	590	miss	miss	cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase, dipeptidyl carboxypeptidase and mitochondrial intermediate peptidase.  The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases.  The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, ...
CDD:189013	546	PRK	Bacteria:65,Environmental:2	cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F (PepF).  Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus ...
CDD:189014	581	PRK	Bacteria:57	cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).  Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most ...
CDD:189015	538	PRK	Bacteria:111	cd09608, M3B_PepF_3, Peptidase family M3B Oligopeptidase F (PepF).  Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most ...
CDD:189016	586	PRK	Bacteria:32	cd09609, M3B_PepF_4, Peptidase family M3B Oligopeptidase F (PepF).  Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most ...
CDD:189017	472	EUKprk	Bacteria:23,Environmental:1,Invertebrates:1,Plants:1	cd09610, M3B_PepF_5, Peptidase family M3B Oligopeptidase F (PepF).  Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy ...
CDD:187707	128	EUKprk	Bacteria:1,Invertebrates:1,Plants:1,Primates:1,Rodents:2,Vertebrates:2	cd09611, Jacalin_ZG16_like, Jacalin-like lectin domain of the zymogen granule protein 16 and related proteins.  ZG16p is a conserved secreted vertebrate protein with tissue-specific expression profiles, which might play a role in glycoprotein secretion, perhaps as a linker protein that participates in the formation and/or transport of the zymogen granule. Its paralog ZG16b (PAUF) has been associated with ...
CDD:187708	130	EUK	Plants:16	cd09612, Jacalin, Jacalin-like plant lectin domain.  Jacalin-like lectins are sugar-binding protein domains mostly found in plants. They adopt a beta-prism topology consistent with a circularly permuted three-fold repeat of a structural motif. Proteins containing this domain may bind mono- or oligosaccharides with high specificity. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other ...
CDD:187710	128	EUKprk	Bacteria:6,Plants:1	cd09614, griffithsin_like, Jacalin-like lectin domain of griffithsin and related proteins.  Griffithsin is a lectin isolated from a red alga, which has shown potential as an inhibitor of viral entry, exhibiting antiviral activity against HIV and SARS. The biological functions of griffithsin and griffithsin-like proteins with respect to their source organisms are not known.
CDD:187737	222	EUK	Invertebrates:9,Plants:8,Primates:2,Vertebrates:2	cd09616, Peptidase_C12_UCH_L1_L3, Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families L1 and L3.  This ubiquitin C-terminal hydrolase (UCH) family includes UCH-L1 and UCH-L3, the two members sharing around 53% sequence identity as well as conserved catalytic residues. Both enzymes hydrolyze carboxyl terminal esters and amides of ubiquitin (Ub). UCH-L1, in dimeric form, has additional enzymatic ...
CDD:187738	219	EUK	Invertebrates:6,Plants:8,Primates:1,Rodents:1,Vertebrates:3	cd09617, Peptidase_C12_UCH37_BAP1, Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1.  This ubiquitin C-terminal hydrolase (UCH) family includes UCH37 (also known as UCH-L5) and BRCA1-associated protein-1 (BAP1). They contain a UCH catalytic domain as well as an additional C-terminal extension which plays a role in protein-protein interactions. UCH37 is ...
CDD:187676	186	PRK	Bacteria:41,nodiv:1	cd09618, CBM9_like_2, DOMON-like type 9 carbohydrate binding module.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues ...
CDD:187677	187	PRK	Bacteria:13	cd09619, CBM9_like_4, DOMON-like type 9 carbohydrate binding module.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and ...
CDD:187678	200	EUKprk	Bacteria:39,Invertebrates:4,Plants:5	cd09620, CBM9_like_3, DOMON-like type 9 carbohydrate binding module.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly ...
CDD:187679	188	PRK	Bacteria:7	cd09621, CBM9_like_5, DOMON-like type 9 carbohydrate binding module.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and ...
CDD:187680	265	PRK	Bacteria:16	cd09622, CBM9_like_HisKa, DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases.  Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions ...
CDD:187681	224	PRK	Bacteria:13	cd09623, DOMON_EBDH, Heme-binding domain of bacterial ethylbenzene dehydrogenase.  Ethylbenzene dehydrogenase (EBDH) is a bacterial molybdopterin enzyme. It catalyzes anaerobic hydroxylation of alkylaromatic compounds to secondary alcohols. The DOMON domain in EBDH and related proteins, typically called the gamma subunit, binds a heme; its function in the catalytic mechanism is unclear. It co-occurs with a molybdopterin-binding subunit and an iron-sulfur protein. ...
CDD:187683	348	PRK	Bacteria:22	cd09625, DOMON_like_cytochrome, DOMON-like domain of an uncharacterized protein family.  This family of uncharacterized bacterial proteins contains a DOMON-like domain and an N-terminal B- or C-type cytochrome domain. DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They ...
CDD:187684	220	PRK	Bacteria:27	cd09626, DOMON_glucodextranase_like, DOMON-like domain of various glycoside hydrolases.  This DOMON-like domain is found at the C-terminus of various bacterial proteins that play roles in metabolizing carbohydrates, such as glucodextranase (hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end), glucan alpha-1,4-glucosidase, pullulanase (degrades pullulan, a polysaccharide built from maltotriose units), arabinogalactan ...
CDD:187685	179	PRK	Bacteria:29	cd09627, DOMON_murB_like, Domon-like domain of UDP-N-acetylenolpyruvoylglucosamine reductase.  UDP-N-acetylenolpyruvoylglucosamine reductase (murB) catalyzes an essential step in peptidoglycan biosynthesis, the reduction of UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramate. A subset of these FAD-dependent enzymes contains a C-terminal DOMON-like domain. DOMON domains can be found in all three kindgoms of life and are a diverse group of ligand binding ...
CDD:187686	169	EUK	Invertebrates:9,Mammals:1,Vertebrates:1	cd09628, DOMON_SDR_2_like, DOMON domain of stromal cell-derived receptor 2 (ferric chelate reductase 1) and related proteins.  Stromal cell-derived receptor 2 (or ferric chelate reductase 1) reduces Fe(3+) to Fe(2+) ahead of iron transport from the endosome to the cytoplasm. This transmembrane protein is a member of the cytochrome b561 family and contains a DOMON domain which may bind to heme or another ligand. DOMON-like domains can be ...
CDD:187687	152	EUK	Plants:14	cd09629, DOMON_CIL1_like, DOMON-like domain of Brassica carinata CIL1 and similar proteins.  Brassica carinata CIL1 has been described as involved in suppression of axillary meristem development. It contains a single DOMON domain, the function of which is unclear. Members in this diverse family of plant proteins may have a cytochrome b561 domain C-terminal to the DOMON domain, some members from Arabidopsis have been characterized as auxin-responsive or auxin-induced ...
CDD:187688	168	EUK	Plants:29	cd09630, CDH_like_cytochrome, Heme-binding cytochrome domain of fungal cellobiose dehydrogenases.  Cellobiose dehydrogenase (CellobioseDH or CDH) is an extracellular fungal oxidoreductase that degrades both lignin and cellulose. Specifically, CDHs oxidize cellobiose, cellodextrins, and lactose to corresponding lactones, utilizing a variety of electron acceptors. Class-II CDHs are monomeric hemoflavoenzymes that are comprised of a b-type cytochrome domain linked to a ...
CDD:187689	138	EUKprk	Bacteria:10,Environmental:1,Invertebrates:23,Mammals:1,Plants:17,Primates:1,Vertebrates:3	cd09631, DOMON_DOH, DOMON-like domain of copper-dependent monooxygenases and related proteins.  This diverse family characterizes DOMON domains found in dopamine beta-hydroxylase (DBH), monooxygenase X (MOX), and various other proteins, some of which contain DOMON domains exclusively; the family is not restricted to eukaryotes. DBH is a membrane-bound enzyme that converts dopamine to ...
CDD:193606	109	PRK	Bacteria:16	cd09632, PliI_like, Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins.  Aeromonas hydrophila PliI is a dimeric periplasmic protein that enables bacteria to resist permeabilization of the outer membrane by the bactericidal action of lysozyme. PliI may be a direct inhibitor of lysozyme that inserts a conserved loop into the active site of type I (invertebrate) lysozymes.
CDD:193607	131	EUK	Invertebrates:18,Plants:5,Primates:1,Vertebrates:3	cd09633, Deltex_C, Domain found at the C-terminus of deltex-like.  The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a ...
CDD:187766	317	PRK	Bacteria:107,Environmental:1	cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold ...
CDD:187767	260	PRK	Bacteria:2	cd09636, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a ...
CDD:187768	178	miss	miss	cd09637, Cas4_I-A_I-B_I-C_I-D_II-B, CRISPR/Cas system-associated protein Cas4.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster.
CDD:187769	90	miss	miss	cd09638, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.
CDD:187770	353	miss	miss	cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I.
CDD:193608	200	PRK	Bacteria:166,Environmental:1	cd09641, Cas3''_I, CRISPR/Cas system-associated protein Cas3''.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I.
CDD:187773	574	miss	miss	cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-C subtype; also known as Csd1 family.
CDD:187774	799	PRK	Bacteria:2	cd09643, Csn1, CRISPR/Cas system-associated protein Cas9.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II.
CDD:213407	223	PRK	Bacteria:12	cd09644, Csn2, CRISPR/Cas system-associated protein Csn2.  Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage ...
CDD:187776	137	PRK	Bacteria:49,Environmental:1	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.
CDD:187778	95	PRK	Bacteria:1	cd09647, Csm2_III-A, CRISPR/Cas system-associated protein Csm2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-A.
CDD:187780	143	PRK	Bacteria:13	cd09649, Cas5_I-A, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.
CDD:187781	189	PRK	Bacteria:1	cd09650, Cas7_I, CRISPR/Cas system-associated RAMP superfamily protein Cas7.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as MJ0381 family.
CDD:187782	198	PRK	Bacteria:34	cd09651, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.
CDD:187783	190	PRK	Bacteria:1	cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex; RAMP superfamily protein; Possesses double RRM/ferredoxin fold.
CDD:187785	127	PRK	Bacteria:4	cd09654, Cmr5_III-B, CRISPR/Cas system-associated protein Cmr5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-B.
CDD:187786	198	miss	miss	cd09655, CasRa_I-A, CRISPR/Cas system-associated transcriptional regulator CasRa.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system.
CDD:187787	318	PRK	Bacteria:10	cd09656, Cmr3_III-B, CRISPR/Cas system-associated RAMP superfamily protein Cmr3.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex.
CDD:187788	132	miss	miss	cd09657, Cmr1_III-B, CRISPR/Cas system-associated RAMP superfamily protein Cmr1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex.
CDD:187791	394	miss	miss	cd09660, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187792	210	PRK	Bacteria:1	cd09661, Cmr6_III-B, CRISPR/Cas system-associated RAMP superfamily protein Cmr6.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex.
CDD:187793	365	miss	miss	cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein.
CDD:187794	301	miss	miss	cd09663, Csm4_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm4.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein.
CDD:187800	477	PRK	Bacteria:1	cd09669, Cse1_I-E, CRISPR/Cas system-associated protein Cse1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; subunit of the Cascade complex; signature gene for I-E subtype; also known as Cse1/CasA/YgcL family.
CDD:187801	152	PRK	Bacteria:1	cd09670, Cse2_I-E, CRISPR/Cas system-associated protein Cse2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype;.
CDD:187802	346	PRK	Bacteria:1	cd09671, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187810	475	PRK	Bacteria:14	cd09679, Cas10_III, CRISPR/Cas system-associated protein Cas10.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; MTH326-like has inactivated polymerase catalytic domain; alr1562 and slr7011 - predicted only on the basis of size, presence ...
CDD:187811	650	PRK	Bacteria:19	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family.
CDD:187813	242	miss	miss	cd09682, Cmr4_III-B, CRISPR/Cas system-associated RAMP superfamily protein Cmr4.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex.
CDD:187815	215	miss	miss	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein.
CDD:187818	302	miss	miss	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Cst2/DevR family.
CDD:187822	381	miss	miss	cd09691, Cas8b_I-B, CRISPR/Cas system-associated protein Cas8b.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-B subtype; also known as Csh1 family.
CDD:187824	202	PRK	Bacteria:12	cd09693, Cas5_I, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.
CDD:187832	909	PRK	Bacteria:10	cd09701, Cas10_III, CRISPR/Cas system-associated protein Cas10.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, inactivated palm domain and Zn-ribbon; signature gene for type III.
CDD:187850	262	miss	miss	cd09719, Cas1_I-E, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal ...
CDD:187851	275	PRK	Bacteria:1	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer intergration. Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a ...
CDD:187852	338	PRK	Bacteria:1	cd09721, Cas1_I-C, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a ...
CDD:187853	320	PRK	Bacteria:1	cd09722, Cas1_I-B, CRISPR/Cas system-associated protein Cas1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a ...
CDD:187856	79	PRK	Bacteria:89	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.
CDD:187857	177	PRK	Bacteria:66	cd09726, RAMP_I_III, CRISPR/Cas system-associated RAMP superfamily protein.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily proteins.
CDD:187858	210	PRK	Bacteria:47,Environmental:1	cd09727, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas6e.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6e is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-E subtype; Homologous to Cas6 (RAMP superfamily protein); Possesses double ...
CDD:187859	400	PRK	Bacteria:15	cd09728, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187860	465	PRK	Bacteria:51,Environmental:1	cd09729, Cse1_I-E, CRISPR/Cas system-associated protein Cse1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; subunit of the Cascade complex; signature gene for I-E subtype; also known as Cse1/CasA/YgcL family.
CDD:187861	579	PRK	Bacteria:16	cd09730, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family.
CDD:187862	141	PRK	Bacteria:53,Environmental:1	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype;.
CDD:187863	221	PRK	Bacteria:19	cd09732, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187864	193	PRK	Bacteria:8,Environmental:1	cd09733, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex; RAMP superfamily protein; Possesses double RRM/ferredoxin fold; also known as AF0072 family.
CDD:187866	377	PRK	Bacteria:18	cd09735, Csy1_I-F, CRISPR/Cas system-associated protein Csy1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins; Predicted subunit of the Cascade complex; signature gene for I-F subtype; also known as Csy1 family.
CDD:187867	289	PRK	Bacteria:25	cd09736, Csy2_I-F, CRISPR/Cas system-associated RAMP superfamily protein Csy2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas5 ortholog.
CDD:187868	329	PRK	Bacteria:23	cd09737, Csy3_I-F, CRISPR/Cas system-associated RAMP superfamily protein Csy3.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas7 ortholog.
CDD:187870	185	PRK	Bacteria:31	cd09739, Cas6_I-F, CRISPR/Cas system-associated RAMP superfamily protein Cas6f.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6f is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-F subtype; Possesses RRM fold; also known as Csy4 family.
CDD:187872	219	PRK	Bacteria:15	cd09741, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187873	183	PRK	Bacteria:25	cd09742, Csm6_III-A, CRISPR/Cas system-associated protein Csm6.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems; also known as APE2256 family.
CDD:187878	378	PRK	Bacteria:10	cd09747, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with ...
CDD:187879	356	PRK	Bacteria:21	cd09748, Cmr3_III-B, CRISPR/Cas system-associated RAMP superfamily protein Cmr3.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex.
CDD:187880	119	PRK	Bacteria:17	cd09749, Cmr5_III-B, CRISPR/Cas system-associated protein Cmr5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-B.
CDD:187534	198	miss	miss	cd09752, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.
CDD:187883	147	miss	miss	cd09753, Cas5_I-A, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.
CDD:187884	65	PRK	Bacteria:10	cd09754, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family.
CDD:187885	62	PRK	Bacteria:29,Environmental:1	cd09755, Cas2_I-E, CRISPR/Cas system-associated protein Cas2.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.
CDD:187886	135	miss	miss	cd09756, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.
CDD:187887	569	PRK	Bacteria:35	cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-C subtype; also known as Csd1 family.
CDD:187735	101	PRK	Bacteria:14	cd09766, Csx15_I-U, CRISPR/Cas system-associated protein Csx15.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein loosely associated with CRISPR/Cas systems; some are fused to AAA ATPase domain, also known as TTE2665 family.
CDD:187705	652	PRK	Bacteria:3	cd09767, Csx17_I-U, CRISPR/Cas system-associated protein Csx17.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins; Predicted subunit of the Cascade complex;.
CDD:188874	301	EUK	Invertebrates:7,Vertebrates:2	cd09768, Luminal_EIF2AK3, The Luminal domain, a dimerization domain, of the Serine/Threonine protein kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 3.  The Luminal domain is a dimerization domain present in eukaryotic translation Initiation Factor 2-Alpha Kinase 3 (EIF2AK3), also called PKR-like Endoplasmic Reticulum Kinase (PERK). EIF2AK3 is a serine/threonine protein kinase (STK) and a type I transmembrane protein that is ...
CDD:188875	295	EUK	Invertebrates:11,Plants:14,Primates:1,Vertebrates:2	cd09769, Luminal_IRE1, The Luminal domain, a dimerization domain, of the Serine/Threonine protein kinase, Inositol-requiring protein 1.  The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), a serine/threonine protein kinase (STK) and a type I transmembrane protein that is localized in the endoplasmic reticulum (ER). IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling ...
CDD:197361	87	EUK	Invertebrates:5,Primates:1,Rodents:2,Vertebrates:4	cd09803, UBAN, polyubiquitin binding domain of NEMO and related proteins.  NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this ...
CDD:197362	121	EUK	Invertebrates:23,Plants:23,Primates:1,Vertebrates:3	cd09804, Dcp1, mRNA decapping enzyme 1 (Dcp1).  mRNA decapping enzyme 1 (Dcp1), together with Dcp2, is part of the decapping complex which catalyzes the removal of the 5' cap structure of mRNA. This decapping reaction is an essential step in mRNA degradation, by exposing the 5' end for exonucleolytic digestion. Dcp1 binds to the N-terminal helical domain of catalytic subunit Dcp2 and enhances its function by promoting Dsp2's ...
CDD:187665	281	EUK	Invertebrates:1,Primates:1,Rodents:1,Vertebrates:3	cd09805, type2_17beta_HSD-like_SDR_c, human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs.  17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. This classical-SDR subgroup includes the human proteins: type 2 17beta-HSD, type 6 17beta-HSD,  type 2 11beta-HSD, dehydrogenase/reductase SDR family member 9,  ...
CDD:187673	335	EUK	Invertebrates:1,Plants:5,Primates:1	cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid dehydrogenase-like protein)-like, extended (e) SDRs.  This subgroup includes human NSDHL and related proteins. These proteins have the characteristic active site tetrad of extended SDRs, and also have a close match to their  NAD(P)-binding motif.  Human NSDHL is a 3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which functions in the cholesterol biosynthetic pathway.  3 beta-HSD ...
CDD:212499	224	PRK	Bacteria:23	cd09815, TP_methylase, S-AdoMet dependent tetrapyrrole methylases.  This family uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt ...
CDD:188648	490	EUKprk	Bacteria:11,Invertebrates:5,Rodents:1,Vertebrates:3	cd09816, prostaglandin_endoperoxide_synthase, Animal prostaglandin endoperoxide synthase and related bacterial proteins.  Animal prostaglandin endoperoxide synthases, including prostaglandin H2 synthase and a set of similar bacterial proteins which may function as cyclooxygenases. Prostaglandin H2 synthase catalyzes the synthesis of prostaglandin H2 from arachidonic acid. In two reaction steps, arachidonic acid is ...
CDD:188649	550	EUK	Plants:14	cd09817, linoleate_diol_synthase_like, Linoleate (8R)-dioxygenase and related enzymes.  These fungal enzymes, related to animal heme peroxidases, catalyze the oxygenation of linoleate and similar targets. Linoleate (8R)-dioxygenase, also called linoleate:oxygen 7S,8S-oxidoreductase, generates (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate as a product. Other members are 5,8-linoleate dioxygenase (LDS, ppoA) and linoleate 10R-dioxygenase (ppoC), involved in the ...
CDD:188650	484	EUKprk	Bacteria:11,Invertebrates:2,Plants:4	cd09818, PIOX_like, Animal heme oxidases similar to plant pathogen-inducible oxygenases.  This is a diverse family of oxygenases related to the animal heme peroxidases, with members from plants, animals, and bacteria. The plant pathogen-inducible oxygenases (PIOX) oxygenate fatty acids into 2R-hydroperoxides. They may be involved in the hypersensitive reaction, rapid and localized cell death induced by infection with pathogens, and the ...
CDD:188651	465	PRK	Bacteria:23	cd09819, An_peroxidase_bacterial_1, Uncharacterized bacterial family of heme peroxidases.  Animal heme peroxidases are diverse family of enzymes which are not restricted to metazoans; members are also found in fungi, and plants, and in bacteria - like this family of uncharacterized proteins.
CDD:188652	558	EUK	Invertebrates:6,Primates:1,Vertebrates:2	cd09820, dual_peroxidase_like, Dual oxidase and related animal heme peroxidases.  Animal heme peroxidases of the dual-oxidase like subfamily play vital roles in the innate mucosal immunity of gut epithelia. They provide reactive oxygen species which help control infection.
CDD:188653	570	PRK	Bacteria:10	cd09821, An_peroxidase_bacterial_2, Uncharacterized bacterial family of heme peroxidases.  Animal heme peroxidases are diverse family of enzymes which are not restricted to metazoans; members are also found in fungi, and plants, and in bacteria - like this family of uncharacterized proteins.
CDD:188654	420	EUKprk	Bacteria:12,Invertebrates:2,Plants:1,nodiv:1	cd09822, peroxinectin_like_bacterial, Uncharacterized family of heme peroxidases, mostly bacterial.  Animal heme peroxidases are diverse family of enzymes which are not restricted to animals. Members are also found in metazoans, fungi, and plants, and also in bacteria - like most members of this family of uncharacterized proteins.
CDD:188655	378	EUK	Invertebrates:17,Primates:1	cd09823, peroxinectin_like, peroxinectin_like animal heme peroxidases.  Peroxinectin is an arthropod protein that plays a role in invertebrate immunity mechanisms. Specifically, peroxinectins are secreted as cell-adhesive and opsonic peroxidases. The immunity mechanism appears to involve an interaction between peroxinectin and a transmembrane receptor of the integrin family. Human myeloperoxidase, which is included in this wider family, has also ...
CDD:188658	440	EUK	Invertebrates:9,Primates:1,Vertebrates:1	cd09826, peroxidasin_like, Animal heme peroxidase domain of peroxidasin and related proteins.  Peroxidasin is a secreted heme peroxidase which is involved in hydrogen peroxide metabolism and peroxidative reactions in the cardiovascular system. The domain co-occurs with extracellular matrix domains and may play a role in the formation of the extracellular matrix.
CDD:193604	88	EUK	Invertebrates:7,Mammals:1,Rodents:2,Vertebrates:3	cd09829, PET_testin, The PET domain of Testin.  The PET domain of Testin: Testin contains a PET domain at the N-terminus and three C-terminal LIM domains. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and is ...
CDD:193605	83	EUK	Invertebrates:5	cd09830, PET_LIMPETin_LIM-9, The PET domain of protein LIMPETin and LIM-9.  The PET domain of protein LIMPETin and LIM-9: Members of this family contain an N-terminal PETdomain and five to six LIM domains at the C-terminus. Four of the six LIM domains are highly homologous to the four-and-half LIM (FHL) domain family while the other two show sequence similarity to LIM domains of the Testin family. Thus, proteins of this family may be the recombinant product of ...
CDD:189018	507	EUK	Invertebrates:5,Plants:5,Primates:1,Vertebrates:1	cd09839, M1_TAF2, TATA binding protein (TBP) associated factor 2.  This family includes TATA binding protein (TBP) associated factor 2 (TAF2, TBP-associated factor TAFII150, transcription initiation factor TFIID subunit 2, RNA polymerase II TBP-associated factor subunit B), and has homology to the aminopeptidase N (APN) subfamily, belonging to the M1 gluzincin family. TAF2 is part of the TFIID multidomain subunit complex ...
CDD:197363	81	PRK	Bacteria:29	cd09846, DUF1312, N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312.  Domains of Unknown Function 1312 (DUF1312) are represented in at least 71 bacterial species with no functional annotation. Included in this family are N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431, having similar structure and surface features that appear to be conserved across these domain families, suggesting similar function. NusG ...
CDD:193573	388	miss	miss	cd09849, M20_Acy1L2_like_2, M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family.  Peptidase M20 family, Aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase)-like subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli , to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate ...
CDD:197368	78	EUKprk	Mammals:3,Primates:5,Rodents:1,Vertebrates:1,Viruses:8,nodiv:1	cd09851, HTLV-1-like_HR1-HR2, heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human T-cell leukemia virus type 1 (HTLV-1), and related domains.  This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane(TM) subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including HTLV-1, HTLV -2, primate Mason-Pfizer monkey virus, ...
CDD:189022	120	EUKprk	Bacteria:11,Invertebrates:1,Plants:3,Primates:1	cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily.  PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties ...
CDD:189025	128	PRK	Bacteria:8	cd09855, PIN_VapC-Smg6-like, PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, Archaeoglobus fulgidus AF0591 protein and homologs.  PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease are included in this family. Also included are the PIN domains of the ...
CDD:189027	210	EUK	Invertebrates:5,Plants:6	cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs.  Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 ...
CDD:189028	215	EUK	Invertebrates:3,Plants:9	cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs.  The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the ...
CDD:189029	174	EUKprk	Bacteria:79,Plants:1	cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs.  The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family.  Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves ...
CDD:189030	170	PRK	Phages:1	cd09860, PIN_T4-like, PIN domain of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs.  PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a ...
CDD:189031	123	PRK	Bacteria:82,Environmental:1	cd09861, PIN_VapC-like, PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs.  PIN (PilT N terminus) domain of ribonucleases (toxins) of prokaryotic toxin/antitoxin (TA) operons, involved in growth inhibition by regulating translation, are included in this family. They include the Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA ...
CDD:189032	182	EUK	Invertebrates:5,Plants:11,Primates:1,Vertebrates:2	cd09862, PIN_Rrp44, PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic homologs.  PIN (PilT N terminus) domain of the Saccharomyces cerevisiae exosome subunit Rrp44 (Ribosomal RNA-processing protein 44 or Protein Dis3 homolog) and other similar eukaryotic homologs are included in this family. The eukaryotic exosome is a conserved macromolecular complex responsible for many RNA-processing and ...
CDD:189033	125	EUK	Plants:3	cd09863, PIN_Smg6-like, PIN domain of human telomerase-binding protein EST1, Smg6, and ribosome assembly factor, Nob1, Archaeoglobus fulgidus AF0591 protein and other eukaryotic, bacterial, and archaeal homologs.  PIN (PilT N terminus) domains of eukaryotic ribonucleases such as Smg5 and Smg6, essential factors in nonsense-mediated mRNA decay (NMD), and Nob1, a ribosome assembly factor critical in pre-rRNA processing, as well as, the uncharacterized archaeal ...
CDD:189034	143	EUK	Invertebrates:13,Plants:13,Primates:1,Vertebrates:2	cd09864, PIN_Fcf1, PIN domain of rRNA-processing protein, Fcf1 (Utp24, YDR339C), and other eukaryotic homologs.  Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Component of the small subunit (SSU) processome, Fcf1 is an essential nucleolar protein that is required for processing of the 18S pre-rRNA at sites A0-A2. ...
CDD:189035	148	EUK	Plants:8	cd09865, PIN_Utp23, PIN domain of rRNA-processing protein, Utp23 (YOR004W), and other fungal homologs.  Saccharomyces cerevisiae Utp23 (U three-associated protein 23), component of the small subunit (SSU) processome, is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. The PIN (PilT N terminus) domain of this protein is a homolog of flap endonuclease-1 (FEN1)-like PIN domains, but apparently lack the H3TH domain or extensive ...
CDD:189036	147	EUK	Invertebrates:15,Plants:8,Vertebrates:2	cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi.  PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar ...
CDD:189037	261	EUKprk	Bacteria:8,Environmental:2,Invertebrates:4,Plants:1	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs.  Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction ...
CDD:189038	249	EUK	Invertebrates:4,Plants:3	cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs.  The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing ...
CDD:189039	233	EUK	Plants:2	cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs.  Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and ...
CDD:189040	239	EUK	Plants:6	cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and fungal homologs.  Yeast Endonuclease 1 (YEN1) is a Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA ...
CDD:189041	128	PRK	Bacteria:35	cd09871, PIN_UPF0110, PIN domain of the VapC-like UPF0110 protein Mb0640 and homologs.  Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Mycobacterium bovis UPF0110 protein Mb0640 and other uncharacterized homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, ...
CDD:189042	127	EUKprk	Bacteria:52,Plants:1	cd09872, PIN_Sll0205, PIN domain of the VapC-like Sll0205 protein and homologs.  Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, ...
CDD:189043	127	PRK	Bacteria:97,Environmental:3	cd09873, PIN_Pae0151, PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs.  Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Pyrobaculum aerophilum proteins, Pae0151 and Pae2754, and homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and ...
CDD:189044	135	PRK	Bacteria:31	cd09874, PIN_MT3492, PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 and other uncharacterized, annotated PilT protein domain proteins.  Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis CDC1551, hypothetical protein MT3492, and similar bacterial and archaeal proteins are included in this subfamily. They are PIN domain homologs of the Mycobacterium tuberculosis VapC and ...
CDD:189045	121	PRK	Bacteria:13	cd09875, PIN_VapC-FitB-like, PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs.  PIN (PilT N terminus) domain-containing proteins of prokaryotic toxin/antitoxin (TA) operons, such as, Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA operon, and Neisseria gonorrhoeae FitB of the FitAB (fast intracellular ...
CDD:189046	109	EUKprk	Bacteria:4,Invertebrates:7,Plants:18,Vertebrates:2	cd09876, PIN_Nob1, PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein Ta0041-like homologs.  PIN (PilT N terminus) domain of the Saccharomyces cerevisiae ribosome assembly factor, Nob1 (Nin one binding) protein, the Thermoplasma acidophilum DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic and archaeal homologs are included in this family.  The Nob1 PIN domain binds the ...
CDD:189047	127	PRK	Bacteria:30	cd09877, PIN_YacL, PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs.  PIN (PilT N terminus) domain of the conserved membrane protein of unknown function of Thermus Thermophilus Hb8, Bacillus subtilis YacL and other similar homologs are included in this family. These PIN domains are structural homologs of flap endonuclease-1 (FEN1)-like PIN domains, but lack the extensive arch/clamp region  and the H3TH ...
CDD:189048	124	PRK	Bacteria:18	cd09878, PIN_VirB11L-ATPase, PIN domain of the Methanocaldococcus Jannaschii Dsm 2661 protein, Thermococcus sibiricus MM 739 predicted ATPase, and other similar archaeal homologs.  PIN (PilT N terminus) domain present N-terminal of AAA+, VirB11-like ATPases, as well as, the PIN domains of proteins from Methanopyrus kandleri AV19 and Thermococcus sibiricus MM 739, and other similar archaeal homologs are included in this family. Several members of this subfamily ...
CDD:189049	117	PRK	Bacteria:35,Environmental:1	cd09879, PIN_AF0591, PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs.  PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. These PIN domains are structural homologs of flap endonuclease-1 (FEN1)-like PIN domains, but lack the extensive arch/clamp region  and the H3TH (helix-3-turn-helix) domain, an atypical ...
CDD:189050	139	EUKprk	Bacteria:14,Invertebrates:12,Plants:16,Primates:1,Vertebrates:1	cd09880, PIN_Smg5-Smg6-like, PIN domain.  PIN (PilT N terminus) domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and homologs are included in this family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound ...
CDD:189051	127	PRK	Bacteria:155,Environmental:1	cd09881, PIN_VapC-FitB, PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs.  PIN (PilT N terminus) domain-containing proteins of prokaryotic toxin/antitoxin (TA) operons, such as, Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA operon, and Neisseria gonorrhoeae FitB of the FitAB (fast ...
CDD:189052	128	PRK	Bacteria:28	cd09882, PIN_MtRv0301, PIN domain of the Rv0301 toxin of Mycobacterium tuberculosis and other uncharacterized, annotated PilT protein domain proteins.  Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis protein Rv0301 and similar bacterial proteins are included in this subfamily. They are PIN domain homologs of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic ...
CDD:189053	147	PRK	Bacteria:54	cd09883, PIN_PhoHL-ATPase, PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains.  PIN (PilT N terminus) domain of Smg6-like bacterial proteins with C-terminal PhoH-like ATPase domains and other similar homologs are included in this family. Eukaryotic Smg5 and Smg6 nucleases are essential factors in nonsense-mediated mRNA decay (NMD), a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature ...
CDD:189055	182	EUK	Invertebrates:7,Vertebrates:1	cd09885, PIN_Smg6, PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs.  Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, ...
CDD:193575	97	PRK	Bacteria:11	cd09886, NGN_SP, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP).  The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding ...
CDD:193576	82	PRK	Bacteria:9,Environmental:1	cd09887, NGN_Arch, Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain.  The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. ...
CDD:193577	86	EUK	Invertebrates:7,Plants:11,Vertebrates:1	cd09888, NGN_Euk, Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1).  The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that ...
CDD:193578	100	PRK	Bacteria:8	cd09889, NGN_Bact_2, Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2.  The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and ...
CDD:193579	113	EUK	Plants:7	cd09890, NGN_plant, Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain.  The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains a NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein comprising an acidic N-terminus, an NGN domain, and multiple KOW ...
CDD:193580	107	EUKprk	Bacteria:86,Environmental:4,Plants:1	cd09891, NGN_Bact_1, Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1.  The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but ...
CDD:193581	96	PRK	Bacteria:44	cd09892, NGN_SP_RfaH, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH.  RfaH is an operon-specific virulence regulator, thought to have arisen from an early duplication of N-Utilization Substance G (NusG). Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are ...
CDD:193582	95	PRK	Bacteria:9	cd09893, NGN_SP_TaA, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA.  The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons ...
CDD:193583	99	PRK	Bacteria:11	cd09894, NGN_SP_AnfA1, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1.  Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and ...
CDD:193584	95	PRK	Bacteria:46	cd09895, NGN_SP_UpxY, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY.  The N-Utilization Substance G (NusG) proteins are involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding ...
CDD:188617	68	miss	miss	cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases.  The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap ...
CDD:188618	73	miss	miss	cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs.  H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a ...
CDD:188619	74	miss	miss	cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs.  H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA ...
CDD:188620	52	miss	miss	cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG.  The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 ...
CDD:188621	73	miss	miss	cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1.  The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of eukaryotic Flap Endonuclease-1 (FEN1), ...
CDD:188622	81	miss	miss	cd09902, H3TH_MKT1, H3TH domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs.  The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the structure-specific, 5' ...
CDD:188623	65	miss	miss	cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs.  Members of this subgroup include the H3TH (helix-3-turn-helix) domains of archaeal Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes ...
CDD:188624	97	miss	miss	cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease.  The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA ...
CDD:188625	108	miss	miss	cd09905, H3TH_GEN1, H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease.  Gap Endonuclease 1 (GEN1): Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. ...
CDD:188626	105	miss	miss	cd09906, H3TH_YEN1, H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease.  Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and ...
CDD:188627	70	miss	miss	cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs.  Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes ...
CDD:188628	73	miss	miss	cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease.  Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR), recombination, and telomere integrity. EXO1 functions in the MMS2 ...
CDD:197369	128	EUKprk	Mammals:2,Primates:1,Viruses:7	cd09909, HIV-1-like_HR1-HR2, heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains.  This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus ...
CDD:197364	80	PRK	Bacteria:23	cd09910, NGN-insert_like, NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN).  This family contains a unique insert (domain II, DII) found between the highly conserved N-terminal domain (NGN, domain I, D1) and C-terminal Kyrpides Ouzounis and Woese domain (KOW, domain III, DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN) proteins in bacteria ...
CDD:197365	82	PRK	Bacteria:78	cd09911, Lin0431_like, Listerrria innocua Lin0431  is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (DII).  This family contains domains homologous to Listeria innocua Lin0431, a protein that is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (domain II, DII). Lin0431 and Aquifex aeolicus NusG DII (AaeNusG DII ) have similar structure and similar basic charged surface distributions that may bind negatively charged ...
CDD:206739	180	EUKprk	Bacteria:51,Invertebrates:4,Plants:3,Primates:1,Vertebrates:3	cd09912, DLP_2, Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins.  The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an ...
CDD:206740	241	EUK	Invertebrates:9,Plants:2,Primates:1,Vertebrates:3	cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.  Dynamin-like C-terminal Eps15 homology domain (EHD) proteins regulate endocytic events; they have been linked to a number of Rab proteins through their association with mutual effectors, suggesting a coordinate role in endocytic regulation. Eukaryotic EHDs comprise four members (EHD1-4) in mammals and single members in Caenorhabditis elegans (Rme-1), Drosophila ...
CDD:206741	161	EUKprk	Bacteria:2,Environmental:1,Invertebrates:2,Rodents:1,Vertebrates:1	cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family.  RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; ...
CDD:197366	96	PRK	Bacteria:63	cd09916, CpxP_like, CpxP component of the bacterial Cpx-two-component system and related proteins.  This family summarizes bacterial proteins related to CpxP, a periplasmic protein that forms part of a two-component system which acts as a global modulator of cell-envelope stress in gram-negative bacteria. CpxP aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Functioning as a dimer, it inhibits ...
CDD:198174	85	EUK	Invertebrates:15,Plants:17,Primates:1,Vertebrates:2	cd09918, SH2_Nterm_SPT6_like, N-terminal Src homology 2 (SH2) domain found in Spt6.  N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its ...
CDD:198175	115	EUK	Invertebrates:28,Primates:1,Rodents:1,Vertebrates:6	cd09919, SH2_STAT_family, Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) family.  STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus.  STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. ...
CDD:198177	97	EUK	Invertebrates:10,Rodents:1,Vertebrates:2	cd09921, SH2_Jak_family, Src homology 2 (SH2) domain in the Janus kinase (Jak) family.  The Janus kinases (Jak) are a family of 4 non-receptor tyrosine kinases (Jak1, Jak2, Jak3, Tyk2) which respond to cytokine or growth factor receptor activation. To transduce cytokine signaling, a series of conformational changes occur in the receptor-Jak complex upon extracellular ligand binding. This results in trans-activation of the ...
CDD:198178	81	EUK	Invertebrates:19,Primates:1,Rodents:1,Vertebrates:6	cd09923, SH2_SOCS_family, Src homology 2 (SH2) domain found in  suppressor of cytokine signaling (SOCS) family.  SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. ...
CDD:198179	104	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:2	cd09925, SH2_SHC, Src homology 2 (SH2) domain found in SH2 adaptor protein C (SHC).  SHC is involved in a wide variety of pathways including regulating proliferation, angiogenesis, invasion and metastasis, and bone metabolism. An adapter protein, SHC has been implicated in Ras activation following the stimulation of a number of different receptors, including growth factors [insulin, epidermal growth factor (EGF), nerve growth ...
CDD:198182	89	EUK	Invertebrates:8,Plants:7,Primates:1,Vertebrates:1	cd09928, SH2_Cterm_SPT6_like, C-terminal Src homology 2 (SH2) domain found in Spt6.  Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. ...
CDD:198183	121	EUK	Primates:1,Rodents:1,Vertebrates:5	cd09929, SH2_BLNK_SLP-76, Src homology 2 (SH2) domain found in B-cell linker (BLNK) protein and SH2 domain-containing leukocyte protein of 76 kDa (SLP-76).  BLNK (also known as SLP-65 or BASH) is an important adaptor protein expressed in B-lineage cells. BLNK consists of a N-terminal sterile alpha motif (SAM) domain and a C-terminal SH2 domain.  BLNK is a cytoplasmic protein, but a part of it is bound to the plasma membrane through an ...
CDD:198185	99	EUK	Invertebrates:6,Primates:1,Vertebrates:5	cd09931, SH2_C-SH2_SHP_like, C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins.  The SH2 domain phosphatases (SHP-1, SHP-2/Syp, Drosophila corkscrew (csw), and Caenorhabditis elegans Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic signaling enzymes. They are both targeted and regulated by interactions of their SH2 domains with phosphotyrosine docking sites. These proteins contain two SH2 ...
CDD:198186	104	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd09932, SH2_C-SH2_PLC_gamma_like, C-terminal Src homology 2 (C-SH2) domain in Phospholipase C gamma.  Phospholipase C gamma is a signaling molecule that is recruited to the C-terminal tail of the receptor upon autophosphorylation of a highly conserved tyrosine. PLCgamma is composed of a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, 2 catalytic regions of PLC domains that flank 2 tandem SH2 domains ...
CDD:199827	101	EUKprk	Invertebrates:14,Primates:1,Rodents:2,Vertebrates:5,Viruses:1	cd09933, SH2_Src_family, Src homology 2 (SH2) domain found in the Src family of non-receptor tyrosine kinases.  The Src family kinases are nonreceptor tyrosine kinases that have been implicated in pathways regulating proliferation, angiogenesis, invasion and metastasis, and bone metabolism. It is thought that transforming ability of Src is linked to its ability to activate key signaling molecules in these ...
CDD:198190	98	EUK	Invertebrates:8,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd09937, SH2_csk_like, Src homology 2 (SH2) domain found in Carboxyl-Terminal Src Kinase (Csk).  Both the C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK) are members of the CSK-family of protein tyrosine kinases. These proteins suppress activity of Src-family kinases (SFK) by selectively phosphorylating the conserved C-terminal tail regulatory tyrosine by a similar mechanism. CHK is also capable of ...
CDD:198193	102	EUK	Invertebrates:10,Primates:1,Rodents:1	cd09940, SH2_Vav_family, Src homology 2 (SH2) domain found in the Vav family.  Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation.  Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases.  Vav family members have several conserved ...
CDD:199828	95	EUK	Invertebrates:7,Primates:1,Rodents:1,Vertebrates:4	cd09941, SH2_Grb2_like, Src homology 2 domain found in Growth factor receptor-bound protein 2 (Grb2) and similar proteins.  The adaptor proteins here include homologs Grb2 in humans, Sex muscle abnormal protein 5 (Sem-5) in Caenorhabditis elegans, and Downstream of receptor kinase (drk) in Drosophila melanogaster. They are composed of one SH2 and two SH3 domains. Grb2/Sem-5/drk regulates the Ras pathway by linking the tyrosine ...
CDD:198195	110	EUK	Invertebrates:5,Rodents:1,Vertebrates:3	cd09942, SH2_nSH2_p85_like, N-terminal Src homology 2 (nSH2) domain found in p85.  Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. p110, the catalytic subunit, is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain.  The regulatory unit is called p85 and is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, an ...
CDD:197375	181	EUK	Mammals:4,Primates:1,Rodents:1,Vertebrates:4	cd09966, UP_III_II, Uroplakin IIIb, IIIa and II.  Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large ...
CDD:197377	187	EUK	Vertebrates:1	cd09968, UP_III, Uroplakin III.  Uroplakin IIIa and IIIb, the dimerization partners of uroplakin Ib, are a members of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins ...
CDD:197378	184	miss	miss	cd09969, UP_IIIb, Uroplakin IIIb.  Uroplakin IIIb, minor isoform of the dimerization partner of uroplakin Ib, is a members of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins ...
CDD:197380	242	PRK	Bacteria:28	cd09971, SdiA-regulated, SdiA-regulated.  This model represents a bacterial family of proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. The C-terminal domain included in the alignment forms a five-bladed beta-propeller structure. The X-ray structure of Escherichia coli yjiK (C-terminal domain) exhibits binding of calcium ions (Ca++) in what appears to be an evolutionarily conserved site. Sequence analysis suggests a ...
CDD:193586	87	EUK	Invertebrates:23,Vertebrates:3,nodiv:1	cd09972, LOTUS_TDRD_OSKAR, The first LOTUS domain in Oskar and Tudor-containing proteins 5 and 7.  The first LOTUS domain in Oskar and Tudor-containing proteins 5 and 7: The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, ...
CDD:212513	217	EUKprk	Bacteria:7,Invertebrates:1,Primates:1,Rodents:1	cd09987, Arginase_HDAC, Arginase-like and histone-like hydrolases.  Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in ...
CDD:212514	262	EUKprk	Bacteria:87,Environmental:1,Invertebrates:5	cd09988, Formimidoylglutamase, Formimidoylglutamase or HutE.  Formimidoylglutamase (N-formimidoyl-L-glutamate formimidoylhydrolase; formiminoglutamase; N-formiminoglutamate hydrolase; N-formimino-L-glutamate formiminohydrolase; HutE; EC 3.5.3.8) is a metalloenzyme that catalyzes hydrolysis of N-formimidoyl-L-glutamate to L-glutamate and formamide. This enzyme is involved in histidine degradation, requiring Mn as a cofactor while ...
CDD:212515	290	EUKprk	Bacteria:84,Invertebrates:22,Plants:7,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd09989, Arginase, Arginase family.  This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous ...
CDD:212516	275	EUKprk	Bacteria:40,Environmental:1,Plants:3	cd09990, Agmatinase-like, Agmatinase-like family.  Agmatinase subfamily currently includes metalloenzymes such as agmatinase, guanidinobutyrase, guanidopropionase, formimidoylglutamase and proclavaminate amidinohydrolase. Agmatinase (agmatine ureohydrolase; SpeB; EC=3.5.3.11) is the key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield putrescine and urea. This enzyme has been found in ...
CDD:212517	306	EUK	Invertebrates:18,Plants:10,Primates:1,Vertebrates:2	cd09991, HDAC_classI, Class I histone deacetylases.  Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases ...
CDD:212518	291	EUKprk	Bacteria:78,Environmental:1,Invertebrates:5,Plants:11,Primates:1	cd09992, HDAC_classII, Histone deacetylases and histone-like deacetylases, classII.  Class II histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. This group includes animal HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and HDA15 as well as other ...
CDD:212519	275	EUKprk	Bacteria:55,Invertebrates:11,Plants:10,Vertebrates:2	cd09993, HDAC_classIV, Histone deacetylase class IV also known as histone deacetylase 11.  Class IV histone deacetylases (HDAC11; EC 3.5.1.98) are predicted Zn-dependent enzymes. This class includes animal HDAC11, plant HDA2 and related bacterial deacetylases. Enzymes in this subfamily participate in regulation of a number of different processes through protein modification (deacetylation). They catalyze hydrolysis of ...
CDD:212520	313	PRK	Bacteria:43	cd09994, HDAC_AcuC_like, Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes.  AcuC (Acetoin utilization protein) is a class I deacetylase found only in bacteria and is involved in post-translational control of the acetyl-coenzyme A synthetase (AcsA). Deacetylase AcuC works in coordination with deacetylase SrtN (class III), possibly to maintain AcsA in active (deacetylated) form and let the cell grow under low concentration of acetate. B. ...
CDD:212521	359	EUKprk	Bacteria:27,Environmental:2,Plants:6	cd09996, HDAC_classII_1, Histone deacetylases and histone-like deacetylases, classII.  This subfamily includes bacterial as well as eukaryotic Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Included in this family is a ...
CDD:212523	272	EUKprk	Bacteria:60,Invertebrates:3,Plants:5	cd09999, Arginase-like_1, Arginase-like amidino hydrolase family.  This family includes arginase, also known as arginase-like amidino hydrolase family, as well as arginase-like proteins and are found in bacteria, archaea and eykaryotes, but does not include metazoan arginases. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth ...
CDD:212525	298	EUKprk	Bacteria:62,Invertebrates:1	cd10001, HDAC_classII_APAH, Histone deacetylase class IIa.  This subfamily includes bacterial acetylpolyamine amidohydrolase (APAH) as well as other Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Mycoplana ramosa APAH exhibits broad ...
CDD:212526	336	EUK	Invertebrates:7,Primates:1,Vertebrates:1	cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6, domain 1 and histone deacetylase 10.  Histone deacetylases 6 and 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to ...
CDD:212527	350	EUK	Invertebrates:5,Vertebrates:2,nodiv:1	cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2.  Histone deacetylase 6 is a class IIb Zn-dependent enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. ...
CDD:193609	188	PRK	Bacteria:7	cd10013, Cas3''_I, CRISPR/Cas system-associated protein Cas3''.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I.
CDD:199900	47	EUK	Invertebrates:13,Plants:20,Primates:1,Vertebrates:3	cd10014, TFIIA_gamma_C, Gamma subunit of transcription initiation factor IIA, C-terminal domain.  Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from ...
CDD:197382	142	PRK	Bacteria:11	cd10016, EcoRII_N, N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins.  N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require ...
CDD:197383	98	EUK	Plants:22	cd10017, B3_DNA, Plant-specific B3-DNA binding domain.  The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more ...
CDD:198425	201	EUKprk	Bacteria:80,Invertebrates:6,Plants:8,Vertebrates:2,Viruses:5,nodiv:1	cd10027, UDG_F1, Family 1 of Uracil-DNA glycosylase (UDG) enzymes.  Uracil-DNA glycosylases (UDGs) are DNA repair enzymes that catalyze the removal of mismatched uracil from DNA to initiate DNA base excision repair pathway. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water ...
CDD:198426	162	EUKprk	Bacteria:43,Invertebrates:2,Plants:6,Primates:1,Vertebrates:2	cd10028, UDG_F2_MUG, G:T/U mismatch specific DNA glcosylase (MUG).  G:T/U mismatch specific DNA glycosylases (MUG) are classified as Family 2 of Uracil DNA glycosylase enzymes. MUG catalyzes the removal of thymine or uracil bases mispaired with guanine through the hydrolysis of their N-glycosidic bond, generating abasic sites in DNA to initiate the base excision repair pathway. G:U and G:T mismatched base pairs ...
CDD:198427	233	EUKprk	Bacteria:11,Environmental:1,Invertebrates:3,Primates:1,Vertebrates:1	cd10029, UDG_F3_SMUG, SMUG: single-strand-selective monofunctional uracil-DNA glycosylase.  SMUG (single-strand-selective monofunctional uracil-DNA glycosylase) is classified as Family 3 of Uracil-DNA glycosylase (UDG) enzymes.  SMUG is a DNA repair enzyme that catalyzes the removal of mismatched uracil and its derivatives from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a ...
CDD:198428	164	PRK	Bacteria:142,Environmental:3	cd10030, UDG_F4_TTUDGA_like, Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms.  The enzymes of Family 4 Uracil-DNA glycosylase (UDG), found only in thermophilic organisms, are thermostable enzymes. Uracil-DNA glycosylases (UDGs) are DNA repair enzymes that catalyze the removal of mismatched uracil from DNA to initiate DNA base excision repair pathway. The Thermus thermophilus enzyme TTUDGA removes uracil from both, ...
CDD:198429	203	PRK	Bacteria:34	cd10031, UDG_F5_TTUDGB_like, Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms.  Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms, are DNA base excision repair enzymes.  This family is represented by the enzyme TTUDGB from Thermus thermophilus HB8. Members of this family exhibit high structural and sequence similarity to Family 4 UDGs, which are also found in thermophilic organisms.  However, Family 4 and Family 5 ...
CDD:198430	140	EUKprk	Bacteria:105,Environmental:1,Invertebrates:1	cd10032, UDG_MUG_like, MUG-like Uracil-DNA glycosylase enzyme family.  MUG-like subfamily of Uracil-DNA glycosylase superfamily: Uracil-DNA glycosylases (UDG) catalyze the removal of uracil from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major ...
CDD:198431	172	PRK	Bacteria:39,nodiv:1	cd10033, UDG_like_1, Uncharacterized subfamily of Uracil-DNA glycosylases.  This is a subfamily of Uracil-DNA glycosylase superfamily. Uracil-DNA glycosylases (UDG) catalyze the removal of uracil from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing ...
CDD:198432	141	PRK	Bacteria:16	cd10034, UDG_like_2, Uncharacterized subfamily of Uracil-DNA glycosylases.  This is a subfamily of Uracil-DNA glycosylase superfamily. Uracil-DNA glycosylases (UDG) catalyze the removal of uracil from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T ...
CDD:198433	133	PRK	Bacteria:27	cd10035, UDG_like_3, Uncharacterized subfamily of Uracil-DNA glycosylases.  This is a subfamily of Uracil-DNA glycosylase superfamily. Uracil-DNA glycosylases (UDG) catalyze the removal of uracil from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T ...
CDD:199901	49	EUK	Invertebrates:3,Plants:2	cd10145, TFIIA_gamma_N, Gamma subunit of transcription initiation factor IIA, N-terminal helical domain.  Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less ...
CDD:199214	69	EUKprk	Bacteria:182,Invertebrates:1,Plants:11	cd10146, LabA_like_C, C-terminal domain of LabA_like proteins.  This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related ...
CDD:199902	144	PRK	Bacteria:264,Environmental:2	cd10147, Wzt_C-like, C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins.  The Escherichia coli ABC protein Wzt consists of 2 domains, a conventional ABC domain that binds ATP and utilizes its energy to transport molecules across membranes, and a C terminal domain which is responsible for its target molecule specificity. Wzt is part of the ATP-binding-cassette (ABC) transporter complex, responsible for the ...
CDD:197385	80	PRK	Bacteria:121	cd10148, CsoR-like_DUF156, Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156.  This superfamily includes various transcriptional regulators that respond to stressors including Cu(I), Ni(I), sulfite, and formaldehyde. It includes CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), Bacillus subtilis (BsCsoR), Thermus ...
CDD:199903	910	EUKprk	Bacteria:87,Environmental:1,Plants:4	cd10150, CobN_like, CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins.  Cobaltochelatase is a complex enzyme that catalyzes the insertion of cobalt into hydrogenobyrinic acid a,c-diamide, resulting in cobyrinic acid, as demonstrated for Pseudomonas denitrificans. This is an essential step in the bacterial synthesis of cobalamine (B12). The insertion of cobalt requires a complex ...
CDD:197386	82	PRK	Bacteria:9	cd10151, TthCsoR-like_DUF156, Thermus thermophilus CsoR, a Cu(I)-sensing transcriptional regulator, and related domains; this domain family was previously known as part of DUF156.  This domain family contains various Cu(I)-inducible transcriptional regulators including CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), and Thermus thermophilus (TthCsoR). CsoR regulates the expression of genes involved in copper homeostasis. For ...
CDD:197388	88	EUKprk	Bacteria:44,Plants:2,nodiv:1	cd10153, RcnR-FrmR-like_DUF156, Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156.  This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses ...
CDD:197389	86	EUKprk	Bacteria:14,Plants:1	cd10154, NreA-like_DUF156, Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156.  This domain family includes Alcaligenes xylosoxidans NreA, Psudomonas putida MreA, and related domains. The gene encoding Alcaligenes xylosoxidans NreA is part of the nre nickel resistance locus located on the pTOM9 plasmid from this bacteria; it confers low-level nickel resistance on both Ralstonia and Escherichia ...
CDD:197390	82	PRK	Bacteria:20	cd10155, BsYrkD-like_DUF156, Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156.  This domain family contains an uncharacterized protein YrkD from Bacillus subtilis and related proteins. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs ...
CDD:197391	86	PRK	Bacteria:12	cd10156, FpFrmR-Cterm-like_DUF156, C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this domain family was previously known as part of DUF156.  This domain family contains the C-terminal domain of the functionally uncharacterized protein Faecalibacterium prausnitzii A2-165 FrmR, and related domains. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such ...
CDD:197393	81	PRK	Bacteria:16	cd10158, CsoR-like_DUF156_1, Uncharacterized family 1; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156.  Uncharacterized family 1, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs ...
CDD:197394	82	PRK	Bacteria:23	cd10159, CsoR-like_DUF156_2, Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156.  Uncharacterized family 2, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs ...
CDD:212667	369	EUKprk	Bacteria:107,Environmental:1,Invertebrates:13,Mammals:1,Plants:14,Primates:1,Rodents:2,Viruses:2	cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.  HSP70 (70-kDa heat shock protein) family chaperones assist in protein folding and assembly and can direct incompetent "client" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two ...
CDD:212668	320	PRK	Bacteria:87	cd10225, MreB_like, MreB and similar proteins.  MreB is a bacterial protein which assembles into filaments resembling those of eukaryotic F-actin. It is involved in determining the shape of rod-like bacterial cells, by assembling into large fibrous spirals beneath the cell membrane. MreB has also been implicated in chromosome segregation; specifically MreB is thought to bind to and segregate the replication origin of bacterial chromosomes.
CDD:212669	312	PRK	Bacteria:124	cd10227, ParM_like, Plasmid segregation protein ParM and similar proteins.  ParM is a plasmid-encoded bacterial homolog of actin, which polymerizes into filaments similar to F-actin, and plays a vital role in plasmid segregation. ParM filaments segregate plasmids paired at midcell into the individual daughter cells. This subfamily also contains Thermoplasma acidophilum Ta0583, an active ATPase at physiological temperatures, which has a propensity to form filaments.
CDD:212670	381	EUK	Invertebrates:27,Plants:15,Primates:1,nodiv:1	cd10228, HSPA4_like_NDB, Nucleotide-binding domain of 105/110 kDa heat shock proteins including HSPA4 and similar proteins.  This subgroup includes the human proteins, HSPA4 (also known as 70-kDa heat shock protein 4, APG-2, HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps to 5q31.1), HSPA4L (also known as 70-kDa heat shock protein 4-like, APG-1, HSPH3, and OSP94; the human HSPA4L gene maps to 4q28), and HSPH1 (also known ...
CDD:212671	404	EUKprk	Bacteria:1,Invertebrates:6,Plants:23,Primates:1,Vertebrates:1	cd10229, HSPA12_like_NBD, Nucleotide-binding domain of HSPA12A, HSPA12B and similar proteins.  Human HSPA12A (also known as 70-kDa heat shock protein-12A) and HSPA12B (also known as 70-kDa heat shock protein-12B, chromosome 20 open reading frame 60/C20orf60, dJ1009E24.2) belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ...
CDD:212672	388	EUK	Invertebrates:20,Plants:25,Primates:1,Vertebrates:3	cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1 and similar proteins.  This subgroup includes human HYOU1 (also known as human hypoxia up-regulated 1, GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian HYOU1 functions as a nucleotide exchange factor (NEF) for HSPA5 (alos known as BiP, Grp78 or HspA5) ...
CDD:212673	415	PRK	Bacteria:62,Environmental:1	cd10231, YegD_like, Escherichia coli YegD, a putative chaperone protein, and related proteins.  This bacterial subfamily includes the uncharacterized Escherichia coli YegD. It belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent "client" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The ...
CDD:212674	386	EUK	Plants:8	cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of Saccharmomyces cerevisiae Ssz1pp and similar proteins.  Saccharomyces cerevisiae Ssz1p (also known as /Pdr13p/YHR064C) belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent "client" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a ...
CDD:212676	376	EUKprk	Bacteria:16,Plants:5	cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human HSPA9 and similar proteins.  This subfamily includes human mitochondrial HSPA9 (also known as 70-kDa heat shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75; HSPA9B; MTHSP75; the gene encoding HSPA9 maps to 5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae Stress-seventy subfamily Q protein 1/Ssq1p (also called Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae Stress-Seventy ...
CDD:212677	339	PRK	Bacteria:32	cd10235, HscC_like_NBD, Nucleotide-binding domain of Escherichia coli HscC and similar proteins.  This subfamily  includes Escherichia coli HscC (also called heat shock cognate protein C, Hsc62, or YbeW) and the the putative DnaK-like protein Escherichia coli ECs0689. It belongs to the heat shock protein 70 (Hsp70) family of chaperones that assist in protein folding and assembly and can direct incompetent "client" proteins towards degradation. Typically, Hsp70s ...
CDD:212678	355	PRK	Bacteria:14	cd10236, HscA_like_NBD, Nucleotide-binding domain of HscA and similar proteins.  Escherichia coli HscA (heat shock cognate protein A, also called Hsc66), belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent "client" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed ...
CDD:199834	358	PRK	Bacteria:13	cd10276, BamB_YfgL, Beta-barrel assembly machinery (Bam) complex component B and related proteins.  BamB (YflG) is a non-essential component of the beta-barrel assembly machinery (Bam), a multi-subunit complex that inserts proteins with beta-barrel topology into the outer membrane. BamB has been found to interact with BamA, which in turn binds and stabilizes pre-folded beta-barrel proteins; it has been suggested that BamB participates in the stabilization.
CDD:199835	529	PRK	Bacteria:15	cd10277, PQQ_ADH_I, Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase).  This bacterial family of homodimeric ethanol dehydrogenases utilize pyrroloquinoline quinone (PQQ) as a cofactor. It represents proteins whose expression may be induced by ethanol, and which are similar to quinoprotein methanol dehydrogenases, but have higher specificities for ethanol and other primary and secondary alcohols. Dehydrogenases with PQQ ...
CDD:199836	553	PRK	Bacteria:16	cd10278, PQQ_MDH, Large subunit of methanol dehydrogenase (moxF).  Methanol dehydrogenase is a key enzyme in the utilization of C1 compounds as a source of energy and carbon by bacteria. It catalyzes the oxidation of methanol to formaldehyde, transfering two electrons per methanol to cytochrome c(L) as the acceptor. Methanol dehydrogenase belongs to a family of dehydrogenases with pyrroloquinoline quinone (PQQ) as cofactor, which also includes dehydrogenases ...
CDD:199837	549	PRK	Bacteria:18,Environmental:1	cd10279, PQQ_ADH_II, PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II).  This family of monomeric and soluble type II alcohol dehydrogenases utilizes pyrroloquinoline quinone (PQQ) as a cofactor and is related to ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller.
CDD:199838	616	PRK	Bacteria:41,Environmental:2	cd10280, PQQ_mGDH, Membrane-bound PQQ-dependent glucose dehydrogenase.  This bacterial subfamily of enzymes belongs to the dehydrogenase family with pyrroloquinoline quinone (PQQ) as cofactor, and is the only subfamily that is bound to the membrane. Glucose dehydrogenase converts D-glucose to D-glucono-1,5-lactone in a reaction that is coupled with the respiratory chain in the periplasmic oxidation of sugars and alcohols in gram-negative bacteria. ...
CDD:197336	253	EUKprk	Bacteria:22,Invertebrates:1	cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases.  This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of ...
CDD:197337	256	EUKprk	Bacteria:5,Invertebrates:6,Mammals:1,Rodents:2,Vertebrates:8	cd10282, DNase1, Deoxyribonuclease 1.  Deoxyribonuclease 1 (DNase1, EC 3.1.21.1), also known as DNase I, is a Ca2+, Mg2+/Mn2+-dependent secretory endonuclease, first isolated from bovine pancreas extracts. It cleaves DNA preferentially at phosphodiester linkages next to a pyrimidine nucleotide, producing 5'-phosphate terminated polynucleotides with a free hydroxyl group on position 3'. It generally produces ...
CDD:197338	266	EUKprk	Bacteria:47,Environmental:1,Invertebrates:2,Plants:1,Vertebrates:3	cd10283, MnuA_DNase1-like, Mycoplasma pulmonis MnuA nuclease-like.  This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a ...
CDD:198438	199	EUK	Mammals:3,Rodents:5,Vertebrates:4	cd10288, prolactin_like, Prolactin (PRL or PRL1), chorionic somatomammotropin, and related pituitary gland hormones.  Prolactin is primarily responsible for stimulating milk production and breast development in mammals. Aside from roles in reproduction, various functions have been attributed to prolactin, more than for other pituitary gland hormones combined. These are roles in growth and development, metamorphosis, metabolism of lipids, ...
CDD:198322	82	EUK	Invertebrates:12,Plants:12,Primates:1,Rodents:1	cd10289, GST_C_AaRS_like, Glutathione S-transferase C-terminal-like, alpha helical domain of various Aminoacyl-tRNA synthetases and similar domains.  Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl-tRNA synthetase (AaRS)-like subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of some eukaryotic AaRSs, as well as similar domains found in proteins involved in protein ...
CDD:198324	110	EUKprk	Bacteria:12,Plants:4	cd10291, GST_C_YfcG_like, C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins.  Glutathione S-transferase (GST) C-terminal domain family, YfcG-like subfamily; composed of the Escherichia coli YfcG and related proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and ...
CDD:198337	100	EUK	Plants:18	cd10304, GST_C_Arc1p_N_like, Glutathione S-transferase C-terminal-like, alpha helical domain of the Aminoacyl tRNA synthetase cofactor 1 and similar proteins.  Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl tRNA synthetase cofactor 1 (Arc1p)-like subfamily; Arc1p, also called GU4 nucleic binding protein 1 (G4p1) or p42, is a tRNA-aminoacylation and nuclear-export cofactor. It contains a domain in the N-terminal region with similarity to the ...
CDD:198338	101	EUK	Invertebrates:11,Plants:2,Vertebrates:3,nodiv:1	cd10305, GST_C_AIMP3, Glutathione S-transferase C-terminal-like, alpha helical domain of Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein 3.  Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein (AIMP) 3 subfamily; AIMPs are non-enzymatic cofactors that play critical roles in the assembly and formation of a macromolecular multi-tRNA ...
CDD:198339	87	EUK	Plants:11	cd10306, GST_C_GluRS_N, Glutathione S-transferase C-terminal-like, alpha helical domain of Glutamyl-tRNA synthetase.  Glutathione S-transferase (GST) C-terminal domain family, Glutamyl-tRNA synthetase (GluRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of GluRS from lower eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This ...
CDD:198341	82	EUK	Invertebrates:9,Plants:2,Primates:1	cd10308, GST_C_eEF1b_like, Glutathione S-transferase C-terminal-like, alpha helical domain of eukaryotic translation Elongation Factor 1 beta.  Glutathione S-transferase (GST) C-terminal domain family, eukaryotic translation Elongation Factor 1 beta (eEF1b) subfamily; eEF1b is a component of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists ...
CDD:198342	81	EUK	Invertebrates:7,Vertebrates:2	cd10309, GST_C_GluProRS_N, Glutathione S-transferase C-terminal-like, alpha helical domain of bifunctional Glutamyl-Prolyl-tRNA synthetase.  Glutathione S-transferase (GST) C-terminal domain family, bifunctional GluRS-Prolyl-tRNA synthetase (GluProRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of GluProRS from higher eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that ...
CDD:197304	156	PRK	Bacteria:34	cd10311, PLDc_N_DEXD_c, N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain.  N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a ...
CDD:198457	209	EUK	Invertebrates:10,Primates:1,Rodents:1,Vertebrates:7	cd10314, FAM20_C, C-terminal putative kinase domain of FAM20 (family with sequence similarity 20) proteins.  This family contains the C-terminal domain of FAM20A, -B, -C and related proteins. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by ...
CDD:199215	100	PRK	Bacteria:49	cd10315, CBM41_pullulanase, Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes.  Pullulanases (EC 3.2.1.41) are a group of starch-debranching enzymes, catalyzing the hydrolysis of the alpha-1,6-glucosidic linkages of alpha-glucans, preferentially pullulan. Pullulan is a polysaccharide in which alpha-1,4 linked maltotriosyl units are combined via an alpha-1,6 linkage. These enzymes are of importance in the starch industry, where they are used to ...
CDD:199904	92	EUKprk	Bacteria:12,Invertebrates:1,Plants:27	cd10316, RGL4_M, Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase.  The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 ...
CDD:199905	161	EUKprk	Bacteria:3,Plants:8	cd10317, RGL4_C, C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase.  The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of ...
CDD:199906	564	EUKprk	Bacteria:23,Invertebrates:1,Plants:1	cd10318, RGL11, Rhamnogalacturonan lyase of the polysaccharide lyase family 11.  The rhamnogalacturonan lyase of the polysaccharide lyase family 11 (RGL11) cleaves glycoside bonds in polygalacturonan as well as RG (rhamnogalacturonan) type-I through a beta-elimination reaction. Functionally characterized members of this family, YesW and YesX from Bacillus subtilis, cleave glycoside bonds between rhamnose and galacturonic acid residues in ...
CDD:198439	177	EUK	Invertebrates:4,Primates:1,Rodents:2	cd10319, EphR_LBD, Ligand Binding Domain of Ephrin Receptors.  Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). They are subdivided into 2 groups, A and B type receptors, depending on their ligand ephrin-A or ephrin-B, respectively. In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with ...
CDD:199907	265	EUKprk	Bacteria:1,Invertebrates:1,Plants:7	cd10320, RGL4_N, N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase.  The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination ...
CDD:199216	127	EUK	Invertebrates:5,Plants:1,Primates:1	cd10321, RNase_Ire1_like, RNase domain (also known as the kinase extension nuclease domain) of Ire1 and RNase L.  This RNase domain is found in the multi-functional protein Ire1; Ire1 also contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR). The UPR is activated when protein misfolding is detected ...
CDD:271357	454	EUKprk	Bacteria:181,Environmental:2,Primates:1	cd10322, SLC5sbd, Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain.  This family represents the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporter family or solute sodium symporter family) that co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. Family members include: the human glucose (SGLT1, 2, 4, 5), chiro-inositol (SGLT5), ...
CDD:271358	414	PRK	Bacteria:16	cd10323, SLC-NCS1sbd, nucleobase-cation-symport-1 (NCS1) transporters; solute-binding domain.  NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. This family includes Microbacterium liquefaciens Mhp1, a transporter that mediates the uptake of indolyl methyl- and benzyl-hydantoins as part of a metabolic salvage pathway for their conversion ...
CDD:271359	415	EUKprk	Bacteria:11,Environmental:1,Invertebrates:23,Plants:1,Primates:1,Vertebrates:2	cd10324, SLC6sbd, Solute carrier 6 family, neurotransmitter transporters; solute-binding domain.  This family represents the solute-binding domain of SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family). These use sodium and chloride electrochemical gradients to catalyze the thermodynamically uphill movement of ...
CDD:271360	523	PRK	Bacteria:13	cd10325, SLC5sbd_vSGLT, Vibrio parahaemolyticus Na(+)/galactose cotransporter (vSGLT) and related proteins; solute binding domain.  vSGLT transports D-galactose, D-glucose, and alpha-D-fucose, with a sugar specificity in the order of D-galactose >D-fucose >D-glucose. It transports one Na+ ion for each sugar molecule, and appears to function as a monomer. vSGLT has 13 transmembrane helices (TMs): TM-1, an inverted topology repeat: TMs1-5 and TMs6-10, and TMs 11-12 ...
CDD:271361	472	PRK	Bacteria:35	cd10326, SLC5sbd_NIS-like, Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain.  NIS (product of the SLC5A5 gene) transports I-, and other anions including ClO4-, SCN-, and Br-. SMVT (product of the SLC5A6 gene) transports biotin, pantothenic acid and lipoate. This subfamily also includes SMCT1 and 2. SMCT1(the product of the SLC5A8 gene) is a high-affinity transporter of various monocarboxylates including ...
CDD:212037	472	PRK	Bacteria:17	cd10327, SLC5sbd_PanF, Na(+)/pantothenate cotransporters: PanF of Escherichia coli and related proteins; solute binding domain.  PanF catalyzes the Na+-coupled uptake of extracellular pantothenate for coenzyme A biosynthesis in cells. This subfamily belongs to the solute carrier 5 (SLC5) transporter family.
CDD:271362	472	PRK	Bacteria:25	cd10328, SLC5sbd_YidK, uncharacterized SLC5 subfamily, Escherichia coli YidK-like; solute binding domain.  Uncharacterized subfamily of the solute binding domain of the solute carrier 5 (SLC5) transporter family (also called the sodium/glucose cotransporter family or solute sodium symporter family) that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and ...
CDD:271363	538	EUKprk	Bacteria:17,Environmental:1,Invertebrates:5,Primates:1,Rodents:1	cd10329, SLC5sbd_SGLT1-like, Na(+)/glucose cotransporter SGLT1 and related proteins; solute binding domain.  This subfamily includes the solute-binding domain of SGLT proteins that cotransport Na+ with various solutes. Its members include: the human glucose (SGLT1, -2, -4, -5 ), chiro-inositol (SGLT5), and myo-inositol (SMIT) cotransporters. It also includes human SGLT3 which has been characterized as a ...
CDD:271364	531	EUK	Invertebrates:7,Primates:1,Vertebrates:1	cd10332, SLC6sbd-B0AT-like, System B(0) neutral amino acid transporter AT1, 2 and 3, and related proteins; solute-binding domain.  This subgroup includes the solute-binding domain of transmembrane transporters, which transport, i) neutral amino acids: NTT4 (also called XT1), SBAT1 (also called B0AT2, v7-3, NTT7-3), and B0AT1 (also called HND); the human genes encoding these are SLC6A17, SLC6A15, and SLC6A19 respectively, ii) glycine: ...
CDD:271365	496	PRK	Bacteria:10	cd10333, LeuT-like_sbd, Aquifex aeolicus LeuT and related proteins; solute binding domain.  LeuT is a bacterial amino acid transporter with specificity for the hydrophobic amino acids glycine, alanine, methionine, and leucine. This subgroup belongs to the solute carrier 6 (SLC6) transporter family; LeuT has been used as a structural template for understanding fundamental aspects of SLC6 function. It has an arrangement of 12 transmembrane helices (TMs), which ...
CDD:271366	480	PRK	Bacteria:62	cd10334, SLC6sbd_u1, uncharacterized bacterial and archaeal solute carrier 6 subfamily; solute-binding domain.  SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and ...
CDD:271367	440	PRK	Bacteria:202,Environmental:2,nodiv:1	cd10336, SLC6sbd_Tyt1-Like, solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain.  SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), ...
CDD:198200	136	EUK	Invertebrates:5,Primates:2,Vertebrates:3	cd10337, SH2_BCAR3, Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3.  BCAR3 is part of a growing family of guanine nucleotide exchange factors is responsible for activation of Ras-family GTPases, including Sos1 and 2, GRF1 and 2, CalDAG-GEF/GRP1-4, C3G, cAMP-GEF/Epac 1 and 2, PDZ-GEFs, MR-GEF, RalGDS family members, RalGPS, RasGEF, Smg GDS, and phospholipase C(epsilon). 12102558  21262352  BCAR3 binds ...
CDD:199829	99	EUK	Rodents:1,Vertebrates:1	cd10341, SH2_N-SH2_PLC_gamma_like, N-terminal Src homology 2 (N-SH2) domain in Phospholipase C gamma.  Phospholipase C gamma is a signaling molecule that is recruited to the C-terminal tail of the receptor upon autophosphorylation of a highly conserved tyrosine.  PLCgamma is composed of a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, 2 catalytic regions of PLC domains that flank 2 tandem SH2 domains (N-SH2, C-SH2), and ...
CDD:198224	90	EUK	Invertebrates:6,Vertebrates:3	cd10361, SH2_Fps_family, Src homology 2 (SH2) domain found in feline sarcoma, Fujinami poultry sarcoma, and fes-related (Fes/Fps/Fer) proteins.  The Fps family consists of members Fps/Fes and Fer/Flk/Tyk3. They are cytoplasmic protein-tyrosine kinases implicated in signaling downstream from cytokines, growth factors and immune receptors.  Fes/Fps/Fer contains three coiled-coil regions, an SH2 (Src-homology-2) and a TK (tyrosine kinase catalytic) ...
CDD:198251	101	EUK	Invertebrates:13,Mammals:2,Rodents:1,Vertebrates:1	cd10388, SH2_SOCS7, Src homology 2 (SH2) domain found in  suppressor of cytokine signaling (SOCS) proteins.  SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS ...
CDD:199217	129	EUK	Invertebrates:4,Plants:15,Vertebrates:1	cd10422, RNase_Ire1, RNase domain (also known as the kinase extension nuclease domain) of Ire1.  The model represents the C-terminal endoribonuclease domain of the multi-functional protein Ire1; Ire1 in addition contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR), which acts as an ER stress ...
CDD:259896	130	EUK	Invertebrates:1,Primates:1,Rodents:1,Vertebrates:4	cd10425, Ephrin-A_Ectodomain, Ectodomain of Ephrin A.  Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin (Eph) ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, ...
CDD:198378	487	PRK	Bacteria:12	cd10427, FGGY_GK_1, Uncharacterized subgroup; belongs to the glycerol kinases subfamily of the FGGY family of carbohydrate kinases.  This subgroup contains uncharacterized bacterial proteins belonging to the glycerol kinase subfamily of the FGGY family of carbohydrate kinases. The glycerol kinase subfamily includes glycerol kinases (GK; EC 2.7.1.30), and glycerol kinase-like proteins from all three kingdoms of living organisms. Glycerol is an important intermediate ...
CDD:198410	217	EUK	Invertebrates:10,Mammals:1,Primates:1,Rodents:1,Vertebrates:4	cd10428, LFG_like, Proteins similar to and including lifeguard (LFG), a putative regulator of apoptosis.  Lifeguard (LFG) inhibits Fas-mediated apoptosis and interacts with the death receptor FasR/CD95/Apo1. LFG has been shown to interact with Bax and is supposed to be integral to cellular membranes such as the ER. A close homolog, PP1201 or RECS1, appears located in the Golgi compartment and also interacts with the ...
CDD:198411	233	EUK	Invertebrates:3,Plants:11,Primates:1,Vertebrates:3	cd10429, GAAP_like, Golgi antiapoptotic protein.  GAAP (or transmembrane BAX inhibitor motif containing 4) is a regulator of apoptosis that is related to the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another ...
CDD:198412	213	EUK	Invertebrates:9,Plants:5,Primates:1,Vertebrates:2	cd10430, BI-1, BAX inhibitor (BI)-1.  Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an ...
CDD:198414	211	PRK	Bacteria:60	cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor (BI)-1/YccA-like proteins.  This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, ...
CDD:198415	205	PRK	Bacteria:23	cd10433, YccA_like, YccA-like proteins.  A prokaryotic member of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.
CDD:198381	81	PRK	Bacteria:94,Environmental:1	cd10434, GIY-YIG_UvrC_Cho, Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins.  UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding ...
CDD:198383	97	PRK	Bacteria:12,Phages:6	cd10436, GIY-YIG_EndoII_Hpy188I_like, Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins.  This family includes two different GIY-YIG enzymes, coliphage T4 non-specific endonuclease II (EndoII), and type II restriction endonuclease R.Hpy188I. They display high sequence similarity to each other, and both of them contain an extra N-terminal hairpin that lacks counterparts in ...
CDD:198384	90	EUKprk	Bacteria:13,Plants:5,nodiv:1	cd10437, GIY-YIG_HE_I-TevI_like, N-terminal catalytic domain of GIY-YIG intron endonuclease I-TevI, I-BmoI, I-BanI, I-BthII and similar proteins.  I-TevI is a site-specific GIY-YIG homing endonuclease encoded within the group I intron of the thymidylate synthase gene (td) from Escherichia coli phage T4. It functions as an endonuclease that catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele ...
CDD:198386	80	PRK	Bacteria:31	cd10439, GIY-YIG_COG3410, GIY-YIG domain of uncharacterized bacterial protein structurally related to COG3410.  This family contains a group of uncharacterized bacterial proteins. Although their function roles have not been recognized, these proteins contain a putative GIY-YIG domain in their N-terminus. Moreover, a  conserved domain COG3410 with unknown function has been found in the C-terminus of most family members.
CDD:198387	94	PRK	Bacteria:33	cd10440, GIY-YIG_COG3680, GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs.  This family includes a group of functionally uncharacterized proteins from bacteria and their eukaryotic homologs which are present only in metazoa. These proteins might have nuclease activities and possibly be engaged in DNA repair or recombination, since they share sequence homology with the catalytic GIY-YIG domain of bacterial UvrC DNA repair ...
CDD:198388	112	PRK	Bacteria:78	cd10441, GIY-YIG_COG1833, GIY-YIG domain of hypothetical proteins from archaea and their bacterial homologs.  This family includes a group of functionally uncharacterized hypothetical proteins from archaea and their bacterial homologs. These proteins contain a putative GIY-YIG domain that shows sequence homology with bacterial UvrC DNA repair proteins. Meanwhile, all of them share a C-terminal extension with semi-conserved Cys and His residues, which suggests that ...
CDD:198389	92	EUK	Invertebrates:8,Vertebrates:2	cd10442, GIY-YIG_PLEs, Catalytic GIY-YIG endonuclease domain of penelope-like elements and similar proteins.  This model corresponds to the EN domain of PLEs that contains catalytic module of the GIY-YIG endonucleases of group I bacterial/organellar introns, as well as bacterial UvrC DNA repair proteins. It can cleave DNA with low nucleotide sequence specificity. However, the PLEs EN domain is distinct from other GIY-YIG endonucleases by the ...
CDD:198390	90	EUKprk	Bacteria:21,Invertebrates:1,Viruses:7	cd10443, GIY-YIG_HE_Tlr8p_PBC-V_like, GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria.  The family includes a group of diverse uncharacterized hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of ...
CDD:198391	85	PRK	Bacteria:6,Phages:3	cd10444, GIY-YIG_SegABCDEFG, N-terminal catalytic GIY-YIG domain of bacteriophage T4 segABCDEFG gene encoding proteins.  The prototypes of Seg family are proteins SegA, B, C, D, E, F, and G encoded by five seg genes segA, B, C, D, E, F, and G in the bacteriophage T4 genome, respectively. SegA, B, C, D, E, F, and G are not encoded by introns, but free-standing homologs of the GIY-YIG family of endonucleases encoded by group I introns, which are thought to ...
CDD:198392	88	EUK	Plants:22	cd10445, GIY-YIG_bI1_like, Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins.  The prototype of this family is a putative intron-encoded mitochondrial DNA endonuclease bI1 found in mitochondrion Ustilago maydis. This protein may arise from proteolytic cleavage of an in-frame translation of COB exon 1 plus intron 1, containing the bI1 open reading frame. It contains an N-terminal truncated non-functional cytochrome b region and a ...
CDD:198393	103	PRK	Bacteria:28	cd10446, GIY-YIG_unchar_1, GIY-YIG domain of uncharacterized hypothetical protein found in bacteria.  The family includes a group of uncharacterized bacterial hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease  I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.
CDD:198394	80	PRK	Bacteria:52	cd10447, GIY-YIG_unchar_2, GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea.  The family includes a group of uncharacterized hypothetical proteins, mainly found in bacteria and a few found in archaea, with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair ...
CDD:198395	87	PRK	Bacteria:52	cd10448, GIY-YIG_unchar_3, GIY-YIG domain of uncharacterized hypothetical protein found in bacteria.  The family includes a group of uncharacterized bacterial proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease  I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.
CDD:198396	67	EUKprk	Bacteria:30,Vertebrates:1	cd10449, GIY-YIG_SLX1_like, Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs.  Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has ...
CDD:198397	70	EUKprk	Bacteria:6,Plants:7	cd10450, GIY-YIG_AtGrxS16_like, GIY-YIG domain found in CAXIP1-like proteins, iron-sulfur cluster assembly proteins, and similar proteins.  The family includes CAX-interacting protein-1 (CXIP1)-like proteins and iron-sulfur cluster assembly proteins, both of which contain a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG ...
CDD:198398	101	PRK	Bacteria:49	cd10451, GIY-YIG_LuxR_like, GIY-YIG domain of LuxR and ArsR family transcriptional regulators, and uncharacterized hypothetical proteins found in bacteria.  The family includes some bacterial LuxR and ArsR family transcriptional regulators.  The a C-terminal conserved domain shows sequence similarity to the N-terminal catalytic GIY-YIG domains of intron-encoded homing endonucleases. Besides, they have an N-terminally fused transcriptional regulators module, ...
CDD:198401	114	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd10454, GIY-YIG_COG3680_Meta, GIY-YIG domain of hypothetical proteins from Metazoa.  Members of this family are functionally uncharacterized hypothetical proteins from Metazoa. They have bacterial homologs that display sequence homology with the catalytic GIY-YIG domain of bacterial UvrC DNA repair proteins. However, unlike their bacterial relatives, these Metazoan proteins contain an N-terminal extension that includes the region of ...
CDD:198402	76	EUK	Invertebrates:16,Plants:11,Primates:1,Vertebrates:2	cd10455, GIY-YIG_SLX1, Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs.  Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its ...
CDD:198403	68	PRK	Bacteria:129,Viruses:6	cd10456, GIY-YIG_UPF0213, The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1.  This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, ...
CDD:198417	93	EUK	Invertebrates:7,Vertebrates:3	cd10459, PUB_PNGase, PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase).  This PUB (PNGase/UBA or UBX) domain is found in the p97 adaptor protein PNGase (Peptide:N-glycanase). The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the ...
CDD:198418	102	EUK	Invertebrates:18,Mammals:1,Vertebrates:3,nodiv:1	cd10460, PUB_UBXD1, PNGase/UBA or UBX (PUB) domain of UBXD1.  This PUB  domain is found in p97 adaptor protein UBXD1 (UBX domain-containing protein 1, also called UBXD6). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, ...
CDD:198421	96	EUK	Invertebrates:1,Plants:8	cd10463, PUB_WLM, PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family.  The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through ...
CDD:198456	160	PRK	Bacteria:12,nodiv:1	cd10466, FimH_man-bind, Mannose binding  domain of FimH and related proteins.  This family, restricted to gammaproteobacteria, includes FimH, a mannose-specific adhesin of uropathogenic Escherichia coli strains. The domain appears to bind specifically to D-mannose and mediates cellular adhesion to mannosylated proteins, a prerequisite to colonization and subsequent invasion of epithelial tissues.
CDD:198458	210	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:1	cd10467, FAM20_C_like, C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins.  Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects ...
CDD:198461	206	miss	miss	cd10470, FAM20B_C, C-terminal putative kinase domain of FAM20B xylose kinase.  Experiments with human FAM20B suggest that it is a xylose kinase that participates in proteoglycan production. It may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. The C-terminal domain of FAM20B is a putative kinase domain, based on mutagenesis of the C-terminal domain of Drosophila ...
CDD:199813	119	EUK	Invertebrates:14,Primates:1,Vertebrates:3	cd10489, MH1_SMAD_6_7, N-terminal Mad Homology 1 (MH1) domain in SMAD6 and SMAD7.  The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways.  MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 ...
CDD:199821	165	EUK	Invertebrates:5,Rodents:1	cd10496, MH2_I-SMAD, C-terminal Mad Homology 2 (MH2) domain in Inhibitory SMADs.  The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is ...
CDD:259849	744	EUK	Plants:8	cd10506, RNAP_IV_RPD1_N, Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain.  NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms ...
CDD:259792	47	EUK	Invertebrates:26,Plants:30,Vertebrates:3	cd10507, Zn-ribbon_RPA12, C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I.  The C-terminal zinc ribbon domain (C_ribbon) of subunit A12 (C-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly ...
CDD:259793	49	EUK	Invertebrates:25,Mammals:1,Plants:26,Primates:1,Vertebrates:3	cd10508, Zn-ribbon_RPB9, C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II.  The C-terminal zinc ribbon domain (C_ribbon) of subunit B9 (C-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III ...
CDD:259794	46	EUK	Invertebrates:26,Plants:23,Vertebrates:3	cd10509, Zn-ribbon_RPC11, C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III.  The C-terminal zinc ribbon domain (C_ribbon) of subunit C11 (C-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 have strong homology to ...
CDD:259795	47	miss	miss	cd10511, Zn-ribbon_TFS, C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS).  TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even ...
CDD:240598	126	EUKprk	Bacteria:20,Environmental:1,Vertebrates:1	cd10546, VKOR, Vitamin K epoxide reductase (VKOR) family.  VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. This family includes enzymes that are present in vertebrates, Drosophila, plants, bacteria, and ...
CDD:269973	92	EUK	Invertebrates:15,Plants:1,Rodents:1,Vertebrates:2	cd10569, FERM_C_Talin, Talin FERM domain C-lobe/F3.  Talin (also called filopodin) plays an important role in initiating actin filament growth in motile cell protrusions. It is responsible for linking the cytoplasmic domains of integrins to the actin-based cytoskeleton, and is involved in vinculin, integrin and actin interactions. At the leading edge of motile cells, talin colocalises with the hyaluronan receptor layilin in ...
CDD:269974	95	EUK	Mammals:4,Plants:3,Primates:1,Rodents:1,Vertebrates:3	cd10570, PH-GRAM, Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) ...
CDD:269975	106	EUK	Invertebrates:20,Primates:1,Rodents:1,Vertebrates:5	cd10571, PH_beta_spectrin, Beta-spectrin pleckstrin homology (PH) domain.  Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to inositol-1,4,5-trisphosphate. The PH domain of beta-spectrin is thought to play a role in the association of spectrin with the plasma membrane of ...
CDD:269977	96	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd10573, PH_DAPP1, Dual Adaptor for Phosphotyrosine and 3-Phosphoinositides Pleckstrin homology (PH) domain.  DAPP1 (also known as PHISH/3' phosphoinositide-interacting SH2 domain-containing protein or Bam32) plays a role in B-cell activation and has potential roles in T-cell and mast cell function. DAPP1 promotes B cell receptor (BCR) induced activation of Rho GTPases Rac1 and Cdc42, which feed into mitogen-activated protein kinases ...
CDD:269978	113	EUK	Invertebrates:8,Mammals:1,Primates:1,Vertebrates:3	cd10574, EVH1_SPRED-like, Sprouty-related EVH1 domain-containing-like proteins EVH1 domain.  The Spred family has the following domains: an N-terminal EVH1 domain, a unique KBD (c-Kit kinase binding) domain which that is phosphorylated by the stem cell factor receptor c-Kit, and a C-terminal cysteine-rich SPR (Sprouty-related) domain which is involved in membrane localization. There are 3 Spred proteins: Spred1 which interacts ...
CDD:213020	142	EUKprk	Bacteria:28,Invertebrates:1	cd10585, CE4_SF, Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily.  The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this ...
CDD:199908	65	EUKprk	Bacteria:203,Environmental:5,Invertebrates:32,Plants:37,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd10719, DnaJ_zf, Zinc finger domain of DnaJ and HSP40.  Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. ...
CDD:199909	158	EUKprk	Bacteria:97,Invertebrates:7,Mammals:1,Plants:6,Primates:1,Rodents:1,Vertebrates:2	cd10747, DnaJ_C, C-terminal substrate binding domain of DnaJ and HSP40.  The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of ...
CDD:212098	251	EUKprk	Bacteria:9,Invertebrates:1	cd10786, GH38N_AMII_like, N-terminal catalytic domain of class II alpha-mannosidases and similar proteins; glycoside hydrolase family 38 (GH38).  Alpha-mannosidases (EC 3.2.1.24) are extensively found in eukaryotes and play important roles in the processing of newly formed N-glycans and in degradation of mature glycoproteins.  A deficiency of this enzyme causes the lysosomal storage disease alpha-mannosidosis. Many bacterial and archaeal species ...
CDD:212099	238	EUKprk	Bacteria:154,Environmental:1,Plants:1	cd10787, LamB_YcsF_like, LamB/YcsF family of  lactam utilization protein.  The LamB/YbgL family includes the Aspergillus nidulans protein LamB, and its homologs from all three kingdoms of life. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive ...
CDD:212100	243	EUKprk	Bacteria:15,Vertebrates:1	cd10788, YdjC_like, YdjC-family proteins.  YdjC-family proteins are widely distributed, from human to bacteria. It is represented by an uncharacterised protein YdjC (also known as ChbG), encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. This subfamily also includes hopanoid biosynthesis associated proteins HpnK ...
CDD:212101	252	EUKprk	Bacteria:73,Invertebrates:3,Plants:3,Primates:1	cd10789, GH38N_AMII_ER_cytosolic, N-terminal catalytic domain of endoplasmic reticulum(ER)/cytosolic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38).  The subfamily is represented by Saccharomyces cerevisiae vacuolar alpha-mannosidase Ams1, rat ER/cytosolic alpha-mannosidase Man2C1, and similar proteins. Members in this family share high sequence similarity. None of them have any classical signal sequence or ...
CDD:212103	254	EUKprk	Bacteria:27,Invertebrates:2,Plants:2	cd10791, GH38N_AMII_like_1, N-terminal catalytic domain of mainly uncharacterized eukaryotic proteins similar to alpha-mannosidases; glycoside hydrolase family 38 (GH38).  The subfamily of mainly uncharacterized eukaryotic proteins shows sequence homology with class II alpha-mannosidases (AlphaAMIIs). AlphaAMIIs possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyze the degradation of N-linked oligosaccharides. The N-terminal ...
CDD:212104	412	PRK	Bacteria:59	cd10792, GH57N_AmyC_like, N-terminal catalytic domain of  alpha-amylase ( AmyC ) and similar proteins.  Alpha-amylases (alpha-1,4-glucan-4-glucanohydrolases, EC 3.2.1.1) play essential roles in alpha-glucan metabolism by catalyzing the hydrolysis of polysaccharides such as amylose starch, and beta-limit dextrin. This subfamily is represented by a novel alpha-amylase (AmyC) encoded by hyperthermophilic organism Thermotoga maritime ORF tm1438, and its prokaryotic ...
CDD:212105	279	PRK	Bacteria:35	cd10793, GH57N_TLGT_like, N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57).  4-alpha-glucanotransferase (TLGT, EC 2.4.1.25) plays a key role in the maltose metabolism. It catalyzes the disproportionation of amylose and the formation of large cyclic alpha-1,4-glucan (cycloamylose) from linear amylose. TLGT functions as a homodimer. Each monomer is composed of two domains, an N-terminal catalytic domain with a ...
CDD:212106	305	PRK	Bacteria:12	cd10794, GH57N_PfGalA_like, N-terminal catalytic domain of alpha-galactosidase; glycoside hydrolase family 57 (GH57).  Alpha-galactosidases (GalA, EC 3.2.1.22) catalyze the hydrolysis of alpha-1,6-linked galactose residues from oligosaccharides and polymeric galactomannans. Based on sequence similarity, the majority of eukaryotic and bacterial GalAs have been classified into glycoside hydrolase family GH27, GH36, and GH4, respectively. This subfamily is represented ...
CDD:212107	306	PRK	Bacteria:48	cd10795, GH57N_MJA1_like, N-terminal catalytic domain of a thermoactive alpha-amylase from Methanococcus jannaschii and similar proteins; glycoside hydrolase family 57 (GH57).  The subfamily is represented by a thermostable alpha-amylase (MJA1, EC 3.2.1.1) encoded from the hyperthermophilic archaeon Methanococcus jannaschii locus, M J1611. MJA1 has a broad pH optimum 5.0-8.0. It exhibits extremely thermophilic alpha-amylase activity that catalyzes the hydrolysis of ...
CDD:212108	313	PRK	Bacteria:49	cd10796, GH57N_APU, N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57).  Pullulanases (EC 3.2.1.41) are capable of hydrolyzing the alpha-1,6 glucosidic bonds of pullulan, producing maltotriose.  Amylopullulanases (APU, E.C 3.2.1.1/41) are type II pullulanases which can also degrade both the alpha-1,6 and alpha-1,4 glucosidic bonds of starch, producing oligosaccharides. This subfamily includes GH57 archaeal ...
CDD:212109	327	PRK	Bacteria:29	cd10797, GH57N_APU_like_1, N-terminal putative catalytic domain of mainly uncharacterized prokaryotic proteins similar to archaeal thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57).  This subfamily of mainly uncharacterized bacterial proteins, shows high sequence homology to GH57 archaeal thermoactive amylopullulanases (APU, E.C 3.2.1.1/41). Thermoactive APUs are type II pullulanases with both pullulanolytic and amylolytic activities. They have ...
CDD:212112	233	PRK	Bacteria:30,Environmental:2	cd10801, LamB_YcsF_like_1, uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB.  This mainly bacterial subfamily of the LamB/YbgL family, contains many well conserved uncharacterized proteins. Although their molecular function remains unknown, those proteins show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous ...
CDD:212113	251	PRK	Bacteria:29	cd10802, YdjC_TTHB029_like, Thermus thermophiles TTHB029 and similar proteins.  This subfamily is represented by an YdjC-family protein TTHB029 from Thermus thermophilus HB8; it is similar to Escherichia coli YdjC, a hypothetical protein encoded by the celG gene. TTHB029 functions as a homodimer. Each of monomer consists of (beta/alpha)-barrel fold. The molecular function of TTHB029 is unclear.
CDD:212114	228	PRK	Bacteria:54	cd10803, YdjC_EF3048_like, Enterococcus faecalis EF3048 and similar proteins.  This subfamily is represented by a putative cellobiose-phosphate cleavage protein EF3048 from Enterococcus faecalis v583. It is similar to Escherichia coli YdjC, a hypothetical protein encoded by the celG gene. EF3048 might function as a homodimer. Each of the monomers consists of a (beta/alpha)-barrel fold that forms an active homodimer. The molecular function of the EF3048 is unclear.
CDD:212115	261	PRK	Bacteria:22	cd10804, YdjC_HpnK_like, hopanoid biosynthesis associated protein HpnK and similar proteins.  The subfamily includes some uncharacterized proteins annotated as hopanoid biosynthesis associated proteins, HpnK. They show high sequence similarity to proteins from the YdjC-family, the latter is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which ...
CDD:212116	251	PRK	Bacteria:15	cd10805, YdjC_like_1, uncharacterized YdjC-like family proteins from bacteria.  The subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an ...
CDD:212117	280	EUK	Invertebrates:7,Primates:1,Vertebrates:2,nodiv:1	cd10806, YdjC_like_2, uncharacterized YdjC-like family proteins from eukaryotes.  This eukaryotic subfamily contains hypothetical and uncharacterized proteins, and belongs to the YdjC-like family of uncharacterized proteins. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes ...
CDD:212118	251	PRK	Bacteria:49	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria.  This subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an ...
CDD:212119	259	PRK	Bacteria:21	cd10808, YdjC, Escherichia coli YdjC-like family of  proteins.  Uncharacterized  subfamily of YdjC-like family of proteins. Included in this subfamily is the uncharacterized Escherichia coli protein YdjC (also known as ChbG), encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear.
CDD:212120	340	EUK	Invertebrates:13,Plants:3,Primates:1,nodiv:1	cd10809, GH38N_AMII_GMII_SfManIII_like, N-terminal catalytic domain of Golgi alpha-mannosidase II, Spodoptera frugiperda Sf9 alpha-mannosidase III, and similar proteins; glycoside hydrolase family 38 (GH38).  This subfamily is represented by Golgi alpha-mannosidase II (GMII, also known as mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC 3.2.1.114, Man2A1), a monomeric, membrane-anchored class II alpha-mannosidase existing in ...
CDD:212121	278	EUK	Invertebrates:22,Plants:9,Primates:1,Vertebrates:3	cd10810, GH38N_AMII_LAM_like, N-terminal catalytic domain of lysosomal alpha-mannosidase and similar proteins; glycoside hydrolase family 38 (GH38).  The subfamily is represented by lysosomal alpha-mannosidase (LAM, Man2B1, EC 3.2.1.114), which is a broad specificity exoglycosidase hydrolyzing all known alpha 1,2-, alpha 1,3-, and alpha 1,6-mannosidic linkages from numerous high mannose type oligosaccharides. LAM is expressed ...
CDD:212125	271	PRK	Bacteria:23	cd10814, GH38N_AMII_SpGH38_like, N-terminal catalytic domain of SPGH38, a putative alpha-mannosidase of Streptococcus pyogenes, and its prokaryotic homologs; glycoside hydrolase family 38 (GH38).  The subfamily is represented by SpGH38 of Streptococcus pyogenes,  which has been assigned as a putative alpha-mannosidase, and is encoded by ORF spy1604. SpGH38 appears to exist as an elongated dimer and display alpha-1,3 mannosidase activity. It is active on ...
CDD:212126	270	PRK	Bacteria:38	cd10815, GH38N_AMII_EcMngB_like, N-terminal catalytic domain of Escherichia coli alpha-mannosidase MngB and its bacterial homologs; glycoside hydrolase family 38 (GH38).  The bacterial subfamily is represented by Escherichia coli alpha-mannosidase MngB, which is encoded by the mngB gene (previously called ybgG). MngB exhibits alpha-mannosidase activity that converts 2-O-(6-phospho-alpha-mannosyl)-D-glycerate to mannose-6-phosphate and glycerate in the pathway which ...
CDD:211315	51	EUK	Invertebrates:2	cd10909, ChtBD1_GH18_2, Hevein or type 1 chitin binding domain (ChtBD1) subfamily; in some members co-occurs with family 18 glycosyl hydrolases.  This subfamily includes a Toxoplasma gondii ME49 protein annotated as a putative mannosyl-oligosaccharide glucosidase. ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural ...
CDD:199896	145	EUK	Invertebrates:6,Plants:10,Vertebrates:2	cd10910, limkain_b1_N_like, N-terminal LabA-like domain of limkain b1 and similar proteins.  This eukaryotic subfamily of LabA-like domains contains the N-terminal domain of human limkain b1, a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS ...
CDD:199897	155	PRK	Bacteria:43	cd10911, LabA, LabA_like proteins.  A well conserved group of bacterial and archaeal proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. ...
CDD:199211	348	PRK	Bacteria:4	cd10913, Peptidase_C25_N_gingipain, gingipain subgroup of the Peptidase C25 family N-terminal domain.  Gingipain, produced by Porphyromonas gingivalis, exemplifies the Peptidase family C25, a unique class of cysteine proteases.  P.  gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease also associated with other diseases such as diabetes and cardiovascular disease. The gingipain subgroup contains extracellular Arg- and ...
CDD:213021	247	PRK	Bacteria:13	cd10916, CE4_PuuE_HpPgdA_like, Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and similar proteins.  This family is a member of the very large and functionally diverse carbohydrate esterase 4 (CE4) superfamily. It contains bacterial PuuE (purine utilization E) allantoinases, a peptidoglycan deacetylase from Helicobacter pylori (HpPgdA), Escherichia coli ArnD, and many uncharacterized homologs from all three ...
CDD:213022	171	EUKprk	Bacteria:210,Invertebrates:2,Plants:8	cd10917, CE4_NodB_like_6s_7s, Catalytic NodB homology domain of rhizobial NodB-like proteins.  This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and ...
CDD:213023	157	PRK	Bacteria:236,Environmental:3	cd10918, CE4_NodB_like_5s_6s, Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands.  This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes bacterial ...
CDD:200545	273	EUKprk	Bacteria:4,Invertebrates:2,Plants:4,nodiv:1	cd10919, CE4_CDA_like, Putative catalytic domain of chitin deacetylase-like proteins from insects and similar proteins.  Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been ...
CDD:200548	266	PRK	Bacteria:11	cd10922, CE4_PelA_like_C, C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria.  This family is represented by a protein PelA of unknown function that is encoded by a gene in the pelA-G gene cluster for pellicle production and biofilm formation in Pseudomonas aeruginosa. PelA and most of the family members contain a domain of unknown function, DUF297, in the N-terminus and a C-terminal domain that shows ...
CDD:200549	250	PRK	Bacteria:20	cd10923, CE4_COG5298, Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. Some family members contain an ...
CDD:200550	273	PRK	Bacteria:13	cd10924, CE4_COG4878, Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria.  The family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200551	216	PRK	Bacteria:8	cd10925, CE4_u1, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200552	253	PRK	Bacteria:8	cd10926, CE4_u2, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200554	222	PRK	Bacteria:13,nodiv:1	cd10928, CE4_u4, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200555	263	PRK	Bacteria:23	cd10929, CE4_u5, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200557	224	PRK	Bacteria:45,Environmental:1	cd10931, CE4_u7, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200558	324	PRK	Bacteria:15	cd10932, CE4_u8, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200559	266	PRK	Bacteria:14	cd10933, CE4_u9, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:200561	295	PRK	Bacteria:24	cd10935, CE4_WalW, Putative catalytic domain of lipopolysaccharide biosynthesis protein WalW and its bacterial homologs.  This family corresponds to a group of uncharacterized lipopolysaccharide biosynthesis protein WalW found in bacteria. Although their biochemical properties remain to be determined, members of this family is composed of a seven-stranded barrel with detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which ...
CDD:200562	215	PRK	Bacteria:98,Environmental:1,nodiv:1	cd10936, CE4_DAC2, Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria.  This family contains an uncharacterized protein BH1492 from Bacillus halodurans, an uncharacterized protein ATU2773 from Agrobacterium tumefaciens C58, and other bacterial hypothetical proteins. Although their functions are still unknown, structural superposition and sequence comparison suggest that BH1492 and ATU2773 might be ...
CDD:200563	258	EUKprk	Bacteria:47,Environmental:1,Plants:3	cd10938, CE4_HpPgdA_like, Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins.  This family is represented by a peptidoglycan deacetylase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori. HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. It functions as a homotetramer. ...
CDD:200564	290	PRK	Bacteria:11	cd10939, CE4_ArnD, Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs.  This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of ...
CDD:200565	306	PRK	Bacteria:8	cd10940, CE4_PuuE_HpPgdA_like_1, Putative catalytic domain of uncharacterized bacterial polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA).  This family contains many uncharacterized bacterial polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). PuuE ...
CDD:200566	258	PRK	Bacteria:34,Environmental:1	cd10941, CE4_PuuE_HpPgdA_like_2, Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA).  This family contains many uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase ...
CDD:200569	189	EUKprk	Bacteria:53,Invertebrates:1	cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins.  This family is represented by a putative polysaccharide deacetylase PgdA from the oral pathogen Streptococcus mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN), which are members of the carbohydrate esterase 4 (CE4) superfamily. SmPgdA is an extracellular metal-dependent polysaccharide ...
CDD:200572	223	PRK	Bacteria:16	cd10948, CE4_BsPdaA_like, Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs.  The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA ...
CDD:200574	188	PRK	Bacteria:17	cd10950, CE4_BsYlxY_like, Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis and its bacterial homologs.  The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 ...
CDD:200575	197	EUKprk	Bacteria:1,Invertebrates:1,Plants:18	cd10951, CE4_ClCDA_like, Catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase and similar proteins.  This family is represented by the chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41) from Colletotrichum lindemuthianum (also known as Glomerella lindemuthiana), which is a member of the carbohydrate esterase 4 (CE4) superfamily. ClCDA catalyzes the hydrolysis of N-acetamido groups of ...
CDD:200576	178	EUK	Plants:9	cd10952, CE4_MrCDA_like, Catalytic NodB homology domain of Mucor rouxii chitin deacetylase and similar proteins.  This family is represented by the chitin deacetylase (MrCDA, EC 3.5.1.41) encoded from the fungus Mucor rouxii (also known as Amylomyces rouxii). MrCDA is an acidic glycoprotein with a very stringent specificity for beta1-4-linked N-acetylglucosamine homopolymers. It requires at least four residues (chitotetraose) for catalysis, and can achieve extensive ...
CDD:200578	180	PRK	Bacteria:25	cd10954, CE4_CtAXE_like, Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its bacterial homologs.  This family is represented by Clostridium thermocellum acetylxylan esterase (CtAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. CtAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It ...
CDD:200579	195	PRK	Bacteria:16	cd10955, CE4_BH0857_like, Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs.  This family is represented by a putative polysaccharide deacetylase BH0857 from Bacillus halodurans. Although its biological function still remains unknown, BH0857 shows high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an ...
CDD:200580	194	PRK	Bacteria:8	cd10956, CE4_BH1302_like, Putative catalytic NodB homology domain of uncharacterized BH1302 protein from Bacillus halodurans and its bacterial homologs.  This family is represented by a putative polysaccharide deacetylase BH1302 from Bacillus halodurans. Although its biological function is unknown, BH1302 shows high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular ...
CDD:200581	190	EUKprk	Bacteria:3,Invertebrates:3,Plants:5	cd10958, CE4_NodB_like_2, Catalytic NodB homology domain of uncharacterized chitin deacetylases and hypothetical proteins.  This family includes some uncharacterized chitin deacetylases and hypothetical proteins, mainly from eukaryotes. Although their biological function is unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase (endo-chitin ...
CDD:200582	187	PRK	Bacteria:31	cd10959, CE4_NodB_like_3, Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases.  This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent ...
CDD:200583	238	PRK	Bacteria:25	cd10960, CE4_NodB_like_1, Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases.  This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent ...
CDD:200584	196	PRK	Bacteria:13	cd10962, CE4_GT2-like, Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins.  This family includes many uncharacterized bacterial proteins containing an N-terminal GH18 (glycosyl hydrolase, family 18) domain, a middle NodB-like homology domain, and a C-terminal GT2-like (glycosyl transferase group 2) domain. Although their biological function is unknown, members in this family contain a middle NodB homology ...
CDD:200585	182	PRK	Bacteria:11	cd10963, CE4_RC0012_like, Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs.  This family contains an uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs. Although their biochemical properties remain to be determined, members in this family seems to be composed of a seven-stranded barrel with detectable sequence similarity to the six-stranded barrel rhizobial ...
CDD:200586	193	PRK	Bacteria:4	cd10964, CE4_PgaB_5s, N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins.  This family is represented by an outer membrane lipoprotein, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (PgaB, EC 3.5.1.-), encoded by Escherichia coli pgaB gene from the pgaABCD (formerly ycdSRQP) operon, which affects biofilm development by promoting abiotic surface binding and ...
CDD:213024	164	PRK	Bacteria:18	cd10966, CE4_yadE_5s, Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins.  This family contains an uncharacterized protein yadE from Escherichia coli and its bacterial homologs. Although its molecular function remains unknown, yadE shows high sequence similarity with the catalytic NodB homology domain of outer membrane lipoprotein PgaB and the surface-attached protein intercellular adhesion protein IcaB. Both ...
CDD:200589	202	PRK	Bacteria:47	cd10967, CE4_GLA_like_6s, Putative catalytic NodB homology domain of gellan lyase and similar proteins.  This family is represented by the extracellular polysaccharide-degrading enzyme, gellan lyase (gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme acts on gellan exolytically and releases a tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose with unsaturated glucuronic acid at the nonreducing terminus. The family also includes many uncharacterized ...
CDD:213025	161	PRK	Bacteria:18	cd10968, CE4_Mlr8448_like_5s, Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs.  This family contains Mesorhizobium loti Mlr8448 protein and its bacterial homologs. Although their biochemical properties are yet to be determined, members in this subfamily contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, ...
CDD:213026	218	PRK	Bacteria:29	cd10969, CE4_Ecf1_like_5s, Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins.  This family contains a hypothetical protein Ecf1 from Escherichia coli and its prokaryotic homologs. Although their biochemical properties remain to be determined, members in this family contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial ...
CDD:213027	194	PRK	Bacteria:20	cd10970, CE4_DAC_u1_6s, Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 6-stranded beta/alpha barrel.  This family contains uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial ...
CDD:200593	198	PRK	Bacteria:13	cd10971, CE4_DAC_u2_5s, Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel.  This family contains many uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of this family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology ...
CDD:200594	216	PRK	Bacteria:10	cd10972, CE4_DAC_u3_5s, Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel.  This family contains uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of ...
CDD:213028	157	EUKprk	Bacteria:22,Environmental:1,Plants:1	cd10973, CE4_DAC_u4_5s, Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel.  This family contains many uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the ...
CDD:200596	269	EUK	Invertebrates:6	cd10974, CE4_CDA_like_1, Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding peritrophin-A domain (ChBD) and/or a low-density lipoprotein receptor class A domain (LDLa).  Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer ...
CDD:200597	268	EUK	Invertebrates:10	cd10975, CE4_CDA_like_2, Putative catalytic domain of chitin deacetylase-like proteins.  Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal ...
CDD:200598	299	PRK	Bacteria:8,nodiv:1	cd10976, CE4_CDA_like_3, Putative catalytic domain of uncharacterized bacterial hypothetical proteins similar to insect chitin deacetylase-like proteins.  The family includes many uncharacterized bacterial hypothetical proteins that show high sequence similarity to insect chitin deacetylase-like proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the ...
CDD:200599	273	EUKprk	Bacteria:10,Invertebrates:2,Plants:3	cd10977, CE4_PuuE_SpCDA1, Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins.  Allantoinase (EC 3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms ...
CDD:200601	281	PRK	Bacteria:18,Environmental:1,nodiv:1	cd10979, CE4_PuuE_like, Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases.  The family includes a group of uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases. PuuE allantoinase specifically catalyzes the hydrolysis of (S)-allantoin into ...
CDD:211380	238	EUKprk	Bacteria:18,Plants:1	cd10981, ZnPC_S1P1, Zinc dependent phospholipase C/S1-P1 nuclease.  This model describes both the bacterial and archeal zinc-dependent phospholipase C, a domain found in the alpha toxin of Clostridium perfringens, as well as S1/P1 nucleases, which predominantly act on single-stranded DNA and RNA.
CDD:199912	163	EUKprk	Bacteria:5,Invertebrates:1,Plants:1	cd11006, M35_peptidyl-Lys_like, Peptidase M35 domain of peptidyl-Lys metalloendopeptidases and related proteins.  This family M35 Zn2+-metallopeptidase extracellular domain is mostly found in proteins characterized as peptidyl-Lys metalloendopeptidases (MEP; peptidyllysine metalloproteinase; EC 3.4.24.20), including some well-characterized domains in Aeromonas salmonicida subsp. Achromogenes (AsaP1) and Grifola frondosa (GfMEP). These ...
CDD:199913	183	PRK	Bacteria:18	cd11007, M35_like_1, Peptidase M35-like domain of uncharacterized proteins.  This family contains proteins similar to the M35 Zn2+-metallopeptidases, also known as the deuterolysin family, presumably these are bacterial metalloendopeptidases that have yet to be characterized. Typically, members of this family of extracellular peptidases contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ...
CDD:199914	167	EUK	Plants:37	cd11008, M35_deuterolysin_like, Peptidase M35 domain of deuterolysins and related proteins.  This family M35 Zn2+-metallopeptidase extracellular domain is found in fungal deutrolysins (acid metalloproteinase, neutral proteinase II), including some well-characterized metallopeptidase domains in Aspergillus oryzae (NpII), Aspergillus fumigatus (MEP20), Penicillium roqueforti (protease II) and Emericella nidulans (PepJ peptidase). The neutral proteinase II from ...
CDD:211381	218	PRK	Bacteria:47	cd11009, Zn_dep_PLPC, Zinc dependent phospholipase C (alpha toxin).  This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that ...
CDD:211382	249	EUKprk	Bacteria:93,Environmental:2,Invertebrates:19,Plants:28	cd11010, S1-P1_nuclease, S1/P1 nucleases and related enzymes.  This family summarizes both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity. S1 nuclease is more active on DNA than RNA. Its reaction products are oligonucleotides or single nucleotides with 5' phosphoryl groups. Although its primary substrate is single-stranded, it may also introduce single-stranded breaks ...
CDD:259899	95	EUK	Plants:6	cd11013, Plantacyanin, Plantacyanin is a subclass of phytocyanins, plant type I copper proteins.  Plantacyanins belong to the phytocyanin family of blue copper proteins, a ubiquitous family of plant cupredoxins. Plantacyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. The exact function of plantacyanin is unknown. However plantacyanin is shown to play a role in reproduction in ...
CDD:259905	103	EUK	Invertebrates:1,Plants:8	cd11019, OsENODL1_like, Early nodulin-like protein (OsENODL1) and similar proteins.  This family includes early nodulin-like protein (OsENODL1) from Oryza sativa and similar proteins. It belongs to the phytocyanin family of blue copper proteins, a ubiquitous family of plant cupredoxins. Phytocyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. OsENODL1 expression ...
CDD:259906	119	EUKprk	Bacteria:14,Environmental:2,Invertebrates:1,Plants:1	cd11020, CuRO_1_CuNIR, Cupredoxin domain 1 of Copper-containing nitrite reductase.  Copper-containing nitrite reductase (CuNIR), which catalyzes the reduction of NO2- to NO, is the key enzyme in the denitrification process in denitrifying bacteria. CuNIR contains at least one type 1 copper center and a type 2 copper center, which serves as the active site of the enzyme. A histidine, bound to the Type 2 Cu center, is ...
CDD:259910	119	PRK	Bacteria:18,Environmental:1	cd11024, CuRO_1_2DMCO_NIR_like, The cupredoxin domain 1 of a two-domain laccase related to nitrite reductase.  The two-domain laccase (small laccase) in this family differs significantly from all laccases. It resembles the two domain nitrite reductase in both sequence and structure. It consists of two cupredoxin domains and forms trimers and hence resembles the quaternary structure of nitrite reductases more than that of large laccases. There are ...
CDD:199893	101	PRK	Bacteria:24	cd11234, E_set_GDE_N, N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme.  E or "early" set domains are associated with the catalytic domain of the glycogen debranching enzyme at the N-terminal end. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase, it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose ...
CDD:200496	437	EUK	Invertebrates:4,Primates:1,Rodents:1	cd11235, Sema_semaphorin, The Sema domain, a protein interacting module, of semaphorins.  Semaphorins are regulator molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. They can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in ...
CDD:200497	401	EUK	Invertebrates:17,Primates:1	cd11236, Sema_plexin_like, The Sema domain, a protein interacting module, of Plexins and MET-like receptor tyrosine kinases.  Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestor of semaphorins. Ligand binding activates signal transduction pathways controlling axon guidance in the nervous system and other developmental processes including cell migration and morphogenesis, immune function, and tumor ...
CDD:200498	446	EUK	Invertebrates:9	cd11237, Sema_1A, The Sema domain, a protein interacting module, of semaphorin 1A (Sema1A).  Sema1A is a transmembrane protein. It has been shown to mediate the defasciculation of motor axon bundles at specific choice points. Sema1A binds to its receptor plexin A (PlexA), which in turn triggers downstream signaling events involving the receptor tyrosine kinase Otk, the evolutionarily conserved flavoprotein monooxygenase molecule interacting with CasL (MICAL), ...
CDD:200501	456	EUK	Primates:1,Rodents:1,Vertebrates:4	cd11240, Sema_4, The Sema domain, a protein interacting module, of class 4 semaphorins (Sema4).  Class 4 semaphorins (Sema4s) are transmembrane regulator molecules involved in the development of the nervous system, immune response, cytoskeletal organization, angiogenesis, and cell-cell interactions. There are 7 distinct subfamilies in class 4 semaphorins, named 4A to 4G. Several class 4 subfamilies play important roles in the immune system ...
CDD:200436	88	EUK	Invertebrates:3,Plants:1,Primates:1,Vertebrates:1	cd11280, gelsolin_like, Tandemly repeated domains found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play ...
CDD:200437	136	EUK	Invertebrates:7,Plants:9,Rodents:1,Vertebrates:3,nodiv:1	cd11281, ADF_drebrin_like, ADF homology domain of drebrin and actin-binding protein 1 (abp1).  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Many of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. Abp1 and drebrin (developmentally regulated brain protein) are ...
CDD:200438	114	EUK	Invertebrates:14,Plants:11,Primates:1,Rodents:1,Vertebrates:2	cd11282, ADF_coactosin_like, Coactosin-like members of the ADF homology domain family.  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Many of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. The function of coactosins is not well understood. They appear to ...
CDD:200439	122	EUK	Invertebrates:13,Plants:10,Primates:1,Vertebrates:4,nodiv:1	cd11283, ADF_GMF-beta_like, ADF-homology domain of glia maturation factor beta and related proteins.  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Most of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. The glia maturation factor (GMF), however, does not bind ...
CDD:200440	132	EUK	Invertebrates:14,Plants:24,Rodents:1,Vertebrates:3,nodiv:1	cd11284, ADF_Twf-C_like, C-terminal ADF domain of twinfilin and related proteins.  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Twinfilin contains two ADF domains, and inhibits the assembly of actin filaments by strongly interacting with monomeric ADP-actin (ADP-G-actin) in a 1:1 stochiometry (with it's C-terminal ADF domain, ...
CDD:200441	139	EUK	Invertebrates:5,Plants:7	cd11285, ADF_Twf-N_like, N-terminal ADF domain of twinfilin and related proteins.  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Twinfilin contains two ADF domains, and inhibits the assembly of actin filaments by strongly interacting with monomeric ADP-actin (ADP-G-actin) in a 1:1 stochiometry (with it's C-terminal ADF domain, Twf-C) and inhibiting the actin ...
CDD:200442	133	EUK	Invertebrates:23,Plants:20,Primates:1,Rodents:1,Vertebrates:6,nodiv:2	cd11286, ADF_cofilin_like, Cofilin, Destrin, and related actin depolymerizing factors.  Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. These proteins enhance the turnover rate of actin, and interact with actin monomers (G-actin) as well as actin filaments (F-actin), typically with a preference for ADP-G-actin ...
CDD:200444	92	EUK	Invertebrates:7,Plants:3,Primates:1,Rodents:1,Vertebrates:4	cd11288, gelsolin_S5_like, Gelsolin sub-domain 5-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins ...
CDD:200445	92	EUK	Invertebrates:5,Plants:1,Primates:1,Vertebrates:2	cd11289, gelsolin_S2_like, Gelsolin sub-domain 2-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) ...
CDD:200446	113	EUK	Invertebrates:6,Mammals:1,Plants:2,Primates:1,Vertebrates:3	cd11290, gelsolin_S1_like, Gelsolin sub-domain 1-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins ...
CDD:200447	99	EUK	Plants:1	cd11291, gelsolin_S6_like, Gelsolin sub-domain 6-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and ...
CDD:200448	98	EUK	Plants:1,Primates:1	cd11292, gelsolin_S3_like, Gelsolin sub-domain 3-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the ...
CDD:200449	101	EUK	Invertebrates:1,Plants:2,Vertebrates:2	cd11293, gelsolin_S4_like, Gelsolin sub-domain 4-like domain found in gelsolin, severin, villin, and related proteins.  Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play ...
CDD:199894	83	EUKprk	Bacteria:39,Plants:1	cd11294, E_set_Esterase_like_N, N-terminal Early set domain associated with the catalytic domain of putative esterases.  E or "early" set domains are associated with the catalytic domain of esterase at the N-terminal end. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term esterase can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the ...
CDD:199917	143	EUK	Invertebrates:20,Plants:10,Primates:1,Vertebrates:3	cd11295, Mago_nashi, Mago nashi proteins, integral members of the exon junction complex.  Members of this family, which was originally identified in Drosophila and called mago nashi, are integral members of the exon junction complex (EJC). The EJC is a multiprotein complex that is deposited on spliced mRNAs after intron removal at a conserved position upstream of the exon-exon junction, and transported to the cytoplasm where ...
CDD:211383	206	EUKprk	Bacteria:10,Invertebrates:8,Plants:29,Rodents:1,Vertebrates:1	cd11296, O-FucT_like, GDP-fucose protein O-fucosyltransferase and related proteins.  O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth ...
CDD:199898	133	EUKprk	Bacteria:23,Plants:1	cd11297, LabA_like_N_1, Uncharacterized subfamily of N-terminal LabA-like domains.  This N-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of ...
CDD:211384	374	EUK	Invertebrates:24,Mammals:1,Vertebrates:2,nodiv:1	cd11298, O-FucT-2, GDP-fucose protein O-fucosyltransferase 2.  O-FucT-2 adds O-fucose to thrombospondin type 1 repeats (TSRs), and appears conserved in bilateria. The O-fucosylation of TSRs appears to play a role in regulating secretion of metalloproteases of the ADAMTS superfamily. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ...
CDD:211385	290	EUK	Plants:8	cd11299, O-FucT_plant, GDP-fucose protein O-fucosyltransferase, plant specific subfamily.  Some members of this plant-specific family of O-fucosyltransferases have been annotated as auxin-independent growth promotors. The function of the protein seems unclear. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a ...
CDD:211386	328	EUK	Invertebrates:19,Vertebrates:3,nodiv:1	cd11300, Fut8_like, Alpha 1-6-fucosyltransferase.  Alpha 1,6-fucosyltransferase (Fut8) transfers a fucose moiety from GDP-fucose to the reducing terminal N-acetylglucosamine of the core structure of Asn-linked oligosaccharides, in a process termed core fucosylation. Core fucosylation is essential for the function of growth factor receptors. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family ...
CDD:211387	265	EUKprk	Bacteria:84,Invertebrates:7,Vertebrates:2	cd11301, Fut1_Fut2_like, Alpha-1,2-fucosyltransferase.  Alpha-1,2-fucosyltransferases (Fut1, Fut2) catalyze the transfer of alpha-L-fucose to the terminal beta-D-galactose residue of glycoconjugates via an alpha-1,2-linkage, generating carbohydrate structures that exhibit H-antigenicity for blood-group carbohydrates. These structures also act as ligands for morphogenesis, the adhesion of microbes, and metastasizing cancer cells. ...
CDD:211388	347	EUK	Invertebrates:19,Primates:1,Vertebrates:3,nodiv:1	cd11302, O-FucT-1, GDP-fucose protein O-fucosyltransferase 1.  The protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds O-fucose to EGF (epidermal growth factor-like) repeats. The O-fucsosylation of the Notch receptor signaling protein is dependent on this enzyme, which requires GDP-fucose as a substrate. O-fucose residues added to the target of O-FucT-1 may be further elongated by other glycosyltransferases. On top of ...
CDD:206636	99	EUKprk	Bacteria:2,Invertebrates:9,Mammals:1,Plants:1,Primates:1,Rodents:1,Vertebrates:4	cd11303, Dystroglycan_repeat, Cadherin-like repeat domain of alpha dystroglycan.  Dystroglycan is a glycoprotein widely distributed in skeletal muscle and other tissues; the pre-protein is cleaved into two subunits (alpha and beta) that form a complex which links the extracellular matrix to the cytoskeleton. Cadherin-like dystroglycan repeats are present in the extracellular alpha-dystroglycan ...
CDD:206637	98	EUK	Invertebrates:2,Mammals:4,Primates:2,Rodents:2,Vertebrates:3	cd11304, Cadherin_repeat, Cadherin tandem repeat domain.  Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, ...
CDD:206765	124	EUK	Invertebrates:6,Vertebrates:1	cd11305, alpha_DG_C, C-terminal domain of alpha dystroglycan.  Dystroglycan is a glycoprotein widely distributed in skeletal muscle and other tissues; the pre-protein is cleaved into two subunits (alpha and beta) that form a complex which links the extracellular matrix to the cytoskeleton. This C-terminal domain of the alpha-subunit appears to contact neighboring cadherin-like repeats of alpha dystroglycan, and may also be involved in interactions ...
CDD:199916	179	EUK	Plants:14	cd11307, M35_Asp_f2_like, Peptidase M35 domain of Asp f2, a major allergen from Aspergillus fumigatus, and related proteins; non catalytic.  In this domain subgroup the unique zinc-binding motif (the aspzincin motif, characteristic of the M35 deuterolysin family, and defined as the "HEXXH + D" motif: two His ligands and Asp as third ligand), is poorly conserved and may not bind Zinc. Members of this subgroup also lack a key conserved Tyr residue which acts as a ...
CDD:200604	76	EUKprk	Bacteria:2,Invertebrates:2,Primates:1,Rodents:1,Vertebrates:5	cd11308, Peptidase_M14NE-CP-C_like, Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain.  This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, ...
CDD:200452	336	PRK	Bacteria:58	cd11313, AmyAc_arch_bac_AmyA, Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes firmicutes, bacteroidetes, and proteobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with ...
CDD:200453	302	EUKprk	Bacteria:23,Plants:11	cd11314, AmyAc_arch_bac_plant_AmyA, Alpha amylase catalytic domain found in archaeal, bacterial, and plant Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes AmyA from bacteria, archaea, water fleas, and plants. The Alpha-amylase family comprises the largest family ...
CDD:200454	352	PRK	Bacteria:27	cd11315, AmyAc_bac1_AmyA, Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with ...
CDD:200455	403	PRK	Bacteria:43,Environmental:1	cd11316, AmyAc_bac2_AmyA, Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes Chloroflexi, Dictyoglomi, and Fusobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the ...
CDD:200456	329	EUKprk	Bacteria:21,Invertebrates:26,Plants:6,Primates:1,Vertebrates:3	cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found in bacterial and eukaryotic Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes AmyA proteins from bacteria, fungi, mammals, insects, mollusks, and nematodes. ...
CDD:200457	391	EUKprk	Bacteria:36,Plants:18	cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes bacterial and fungal proteins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the ...
CDD:200458	375	EUK	Invertebrates:8,Plants:22	cd11319, AmyAc_euk_AmyA, Alpha amylase catalytic domain found in eukaryotic Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes eukaryotic alpha-amylases including proteins from fungi, sponges, and protozoans. The Alpha-amylase family comprises the largest family of ...
CDD:200459	389	PRK	Bacteria:17	cd11320, AmyAc_AmyMalt_CGTase_like, Alpha amylase catalytic domain found in maltogenic amylases, cyclodextrin glycosyltransferase, and related proteins.  Enzymes such as amylases, cyclomaltodextrinase (CDase), and cyclodextrin glycosyltransferase (CGTase) degrade starch to smaller oligosaccharides by hydrolyzing the alpha-D-(1,4) linkages between glucose residues. In the case of CGTases, an additional cyclization reaction is catalyzed yielding mixtures of cyclic ...
CDD:200460	406	EUKprk	Bacteria:3,Invertebrates:4,Plants:1,Vertebrates:1	cd11321, AmyAc_bac_euk_BE, Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes.  Branching enzymes (BEs) catalyze the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a non-reducing end oligosaccharide chain, and subsequent attachment to the alpha-1,6 position. By increasing the number of non-reducing ends, glycogen is ...
CDD:200461	402	PRK	Bacteria:40	cd11322, AmyAc_Glg_BE, Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme).  The glycogen branching enzyme catalyzes the third step of glycogen biosynthesis by the cleavage of an alpha-(1,4)-glucosidic linkage and the formation a new alpha-(1,6)-branch by subsequent transfer of cleaved oligosaccharide. They are part of a group called branching enzymes which catalyze the formation of alpha-1,6 branch ...
CDD:200462	569	EUK	Plants:11	cd11323, AmyAc_AGS, Alpha amylase catalytic domain found in Alpha 1,3-glucan synthase (also called uridine diphosphoglucose-1,3-alpha-glucan glucosyltransferase and 1,3-alpha-D-glucan synthase).  Alpha 1,3-glucan synthase (AGS, EC 2.4.1.183) is an enzyme that catalyzes the reversible chemical reaction of UDP-glucose and [alpha-D-glucosyl-(1-3)]n to form UDP and [alpha-D-glucosyl-(1-3)]n+1. AGS is a component of fungal cell walls. The cell wall of filamentous fungi is ...
CDD:200463	536	EUKprk	Bacteria:40,Plants:1	cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found in Amylosucrase.  Amylosucrase is a glucosyltransferase that catalyzes the transfer of a D-glucopyranosyl moiety from sucrose onto an acceptor molecule. When the acceptor is another saccharide, only alpha-1,4 linkages are produced. Unlike most amylopolysaccharide synthases, it does not require any alpha-D-glucosyl nucleoside diphosphate substrate. In the presence of glycogen it catalyzes ...
CDD:200464	436	EUKprk	Bacteria:47,Invertebrates:4	cd11325, AmyAc_GTHase, Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase).  Glycosyltrehalose trehalohydrolase (GTHase) was discovered as part of a coupled system for the production of trehalose from soluble starch. In the first half of the reaction, glycosyltrehalose synthase (GTSase), an intramolecular glycosyl transferase, converts the glycosidic bond between the ...
CDD:200465	433	EUKprk	Bacteria:52,Plants:1	cd11326, AmyAc_Glg_debranch, Alpha amylase catalytic domain found in glycogen debranching enzymes.  Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities: 4-alpha-D-glucanotransferase (EC 2.4.1.25) and ...
CDD:200466	478	EUK	Invertebrates:18,Plants:10,Primates:1,Vertebrates:2	cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found in glycogen debranching enzymes.  Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities, ...
CDD:200467	470	EUK	Invertebrates:17	cd11328, AmyAc_maltase, Alpha amylase catalytic domain found in maltase (also known as alpha glucosidase) and related proteins.  Maltase (EC 3.2.1.20) hydrolyzes the terminal, non-reducing (1->4)-linked alpha-D-glucose residues in maltose, releasing alpha-D-glucose. In most cases, maltase is equivalent to alpha-glucosidase, but the term "maltase" emphasizes the disaccharide nature of the substrate from which glucose is cleaved, and the term "alpha-glucosidase" ...
CDD:200468	477	EUK	Invertebrates:9	cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family found in maltase.  Maltase (EC 3.2.1.20) hydrolyzes the terminal, non-reducing (1->4)-linked alpha-D-glucose residues in maltose, releasing alpha-D-glucose. The catalytic triad (DED) which is highly conserved in the other maltase group is not present in this subfamily. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on ...
CDD:200469	472	EUKprk	Bacteria:18,Plants:1,nodiv:1	cd11330, AmyAc_OligoGlu, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins.  Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomalto-oligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. The Alpha-amylase ...
CDD:200470	450	EUKprk	Bacteria:14,Invertebrates:1	cd11331, AmyAc_OligoGlu_like, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins.  Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomalto-oligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. The ...
CDD:200471	481	EUKprk	Bacteria:25,Plants:1	cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), trehalose synthase (also called maltose alpha-D-glucosyltransferase), and related proteins.  Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the ...
CDD:200472	428	EUKprk	Bacteria:110,Invertebrates:1,Plants:19	cd11333, AmyAc_SI_OligoGlu_DGase, Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins.  The sucrose isomerases (SIs) Isomaltulose synthase (EC 5.4.99.11) and Trehalose synthase (EC 5.4.99.16) catalyze the isomerization of sucrose and maltose to produce ...
CDD:200473	447	EUKprk	Bacteria:34,Invertebrates:1	cd11334, AmyAc_TreS, Alpha amylase catalytic domain found in Trehalose synthetase.  Trehalose synthetase (TreS) catalyzes the reversible interconversion of trehalose and maltose. The enzyme catalyzes the reaction in both directions, but the preferred substrate is maltose. Glucose is formed as a by-product of this reaction. It is believed that the catalytic mechanism may involve the cutting of the incoming disaccharide and transfer of a glucose to ...
CDD:200474	538	PRK	Bacteria:17	cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in maltosyltransferase.  Maltosyltransferase (MTase), a maltodextrin glycosyltransferase, acts on starch and maltooligosaccharides. It catalyzes the transfer of maltosyl units from alpha-1,4-linked glucans or maltooligosaccharides to other alpha-1,4-linked glucans, maltooligosaccharides or glucose. MTase is a homodimer. The catalytic core domain has the (beta/alpha) 8 barrel fold with the active-site ...
CDD:200475	660	PRK	Bacteria:113	cd11336, AmyAc_MTSase, Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase).  Maltooligosyl trehalose synthase (MTSase) domain. MTSase and maltooligosyl trehalose trehalohydrolase (MTHase) work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-glucosidic linkage at the reducing end of the maltooligosaccharide through an intramolecular transglucosylation reaction, ...
CDD:200476	328	EUKprk	Bacteria:50,Invertebrates:2	cd11337, AmyAc_CMD_like, Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by ...
CDD:200477	389	EUKprk	Bacteria:92,Environmental:2,Invertebrates:1,Plants:1	cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and ...
CDD:200478	344	PRK	Bacteria:24	cd11339, AmyAc_bac_CMD_like_2, Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by ...
CDD:200479	407	PRK	Bacteria:30	cd11340, AmyAc_bac_CMD_like_3, Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by ...
CDD:200480	406	PRK	Bacteria:37	cd11341, AmyAc_Pullulanase_LD-like, Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins.  Pullulanase is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. Pullulanases are very similar to limit ...
CDD:200481	445	PRK	Bacteria:68	cd11343, AmyAc_Sucrose_phosphorylase-like, Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase).  Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family enzymes. The ...
CDD:200482	355	PRK	Bacteria:35	cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in GlgE-like proteins.  GlgE is a (1,4)-a-D-glucan:phosphate a-D-maltosyltransferase, involved in a-glucan biosynthesis in bacteria. It is also an anti-tuberculosis drug target. GlgE isoform I from Streptomyces coelicolor has the same catalytic and very similar kinetic properties to GlgE from Mycobacterium tuberculosis. GlgE from Streptomyces coelicolor forms a homodimer with each subunit comprising ...
CDD:200483	326	EUK	Mammals:1,Vertebrates:5	cd11345, AmyAc_SLC3A2, Alpha amylase catalytic domain found in solute carrier family 3 member 2 proteins.  4F2 cell-surface antigen heavy chain (hc) is a protein that in humans is encoded by the SLC3A2 gene. 4F2hc is a multifunctional type II membrane glycoprotein involved in amino acid transport and cell fusion, adhesion, and transformation. It is related to bacterial alpha-glycosidases, but lacks alpha-glycosidase activity. The Alpha-amylase family ...
CDD:200484	347	EUK	Plants:5	cd11346, AmyAc_plant_IsoA, Alpha amylase catalytic domain family found in plant isoamylases.  Two types of debranching enzymes exist in plants: isoamylase-type (EC 3.2.1.68) and a pullulanase-type (EC 3.2.1.41, also known as limit-dextrinase). These efficiently hydrolyze alpha-(1,6)-linkages in amylopectin and pullulan. This group does not contain the conserved catalytic triad present in other alpha-amylase-like proteins. The Alpha-amylase family comprises the largest ...
CDD:200485	391	EUKprk	Bacteria:23,Invertebrates:6	cd11347, AmyAc_1, Alpha amylase catalytic domain found in an uncharacterized protein family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: ...
CDD:200486	429	PRK	Bacteria:14	cd11348, AmyAc_2, Alpha amylase catalytic domain found in an uncharacterized protein family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a ...
CDD:200487	456	PRK	Bacteria:17	cd11349, AmyAc_3, Alpha amylase catalytic domain found in an uncharacterized protein family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a ...
CDD:200488	390	PRK	Bacteria:21,Environmental:1	cd11350, AmyAc_4, Alpha amylase catalytic domain found in an uncharacterized protein family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, ...
CDD:200489	443	PRK	Bacteria:13	cd11352, AmyAc_5, Alpha amylase catalytic domain found in an uncharacterized protein family.  The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a ...
CDD:200490	366	miss	miss	cd11353, AmyAc_euk_bac_CMD_like, Alpha amylase catalytic domain found in eukaryotic and bacterial cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to ...
CDD:200491	357	miss	miss	cd11354, AmyAc_bac_CMD_like, Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage ...
CDD:200492	433	miss	miss	cd11355, AmyAc_Sucrose_phosphorylase, Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase).  Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family enzymes. The ...
CDD:200493	458	miss	miss	cd11356, AmyAc_Sucrose_phosphorylase-like_1, Alpha amylase catalytic domain found in sucrose phosphorylase-like proteins (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase).  Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family ...
CDD:206766	218	EUKprk	Bacteria:3,Invertebrates:2,Plants:9,Primates:1,nodiv:1	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases.  RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide ...
CDD:200494	456	EUK	Invertebrates:6,Vertebrates:3	cd11359, AmyAc_SLC3A1, Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins.  SLC3A1, also called Neutral and basic amino acid transport protein rBAT or NBAT, plays a role in amino acid and cystine absorption. Mutations in the gene encoding SLC3A1 causes cystinuria, an autosomal recessive disorder characterized by the failure of proximal tubules to reabsorb filtered cystine and dibasic amino acids. The Alpha-amylase ...
CDD:206767	227	PRK	Bacteria:19	cd11362, RNase_PH_bact, Ribonuclease PH.  Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA.
CDD:206768	229	EUKprk	Bacteria:23,Invertebrates:3,Plants:4,Primates:1,Vertebrates:3	cd11363, RNase_PH_PNPase_1, Polyribonucleotide nucleotidyltransferase, repeat 1.  Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase ...
CDD:206769	223	EUKprk	Bacteria:1,Invertebrates:3,Plants:1	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nucleotidyltransferase, repeat 2.  Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA ...
CDD:206770	256	PRK	Bacteria:11,Environmental:2	cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome.  The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 ...
CDD:206771	214	PRK	Bacteria:9,Environmental:1	cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome.  The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 ...
CDD:206772	272	EUK	Invertebrates:16,Plants:8,Vertebrates:3	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome.  The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional ...
CDD:206773	259	EUK	Invertebrates:29,Plants:26,Vertebrates:3,nodiv:1	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome.  The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three ...
CDD:206774	261	EUK	Invertebrates:16,Plants:14,Vertebrates:2	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome.  The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three ...
CDD:206775	226	EUK	Invertebrates:9,Plants:27,Vertebrates:2,nodiv:1	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome.  The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three ...
CDD:206776	210	EUK	Invertebrates:11,Plants:24,Vertebrates:1,nodiv:1	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome.  The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three ...
CDD:206777	199	EUK	Invertebrates:22,Plants:15,Vertebrates:3,nodiv:1	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome.  The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three ...
CDD:200603	226	PRK	Bacteria:22	cd11374, CE4_u10, Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily.  The family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups of cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
CDD:213029	173	EUKprk	Bacteria:55,Invertebrates:10,Plants:12,Primates:1,Rodents:1,Vertebrates:4	cd11375, Peptidase_M54, Peptidase family M54, also called archaemetzincins or archaelysins.  Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and ...
CDD:206778	139	EUKprk	Bacteria:21,Invertebrates:2,Plants:8,Primates:1,Vertebrates:1	cd11377, Pro-peptidase_S53, Activation domain of S53 peptidases.  Members of this family are found in various subtilase propeptides, such as  pro-kumamolysin and tripeptidyl peptidase I, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase.
CDD:211390	113	EUKprk	Bacteria:52,Plants:6	cd11378, DUF296, Domain of unknown function found in archaea, bacteria, and plants.  This domain is found in proteins that contain AT-hook motifs, which suggests a role in DNA-binding for the proteins as a whole. Three conserved histidine residues appear to form a zinc-binding site, and the domain has been observed to form homotrimers. It co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins.
CDD:211392	138	EUKprk	Bacteria:20,Environmental:2,Invertebrates:35,Plants:31,Primates:1,Rodents:1,Vertebrates:3	cd11380, Ribosomal_S8e_like, Eukaryotic/archaeal ribosomal protein S8e and similar proteins.  This family contains the eukaryotic/archaeal ribosomal protein S8, a component of the small ribosomal subunits, as well as the NSA2 gene product.
CDD:211393	257	miss	miss	cd11381, NSA2, pre-ribosomal protein NSA2 (Nop seven-associated 2).  NSA2 appears to be a protein required for the maturation of 27S pre-rRNA in yeast; it has been characterized in mammalian cells as a nucleolar protein that might play a role in the regulation of the cell cycle and in cell proliferation.
CDD:211394	122	miss	miss	cd11382, Ribosomal_S8e, Eukaryotic/archaeal ribosomal protein S8e (RPS8).  The eukaryotic/archaeal ribosomal protein S8 is a component of the small (40S in eukaryotes, 30S in archaea) ribosomal subunits and interacts tightly with 18S rRNA (16S rRNA in archaea, presumably).
CDD:206743	140	miss	miss	cd11383, YfjP, YfjP GTPase.  The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.
CDD:206744	286	EUK	Invertebrates:18,Plants:9,Rodents:1,Vertebrates:2	cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins A and B.  RagA and RagB are closely related Rag GTPases (ras-related GTP-binding protein A and B) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr1. These domains function by forming heterodimers with RagC or RagD, and similarly, Gtr1 dimerizes with ...
CDD:206745	175	EUK	Invertebrates:12,Mammals:1,Plants:13,Primates:1,Vertebrates:3	cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and D.  RagC and RagD are closely related Rag GTPases (ras-related GTP-binding protein C and D) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr2. These domains form heterodimers with RagA or RagB, and similarly, Gtr2 dimerizes with Gtr1 in ...
CDD:206779	200	PRK	Bacteria:9	cd11386, MCP_signal, Methyl-accepting chemotaxis protein (MCP), signaling domain.  Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding ...
CDD:211395	135	EUK	Invertebrates:11,Plants:5,Primates:1,Vertebrates:1	cd11473, W2, C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon.  This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats.
CDD:271368	464	EUKprk	Bacteria:37,Invertebrates:10,Plants:1,Primates:1,Vertebrates:1	cd11474, SLC5sbd_CHT, Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain.  Na+/choline co-transport by CHT is Cl- dependent. Human CHT (also called CHT1) is encoded by the SLC5A7 gene, and is expressed in the central nervous system. hCHT1-mediated choline uptake may be the rate-limiting step in acetylcholine synthesis, and essential for cholinergic transmission. ...
CDD:271369	464	EUKprk	Bacteria:93,Environmental:2,Invertebrates:1	cd11475, SLC5sbd_PutP, Na(+)/proline cotransporter PutP and related proteins; solute binding domain.  Escherichia coli PutP catalyzes the Na+-coupled uptake of proline with a stoichiometry of 1:1. The putP gene is part of the put operon; this operon in addition encodes a proline dehydrogenase, allowing the use of proline as a source of nitrogen and/or carbon. This subfamily also includes the Bacillus subtilis Na+/proline ...
CDD:271370	493	EUKprk	Bacteria:16,Environmental:2,Plants:28	cd11476, SLC5sbd_DUR3, Na(+)/urea-polyamine cotransporter DUR3, and related proteins; solute-binding domain.  Dur3 is the yeast plasma membrane urea transporter. Saccharomyces cerevisiae DUR3 also transports polyamine. The polyamine uptake of S. cerevisiae DUR3 is activated upon its phosphorylation by polyamine transport protein kinase 2 (PTK2). S. cerevisiae DUR3 also appears to play a role in regulating the cellular boron ...
CDD:271371	493	PRK	Bacteria:55,Environmental:2	cd11477, SLC5sbd_u1, Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain.  SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate ...
CDD:271372	496	PRK	Bacteria:14	cd11478, SLC5sbd_u2, Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain.  SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) ...
CDD:271373	454	PRK	Bacteria:19	cd11479, SLC5sbd_u3, Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain.  SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) ...
CDD:271374	488	PRK	Bacteria:86,Environmental:1	cd11480, SLC5sbd_u4, Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain.  SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate ...
CDD:271375	480	EUK	Plants:39	cd11482, SLC-NCS1sbd_NRT1-like, nucleobase-cation-symport-1 (NCS1) transporter NRT1-like; solute-binding domain.  This fungal NCS1 subfamily includes various Saccharomyces cerevisiae transporters: nicotinamide riboside transporter 1 (Nrt1p, also called Thi71p), Dal4p (allantoin permease), Fui1p (uridine permease), Fur4p (uracil permease), and Thi7p (thiamine transporter). NCS1s are essential components of salvage pathways for nucleobases and related metabolites. ...
CDD:271377	406	EUKprk	Bacteria:28,Plants:1	cd11484, SLC-NCS1sbd_CobB-like, nucleobase-cation-symport-1 (NCS1) transporter CobB-like; solute-binding domain.  This NCS1 subfamily includes Escherichia coli CodB (cytosine permease), and the Saccharomyces cerevisiae transporters: Fcy21p (Purine-cytosine permease), and vitamin B6 transporter Tpn1. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and ...
CDD:271378	456	EUKprk	Bacteria:35,Plants:7	cd11485, SLC-NCS1sbd_YbbW-like, uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily, YbbW-like; solute-binding domain.  NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. This subfamily includes the putative allantoin transporter Escherichia coli YbbW (also known as GlxB2). NCS1s belong to a superfamily ...
CDD:271383	522	EUK	Invertebrates:27,Primates:1	cd11492, SLC5sbd_NIS-SMVT, Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain.  NIS (encoded by the SLC5A5 gene) transports I-, and other anions including ClO4-, SCN-, and Br-. SMVT (encoded by the SLC5A6 gene) transports biotin, pantothenic acid and lipoate. This subfamily also includes SMCT1 and -2. SMCT1(encoded by the SLC5A8 gene) is a high-affinity transporter of various monocarboxylates ...
CDD:271384	479	PRK	Bacteria:26	cd11493, SLC5sbd_NIS-like_u1, uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain.  Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1 is a high-affinity transporter while ...
CDD:271385	473	PRK	Bacteria:22	cd11494, SLC5sbd_NIS-like_u2, uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain.  Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters, SMCT1 and 2. SMCT1 is a high-affinity transporter ...
CDD:271386	473	PRK	Bacteria:32	cd11495, SLC5sbd_NIS-like_u3, uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain.  Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1 is a high-affinity transporter while ...
CDD:271387	543	EUK	Invertebrates:8,Primates:1,Vertebrates:3	cd11496, SLC6sbd-TauT-like, Na(+)- and Cl(-)-dependent taurine transporter TauT, and related proteins; solute-binding domain.  This subgroup represents the solute-binding domain of TauT-like Na(+)- and Cl(-)-dependent transporters. Family members include: human TauT which transports taurine, human GAT1, GAT2, and GAT3, and BGT1, which transport gamma-aminobutyric acid (GABA), and human CT1 which transports creatine. This subgroup ...
CDD:271388	537	EUK	Invertebrates:8,Primates:1,Vertebrates:2	cd11497, SLC6sbd_SERT-like, Na(+)- and Cl(-)-dependent monoamine transporters, SERT, NET, DAT1 and related proteins; solute binding domain.  This subgroup represents the solute-binding domain of transmembrane transporters that transport monoamine neurotransmitters from synaptic spaces into presynaptic neurons. Members include: NET which transports norepinephrine, SERT which transports serotonin, and DAT1 which transports dopamine. These ...
CDD:212133	72	PRK	Bacteria:41	cd11523, NTP-PPase, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily.  This superfamily contains enzymes that hydrolyze the alpha-beta phosphodiester bond of all canonical NTPs into monophosphate derivatives and pyrophosphate (PPi). Divalent ions, such as Mg2+ ion(s), are essential to activate a proposed water nucleophile and stabilize the charged intermediates to facilitate catalysis. These enzymes share a conserved divalent ...
CDD:211400	194	EUKprk	Bacteria:72,Invertebrates:1,Plants:13,Primates:1	cd11524, SYLF, The SYLF domain (also called DUF500), a novel lipid-binding module.  The SYLF domain is named after SH3YL1, Ysc84p/Lsb4p, Lsb3p, and plant FYVE, which are proteins that contain it. It is also called DUF500 and is highly conserved from bacteria to mammals. Some members, such as SH3YL1, Ysc84p, and Lsb3p, which represent the best characterized members of the family, also contain an SH3 domain, while family ...
CDD:211401	199	EUK	Invertebrates:4,Plants:10,Vertebrates:4	cd11525, SYLF_SH3YL1_like, The SYLF domain (also called DUF500), a novel lipid-binding module, of SH3 domain containing Ysc84-like 1 (SH3YL1) and similar proteins.  This subfamily is composed of yeast Ysc84 (also called LAS17-binding protein 4, Lsb4p) and Lsb3p proteins, vertebrate SH3YL1 (SH3 domain containing Ysc84-like 1), and similar proteins. They contain an N-terminal SYLF domain (also called DUF500) and a C-terminal SH3 domain. ...
CDD:211402	201	EUK	Plants:11	cd11526, SYLF_FYVE, The SYLF domain (also called DUF500), a novel lipid-binding module, of FYVE zinc finger domain containing proteins.  This subfamily is composed of uncharacterized proteins from plants and stramenopiles containing a FYVE zinc finger domain followed by a SYLF domain (also called DUF500). The SYLF domain of the related protein, SH3YL1, binds phosphoinositides with high affinity, while the N-terminal SYLF domains of both Ysc84p and Lsb3p have been ...
CDD:212134	94	EUKprk	Bacteria:46,Environmental:3,Invertebrates:1	cd11527, NTP-PPase_dUTPase, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins.  dUTPase (dUTP pyrophosphatase; EC 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate. It acts to ensure chromosomal integrity by reducing the effective ratio of dUTP/dTTP. Members in this family are dimeric dUTPases, such ...
CDD:212135	114	PRK	Bacteria:127,Environmental:1	cd11528, NTP-PPase_MazG_Nterm, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs.  MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related ...
CDD:212136	116	PRK	Bacteria:117	cd11529, NTP-PPase_MazG_Cterm, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'.  MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related domains in ...
CDD:212137	88	EUKprk	Bacteria:33,Invertebrates:1	cd11530, NTP-PPase_DR2231_like, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs.  This family includes a MazG-like NTP-PPase from Deinococcus radiodurans (DR2231), a putative NTP-PPase YP_001813558.1 from Exiguobacterium sibiricum and their bacterial homologs. DR2231 shows significant structural resemblance to MazG proteins, but is functionally ...
CDD:212138	93	PRK	Bacteria:19	cd11531, NTP-PPase_BsYpjD, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain putative pyrophosphatase YpjD from Bacillus subtilis and its bacterial homologs.  This family includes a putative pyrophosphatase Ypjd from Bacillus subtilis (BsYpjD) and its homologs. Although its biological role has not been described in detail, BsYpjD shows significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP ...
CDD:212139	95	PRK	Bacteria:65	cd11532, NTP-PPase_COG4997, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from archaea and bacteria.  The family includes some uncharacterized hypothetical proteins from archaea and bacteria. Although their biological roles remain unclear, the family members show significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) ...
CDD:212140	75	PRK	Bacteria:30	cd11533, NTP-PPase_Af0060_like, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in uncharacterized protein from Archaeoglobus fulgidus (Af0060) and its bacterial homologs.  This family includes an uncharacterized protein from Archaeoglobus fulgidus (Af0060) and its homologs from bacteria. Although its biological role remains unclear, Af0060 shows high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate ...
CDD:212141	84	EUKprk	Bacteria:113,Invertebrates:1,Plants:6	cd11534, NTP-PPase_HisIE_like, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs.  This family includes Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase, HisIE, and its homologs from all three kingdoms of life. E. coli HisIE is encoded by the hisIE gene, which is formed by hisE gene fused to hisl. HisIE ...
CDD:212142	76	PRK	Bacteria:26	cd11535, NTP-PPase_SsMazG, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Sulfolobus solfataricus (Ss) and its homologs from archaea and bacteria.  This family includes a MazG-like protein from Sulfolobus solfataricus (SsMazG) and its homologs from archaea and bacteria. Although its biological roles remain still unclear, SsMazG shows significant sequence similarity to the NTP-PPase MazG proteins. However, unlike typical ...
CDD:212144	90	EUKprk	Bacteria:81,Invertebrates:9,Plants:10,Rodents:1,Vertebrates:3	cd11537, NTP-PPase_RS21-C6_like, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs.  RS21-C6 proteins, highly expressed in all vertebrate genomes and green plants, act as house-cleaning enzymes, removing 5-methyl dCTP (m5dCTP) in order to prevent gene silencing. They show significant sequence similarity to the dimeric 2-deoxyuridine ...
CDD:212145	97	PRK	Bacteria:13	cd11538, NTP-PPase_u1, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria.  This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, ...
CDD:212146	85	PRK	Bacteria:31	cd11539, NTP-PPase_u2, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea.  The family corresponds to a group of uncharacterized hypothetical proteins from bacteria and archaea, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical ...
CDD:212147	76	PRK	Bacteria:26	cd11540, NTP-PPase_u3, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea.  This family corresponds to a group of uncharacterized hypothetical proteins from bacteria and archaea, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical ...
CDD:212148	91	PRK	Bacteria:42	cd11541, NTP-PPase_u4, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea.  This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG ...
CDD:212149	99	PRK	Bacteria:15	cd11542, NTP-PPase_u5, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea.  This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG ...
CDD:212150	87	PRK	Bacteria:13	cd11543, NTP-PPase_u6, Nucleoside Triphosphate Pyrophosphohydrolase EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea.  This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG ...
CDD:212152	115	PRK	Bacteria:12	cd11545, NTP-PPase_YP_001813558, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Exiguobacterium sibiricum YP_001813558.1 protein and its bacterial homologs.  This family contains a putative NTP_PPase (YP_001813558.1) from Exiguobacterium sibiricum and its bacterial homologs. Unlike normal dimeric dUTPase-like proteins with a central four-helix bundle forming the active site, YP_001813558.1 displays a very unusual interlaced ...
CDD:212153	84	EUKprk	Bacteria:3,Invertebrates:1,Plants:8	cd11546, NTP-PPase_His4, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in His4-like fungal histidine biosynthesis trifunctional proteins and their homologs.  This family includes fungal histidine biosynthesis trifunctional proteins and their homologs from eukaryotes and bacteria. Some family members contain three domains responsible for phosphoribosyl-AMP cyclohydrolase (PRAMP-CH), phosphoribosyl-ATP ...
CDD:211389	287	EUKprk	Bacteria:8,Invertebrates:1,Plants:1	cd11548, NodZ_like, Alpha 1,6-fucosyltransferase similar to Bradyrhizobium NodZ.  Bradyrhizobium NodZ is an alpha 1,6-fucosyltransferase involved in the biosynthesis of the nodulation factor, a lipo-chitooligosaccharide formed by three-to-six beta-1,4-linked N-acetyl-d-glucosamine (GlcNAc) residues and a fatty acid acyl group attached to the nitrogen atom at the non-reducing end. NodZ transfers L-fucose from the GDP-beta-L-fucose donor to ...
CDD:211403	159	EUK	Invertebrates:12,Primates:1,Rodents:1,Vertebrates:5	cd11549, Serine_rich_CAS, Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module.  CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where ...
CDD:271404	461	PRK	Bacteria:32,Environmental:1	cd11555, SLC-NCS1sbd_u1, uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily; solute-binding domain.  NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and solute carrier 6 family ...
CDD:211407	458	EUK	Invertebrates:15,Primates:1,Vertebrates:3	cd11557, ST7, Suppression of tumorigenicity 7.  ST7 is a metazoan protein that behaves as a tumor suppressor in human cancer cells. It appears to localize to the cytoplasm and plasma membrane, and may mediate tumor suppression by regulating genes that are involved in oncogenic pathways and/or maintain cellular structure. It has been suggested that the suppression of tumorigenicity is associated with a function in mediating the ...
CDD:211396	169	EUK	Invertebrates:27,Plants:42,Vertebrates:2,nodiv:1	cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic translation initiation factor 2B epsilon.  eIF2B is a heteropentameric complex which functions as a guanine nucleotide exchange factor in the recycling of eIF-2 during the initiation of translation in eukaryotes. The epsilon and gamma subunits are sequence similar and both are essential in yeast. Epsilon appears to be the catalytically active subunit, with gamma ...
CDD:211397	134	EUK	Invertebrates:21,Mammals:2,Plants:7,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic translation initiation factor 4 gamma 1 and similar proteins.  eIF4G1 is a component of the multi-subunit eukaryotic translation initiation factor 4F, which facilitates recruitment of the mRNA to the ribosome, a rate-limiting step during translation initiation. This C-terminal domain, whose structure resembles that of a set of concatenated ...
CDD:211398	194	EUK	Invertebrates:15,Plants:13,Vertebrates:3,nodiv:1	cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic translation initiation factor 5C and similar proteins.  eIF5C appears to be essential for the initiation of protein translation; its actual function, and specifically that of the C-terminal W2 domain, are not well understood. The Drosophila ortholog, kra (krasavietz) or exba (extra bases), may be involved in translational inhibition in neural development. The ...
CDD:211399	157	EUK	Invertebrates:32,Plants:41,Vertebrates:3,nodiv:1	cd11561, W2_eIF5, C-terminal W2 domain of eukaryotic translation initiation factor 5.  eIF5 functions as a GTPase acceleration protein (GAP), as well as a GDP dissociation inhibitor (GDI) during translational initiation in eukaryotes. The structure of this C-terminal domain resembles that of a set of concatenated HEAT repeats.
CDD:211408	126	EUK	Invertebrates:2,Mammals:1,Primates:1,Vertebrates:3,nodiv:1	cd11564, FAT-like_CAS_C, C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module.  CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of ...
CDD:211318	84	EUK	Invertebrates:23,Plants:16,Primates:1,Vertebrates:3,nodiv:1	cd11566, eIF1_SUI1, Eukaryotic initiation factor 1.  eIF1/SUI1 (eukaryotic initiation factor 1) plays an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
CDD:211319	76	EUKprk	Bacteria:95,Environmental:4,Plants:4	cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia coli YciH.  Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. The function of non-eukaryotic family members is unclear. Escherichia coli YciH is a non-essential protein and was ...
CDD:211413	99	EUKprk	Bacteria:201,Invertebrates:2,Plants:3	cd11572, RlmI_M_like, Middle domain of the SAM-dependent methyltransferase RlmI and related proteins.  This middle or central domain is typically found between an N-terminal PUA domain and a C-terminal SAM-dependent methyltransferase domain, such as in the Escherichia coli ribosomal RNA large subunit methyltransferase RlmI (YccW). It may be involved in binding to the RNA substrate.
CDD:211414	284	EUKprk	Bacteria:6,Plants:1	cd11573, GH99_GH71_like, Glycoside hydrolase families 71, 99, and related domains.  This superfamily of glycoside hydrolases contains families GH71 and GH99 (following the CAZY nomenclature), as well as other members with undefined function and specificity.
CDD:211415	338	EUKprk	Bacteria:4,Invertebrates:13,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd11574, GH99, Glycoside hydrolase family 99, an endo-alpha-1,2-mannosidase.  This family of glycoside hydrolases 99 (following the CAZY nomenclature) includes endo-alpha-1,2-mannosidase (EC 3.2.1.130), which is an important membrane-associated eukaryotic enzyme involved in the maturation of N-linked glycans. Specifically, it cleaves mannoside linkages internal to N-linked glycan chains by hydrolyzing an ...
CDD:211416	376	EUKprk	Bacteria:15,Invertebrates:1	cd11575, GH99_GH71_like_3, Uncharacterized glycoside hydrolase family 99-like domain.  This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism.
CDD:211417	378	EUKprk	Bacteria:23,Environmental:1,Plants:7	cd11576, GH99_GH71_like_2, Uncharacterized glycoside hydrolase family 99-like domain.  This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism. The domain may co-occur with other domains involved in the binding/processing of glycans.
CDD:211418	283	EUKprk	Bacteria:7,Invertebrates:2,Plants:43	cd11577, GH71, Glycoside hydrolase family 71.  This family of glycoside hydrolases 71 (following the CAZY nomenclature) function as alpha-1,3-glucanases (mutanases, EC 3.2.1.59). They appear to have an endo-hydrolytic mode of enzymatic activity and bacterial members are investigated as candidates for the development of dental caries treatments.The member from fission yeast, endo-alpha-1,3-glucanase Agn1p, plays a vital role in daughter ...
CDD:211419	313	EUKprk	Bacteria:10,Plants:1	cd11578, GH99_GH71_like_1, Uncharacterized glycoside hydrolase family 99-like domain.  This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism.
CDD:211420	347	EUKprk	Bacteria:120,Invertebrates:1,nodiv:1	cd11579, Glyco_tran_WbsX, Glycosyl hydrolase family 99-like domain of WbsX-like glycosyltransferases.  Members of this domain family are found in proteins within O-antigen biosynthesis clusters in Gram negative bacteria, where they may function as glycosyl hydrolases and typically co-occur with glycosyltransferase domains. They bear resemblance to GH71 and the GH99 family of alpha-1,2-mannosidases and may share a similar cataltyic site ...
CDD:211421	72	EUKprk	Bacteria:4,Invertebrates:5,Primates:1	cd11580, eIF2D_N_like, N-terminal domain of eIF2D, malignant T cell-amplified sequence 1 and related proteins.  This N-terminal domain of various proteins co-occurs with a PUA domain. Members of this family are: (1) MCTS-1 (malignant T cell-amplified sequence 1) or MCT-1 (multiple copies T cell malignancies), which may play roles in the regulation of the cell cycle, (2) the eukayotic translation initiation factor 2D, and (3) an ...
CDD:212547	103	EUKprk	Bacteria:1,Invertebrates:1,Plants:2,Primates:1	cd11581, GINS_A, Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3.  The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and ...
CDD:211424	69	EUK	Invertebrates:4,Primates:1,Rodents:1,Vertebrates:4	cd11582, Axin_TNKS_binding, Tankyrase binding N-terminal segment of axin.  This N-terminal region of axin mediates interactions with the ankyrin-repeat clusters 2 and 3 of tankyrase, which controls the turnover of axin via poly-ADP-ribosylation. Axin functions as a negative regulator of the WNT signaling pathway.
CDD:211425	94	EUK	Invertebrates:15,Plants:15,Primates:1,Vertebrates:3	cd11583, Orc6_mid, Middle domain of the origin recognition complex subunit 6.  Orc6 is a subunit of the origin recognition complex in eukaryotes, and it may be involved in binding to DNA. This model describes the central or middle domain of Orc6, whose structure resembles that of TFIIB, a DNA-binding transcription factor. Orc6 appears to form distinct complexes with DNA, and a putative DNA-binding site has been identified.
CDD:211426	100	EUK	Invertebrates:8,Primates:1,Vertebrates:3	cd11585, SATB1_N, N-terminal domain of SATB1 and similar proteins.  SATB1, the special AT-rich sequence-binding protein 1, is involved in organizing chromosomal loci into distinct loops, creating a "loopscape" that has a direct bearing on gene expression. This N-terminal domain, which may be involved in various interactions with chromatin proteins, resembles a ubiquitin domain and has been shown to form tetramers, a function critical to ...
CDD:212155	54	PRK	Bacteria:55	cd11586, VbhA_like, VbhA antitoxin and related proteins.  VbhA is the antitoxin to VbhT. The VbhT toxin of the mammalian pathogen Bartonella schoenbuchensis is responsible for the disruptive adenylation of host proteins. VbhT also induces FIC-domain-mediated growth arrest in bacteria; it is inhibited by this antitoxin which binds to block the ATP binding site of the VbhT FIC domain.
CDD:212537	274	PRK	Bacteria:19,Environmental:1	cd11589, Agmatinase_like_1, Agmatinase and related proteins.  This family includes known and predicted bacterial agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme, belonging to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and ...
CDD:212538	289	EUKprk	Bacteria:48,Invertebrates:3,Plants:16,Primates:1,Vertebrates:3	cd11592, Agmatinase_PAH, Agmatinase-like family includes proclavaminic acid amidinohydrolase.  This agmatinase subfamily contains bacterial and fungal/metazoan enzymes, including proclavaminic acid amidinohydrolase (PAH, EC 3.5.3.22) and Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA). PAH hydrolyzes amidinoproclavaminate to yield proclavaminate and urea in clavulanic acid ...
CDD:212539	263	EUKprk	Bacteria:132,Environmental:2,Plants:3	cd11593, Agmatinase-like_2, Agmatinase and related proteins.  This family includes known and predicted bacterial and archaeal agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme that belongs to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher ...
CDD:212541	288	EUKprk	Bacteria:55,Invertebrates:4,Plants:4	cd11599, HDAC_classII_2, Histone deacetylases and histone-like deacetylases, classII.  This subfamily includes eukaryotic as well as bacterial Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. In D. discoideum, where four ...
CDD:211427	413	EUK	Plants:9,nodiv:2	cd11602, Ndc10, Ndc10 component of the yeast centromere-binding factor 3.  Ndc10 is a multidomain protein conserved in Saccharomycotina that interacts with kinetochore components. This model characterizes the majority of the protein; some family members may have an additional C-terminal domain that is homologous to transcriptional activators (GCR1_C). Ndc10 is part of the centromere-binding factor 3 (CBF3) complex in budding yeast. The CBF3 complex contains ...
CDD:211429	54	EUK	Plants:17	cd11604, RTT106_N, histone chaperone RTT106, regulator of Ty1 transposition protein 106; N-terminal homodimerization domain.  This cd includes the N-terminal homodimerization domain of Saccharomyces cerevisiae Rtt106, a histone chaperone. In addition to this domain, Rtt106 contains two C-terminal pleckstrin-homology (PH) domains. The acetylation of lysine 56 in histone H3 (H3K56ac) is implicated in regulating nucleosome disassembly during gene transcription, and ...
CDD:211320	86	EUK	Invertebrates:28,Plants:24,Primates:1,Vertebrates:3,nodiv:1	cd11607, DENR_C, C-terminal domain of DENR and related proteins.  DENR (density regulated protein), together with MCT-1 (multiple copies T cell malignancies), has been shown to have similar function as eIF2D translation initiation factor (also known as ligatin), which is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner.
CDD:211321	85	EUK	Invertebrates:22,Plants:25,Primates:1,Vertebrates:3	cd11608, eIF2D_C, C-terminal domain of eIF2D and related proteins.  eIF2D translation initiation factor (also known as ligatin) is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner.
CDD:211422	77	EUK	Invertebrates:25,Plants:29,Vertebrates:3,nodiv:1	cd11609, MCT1_N, N-terminal domain of multiple copies T cell malignancies 1 and related proteins.  This N-terminal domain of MCT-1 (multiple copies T cell malignancies 1), also known as MCTS-1 (malignant T cell-amplified sequence 1), co-occurs with a PUA domain. MCT-1, together with DENR (density regulated protein), has been shown to have similar function as eIF2D translation initiation factor (also known as ligatin), which is ...
CDD:211423	76	EUK	Invertebrates:8,Plants:7,Primates:1,Vertebrates:2	cd11610, eIF2D_N, N-terminal domain of eIF2D and related proteins.  This N-terminal domain of eIF2D co-occurs with a PUA domain. eIF2D translation initiation factor (also known as ligatin) is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner.
CDD:212158	80	EUKprk	Bacteria:320,Environmental:3,Invertebrates:1,Plants:2	cd11613, SAF_AH_GD, Domains similar to fish antifreeze type III protein.  Altronate dehydratase (EC 4.2.1.7) converts D-altronate into 2-dehydro-3-deoxy-D-gluconate and is part of a bacterial pathway for the degradation of D-galacturonate. D-galactarate dehydratase (EC 4.2.1.42) eliminates water from D-galactarate to yield 5-dehydro-4-deoxy-D-glucarate, initializing the degradation of D-galactarate. The function of the ...
CDD:212159	61	EUKprk	Bacteria:487,Environmental:2,Plants:1,Vertebrates:1,nodiv:1	cd11614, SAF_CpaB_FlgA_like, SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB.  FlgA is a putative periplasmic chaperone that assists in the formation of the flagellar P ring; CpaB is a protein invoved in the assembly of the flp pili, which are bacterial virulence factors mediating non-specific adherence to surfaces; these proteins appear to contain a single SAF ...
CDD:212160	58	EUKprk	Bacteria:291,Environmental:4,Invertebrates:12,Plants:1,Primates:1,Vertebrates:4	cd11615, SAF_NeuB_like, C-terminal SAF domain of sialic acid synthetase.  Sialic acid synthetase (N-acetylneuraminate synthase or N-acetylneuraminate-9-phosphate synthase) catalyzes the condensation of phosphoenolpyruvate with N-acetylmannosamine (ManNAc, in bacteria) or N-acetylmannosamine-6-phosphate (ManNAc-6P, in mammals), to yield N-acetylneuramic acid (NeuNAc) or N-acetylneuramic ...
CDD:212161	80	EUKprk	Bacteria:75,Environmental:1,Plants:1,nodiv:2	cd11616, SAF_DH_OX_like, SAF domain of putative dehydrogenases or oxidoreductases.  C-terminal SAF domain of an uncharacterized family of putative dehydrogenases or oxidoreductases, which are otherwise members of the NAD(P)-dependent Rossmann-fold superfamily.
CDD:211316	44	EUK	Plants:10	cd11618, ChtBD1_1, Hevein or type 1 chitin binding domain; filamentous ascomycete subfamily.  Hevein or type 1 chitin binding domain (ChtBD1), a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural rubber latex, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin ...
CDD:212009	77	EUK	Invertebrates:12,Primates:1,Vertebrates:2	cd11619, HR1_CIP4-like, Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Cdc42-Interacting Protein 4 and similar proteins.  This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and ...
CDD:212010	72	EUK	Plants:5	cd11620, HR1_PKC-like_2_fungi, Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of fungal Protein Kinase C-like proteins.  This subfamily is composed of fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity. They contain two HR1 domains, C2 and C1 ...
CDD:212011	72	EUK	Plants:2	cd11621, HR1_PKC-like_1_fungi, First Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of fungal Protein Kinase C-like proteins.  This subfamily is composed of fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity. They contain two HR1 domains, C2 and C1 ...
CDD:212012	66	EUK	Invertebrates:10,Primates:1,Vertebrates:5	cd11622, HR1_PKN_1, First Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N.  PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, ...
CDD:212013	71	EUK	Invertebrates:8,Rodents:1,Vertebrates:2	cd11623, HR1_PKN_2, Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N.  PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, ...
CDD:212015	74	EUK	Invertebrates:1,Plants:1,Primates:1	cd11625, HR1_PKN_3, Third Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N.  PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, glucose ...
CDD:212017	71	EUK	Plants:8	cd11627, HR1_Ste20-like, Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Schizosaccharomyces pombe Ste20-like proteins.  This group is composed of predominantly uncharacterized fungal proteins, which contain two known domains: HR1 at the N-terminal region and REM (Ras exchanger motif) at the C-terminal region. One member protein from Schizosaccharomyces pombe is named Ste16 while its gene is called ste20 (a target of rapamycin complex 2 ...
CDD:212163	134	PRK	Bacteria:24	cd11640, HutP, Histidine Utilizing Protein, the hut operon positive regulatory protein.  The HutP protein family regulates the expression of 'hut' structural genes in Bacillus and other bacteria. It forms an anti-termination complex, which recognizes three UAG triplet units, separated by four non-conserved nucleotides on the RNA terminator region. In an L-histidine and Mg2+ dependent manner, HutP binds to the nascent hut mRNA leader transcript, and the ensuing ...
CDD:212500	228	PRK	Bacteria:78,Environmental:2	cd11641, Precorrin-4_C11-MT, Precorrin-4 C11-methyltransferase (CbiF/CobM).  Precorrin-4 C11-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin ...
CDD:212501	233	EUKprk	Bacteria:172,Environmental:8,Invertebrates:2,Plants:11,nodiv:1	cd11642, SUMT, Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT).  SUMT, an enzyme of the cobalamin and siroheme biosynthetic pathway, catalyzes the transformation of uroporphyrinogen III into precorrin-2. It transfers two methyl groups from S-adenosyl-L-methionine to the C-2 and C-7 atoms of uroporphyrinogen III to yield precorrin-2 via the intermediate ...
CDD:212502	247	PRK	Bacteria:18	cd11643, Precorrin-6A-synthase, Precorrin-6A synthase, the cobalamin biosynthesis enzyme CobF.  Precorrin-6A synthase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin ...
CDD:212503	201	PRK	Bacteria:219,Environmental:2	cd11644, Precorrin-6Y-methylase, Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE.  Precorrin-6Y methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not requires oxygen, and cobalt insertion is the first ...
CDD:212504	226	PRK	Bacteria:148,Environmental:1	cd11645, Precorrin_2_C20_MT, Precorrin-2 C20-methyltransferase, also named CobI or CbiL.  Precorrin-2 C20-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step ...
CDD:212505	240	EUKprk	Bacteria:82,Environmental:2,Plants:1	cd11646, Precorrin_3B_C17_MT, Precorrin-3B C(17)-methyltransferase (CobJ/CbiH).  Precorrin-3B C(17)-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards ...
CDD:212506	241	EUKprk	Bacteria:29,Environmental:4,Invertebrates:19,Mammals:1,Plants:16,Vertebrates:2	cd11647, Diphthine_synthase, Diphthine synthase, also known as DPH5.  Diphthine synthase, also known as diphthamide biosynthesis S-adenosylmethionine-dependent methyltransferase, participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. It catalyzes the trimethylation step in diphthamide biosynthesis. ...
CDD:212507	218	EUKprk	Bacteria:204,Environmental:5,Plants:9	cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI.  Proteins in this family catalyze the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA using S-adenosyl-L-methionine (SAM or Ado-Met) as the methyl donor. RsmI proteins employ the 30S subunit (not the 16S rRNA) as a substrate, suggesting that the methylation reaction occurs at a late step during ...
CDD:212508	229	PRK	Bacteria:40,Environmental:1	cd11649, RsmI_like, Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI).  Tetrapyrrole methylase uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. This uncharacterized subfamily exhibits sequence similarity to the ribosomal RNA small subunit methyltransferase I (RsmI), which catalyzes the 2-O-methylation of the ribose of cytidine 1402 ...
CDD:212164	253	EUK	Plants:12	cd11650, AT4G37440_like, Uncharacterized protein domain conserved in plants.  This domain contains an extensive protein sequence fragment that appears conserved in a number of plant proteins, including the gene product of Arabidopsis thaliana locus AT4G37440, which has been identified in transcriptional profiling as expressed at different levels in white cabbage cultivars.
CDD:212165	174	EUK	Plants:34	cd11651, YPK1_N_like, Fungal protein kinase domain similar to the N-terminus of YPK1.  This fungal domain family includes the N-terminal region of the Saccharomyces cerevisiae AGC kinases YPK1 and YPK2, which were found to be essential for the proliferation of yeast. YPK1 is required for cell growth and acts as a downstream kinase in the sphingolipid-mediated signaling pathway of yeast. It also plays a role in efficient endocytosis and in the maintenance of cell wall ...
CDD:212166	233	EUK	Invertebrates:7,Primates:1,Vertebrates:6	cd11652, SSH-N, N-terminal domain conserved in slingshot (SSH) phosphatases.  This domain or region conserved in Bilateria is found N-terminal to the DEK_C-like and catalytic domains of slingshot phosphatases. Slingshot is a cofilin-specific phosphatase. Dephosphorylation reactivates cofilin, which in turn depolymerizes actin and is thus required for actin filament reorganization. Slingshot is a member of the dual-specificity protein ...
CDD:212167	100	EUK	Mammals:1,Plants:16,Primates:2,Rodents:2,Vertebrates:4	cd11653, rap1_RCT, C-terminal domain of RAP1 recruits proteins to telomeres.  The RAP1 (repressor activator protein 1) C-terminal domain (RCT) mediates interactions with other proteins such as TRF2 (human), Rif1, Rif2, Sir3, Sir4 (Saccharomyces cerevisiae), and Taz1 (Schizosaccharomyces pombe) at telomeres and other loci. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere ...
CDD:212553	42	EUK	Mammals:9,Plants:1,Primates:6,Rodents:5,Vertebrates:5	cd11654, TRF2_RBM, RAP1 binding motif of telomere repeat binding factor.  TRF2 (Telomere repeat binding factor 2) functions as part of the 6-component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminus (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA-binding proteins (TRF2, TRF1 and POT1) and 3 recruited proteins that ...
CDD:212554	57	EUK	Invertebrates:2,Plants:52,Primates:1	cd11655, rap1_myb-like, DNA-binding modules of yeast Rap1 and related proteins.  Yeast Rap1 DNA-binding activity is mediated by a pair of DNA-binding modules comprised of 2 3-helix bundles with an N-terminal arm, closely matching the structure of homeodomain and myb-type proteins. Human Rap1 has a single myb-like module, and may not bind DNA directly. Rap1, identified in budding yeast as repressor-activator protein 1, is a conserved telomere ...
CDD:240667	188	EUK	Invertebrates:2,Mammals:1,Primates:1,Vertebrates:6	cd11657, TIN2_N, N-terminal domain of TRF-interacting nuclear factor 2; shelterin complex protein of telomeres.  TIN2 is one of the six proteins of shelterin complex, which acts to protect telomeres from DNA damage repair machinery. TIN2 binds directly to TRF1 and TRF2 and stabilizes TRF2 complex-telomere binding by tethering it to the TRF1 complex. TIN2 binding to TRF2 is primarily via the TRF binding motif (TBM) region and ...
CDD:212557	53	EUK	Invertebrates:14,Plants:13,Primates:1,Vertebrates:2	cd11659, SANT_CDC5_II, SANT/myb-like DNA-binding domain of Cell Division Cycle 5-Like Protein repeat II.  In humans, cell division cycle 5-like protein (CDC5) functions in pre-mRNA splicing in cell cycle control. The DNA-binding, myb-like domain of CDC5 is a member of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix ...
CDD:212558	50	EUK	Invertebrates:15,Plants:24,Primates:1,Vertebrates:4	cd11660, SANT_TRF, Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family.  Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, ...
CDD:212559	46	EUK	Invertebrates:12,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd11661, SANT_MTA3_like, Myb-Like Dna-Binding Domain of MTA3 and related proteins.  Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with ...
CDD:212130	238	EUKprk	Bacteria:5,Plants:8	cd11665, LamB_like, Aspergillus nidulans lactam utilization protein LamB and similar proteins.  This eukaryotic and bacterial subfamily of the LamB/YbgL family, includes Aspergillus nidulans protein LamB. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory ...
CDD:212168	115	EUKprk	Bacteria:21,Invertebrates:1,Plants:1	cd11669, TTHB210-like, Hypothetical protein TTHB210, a sigma(E)-regulated gene product found in Thermus thermophilus, and similar proteins.  TTHB210 is an uncharacterized protein found in Thermus thermophilus, and is controlled by the sigma(E) /anti-sigma(E) regulatory system. It is one of the five proteins of the extracytoplasmic function (ECF) sigma factor sigma(E)-regulated gene products whose physiological function have not been ...
CDD:213032	120	EUK	Invertebrates:10,Primates:1,Vertebrates:3,nodiv:1	cd11672, ADDz, ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain.  The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse ...
CDD:212563	120	EUK	Invertebrates:5	cd11673, hemoglobin_linker_C, Globular domain of extracellular hemoglobin linker.  This family of hemoglobin linker chains is restricted to annelid worms, and participates in the formation of the large erythrocruorin respiratory complex. Via its N-terminal coiled-coil segment (not included in this model), the molecule forms trimers, which are part of a scaffold organizing the overall complex architecture; the latter encompasses 36 linkers and 144 hemoglobins in ...
CDD:212487	63	EUK	Invertebrates:9,Plants:2,Primates:1,Rodents:1,Vertebrates:4	cd11676, Gemin6, Gemin 6.  Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin 7, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring.
CDD:212488	77	EUK	Invertebrates:12,Vertebrates:4,nodiv:1	cd11677, Gemin7, Gemin 7.  Gemins 7, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 7 forms a heterodimer with Gemin 6, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring.
CDD:212490	65	PRK	Bacteria:7,Environmental:1	cd11679, archaeal_Sm_like, archaeal Sm-related protein.  Archaeal Sm-related proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ...
CDD:212543	294	EUK	Invertebrates:1,Plants:10	cd11680, HDAC_Hos1, Class I histone deacetylases Hos1 and related proteins.  Saccharomyces cerevisiae Hos1 is responsible for Smc3 deacetylation. Smc3 is an important player during the establishment of sister chromatid cohesion. Hos1 belongs to the class I histone deacetylases (HDACs). HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes ...
CDD:212544	377	EUK	Invertebrates:10,Primates:1,Vertebrates:1	cd11681, HDAC_classIIa, Histone deacetylases, class IIa.  Class IIa histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) to yield deacetylated histones. This subclass includes animal HDAC4, HDAC5, HDAC7, and HDCA9. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act ...
CDD:212566	392	EUK	Invertebrates:15,Plants:26,Primates:1	cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins.  DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members ...
CDD:212590	101	EUK	Plants:36	cd11691, HRI1_like, Tandem repeat domain of HRI1 and related proteins.  Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that ...
CDD:212591	134	miss	miss	cd11692, HRI1_N_like, N-terminal domain of HRI1 and related proteins.  Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that forms a ...
CDD:212592	90	miss	miss	cd11693, HRI1_C_like, C-terminal domain of HRI1 and related proteins.  Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that forms a ...
CDD:212567	376	EUK	Invertebrates:5,Primates:1,Rodents:1	cd11694, DHR2_DOCK_D, Dock Homology Region 2, a GEF domain, of Class D Dedicator of Cytokinesis proteins.  DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class D, also called the Zizimin subfamily, ...
CDD:212568	368	EUK	Invertebrates:9,Primates:1,Rodents:1,nodiv:1	cd11695, DHR2_DOCK_C, Dock Homology Region 2, a GEF domain, of Class C Dedicator of Cytokinesis proteins.  DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class C, also called the ...
CDD:212570	400	EUK	Invertebrates:10,Primates:1	cd11697, DHR2_DOCK_A, Dock Homology Region 2, a GEF domain, of Class A Dedicator of Cytokinesis proteins.  DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class A includes Dock1, 2 and 5. Class A DOCKs are ...
CDD:240451	118	EUKprk	Bacteria:3,Invertebrates:28,Plants:9,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	cd11709, SPRY, SPRY domain.  SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), ...
CDD:212548	129	EUK	Invertebrates:25,Plants:30,Vertebrates:3	cd11710, GINS_A_psf1, Alpha-helical domain of GINS complex protein Psf1.  Psf1 is a component of the GINS tetrameric protein complex. Psf1 is mainly expressed in highly proliferative tissues, such as blastocysts, adult bone marrow, and testis, in which the stem cell system is active. Loss of Psf1 causes embryonic lethality. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation ...
CDD:212549	119	EUK	Invertebrates:33,Mammals:1,Plants:39,Vertebrates:3,nodiv:1	cd11711, GINS_A_Sld5, Alpha-helical domain of GINS complex protein Sld5.  Sld5 is a component of GINS tetrameric protein complex, and within the complex Sld5 interacts with Psf1 via its N-terminal A-domain, and with Psf2 through a combination of the A and B domains. Sld5 in Drosophila is required for normal cell cycle progression and the maintenance of genomic integrity. GINS is a complex of four subunits (Sld5, Psf1, ...
CDD:212550	119	EUK	Invertebrates:38,Plants:33,Vertebrates:3,nodiv:1	cd11712, GINS_A_psf2, Alpha-helical domain of GINS complex protein Psf2 (partner of Sld5 2).  Psf2 is a component of GINS tetrameric protein complex and has been found to play important roles in normal eye development in Xenopus laevis. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the ...
CDD:212551	109	EUK	Invertebrates:40,Mammals:1,Plants:48,Vertebrates:2,nodiv:1	cd11713, GINS_A_psf3, Alpha-helical domain of GINS complex protein Psf3 (partner of Sld5 3).  Psf3 is a component of GINS, a tetrameric protein complex. Psf3 expression is up regulated in malignant colon cancer and it might be involved in cancer cell proliferation. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome ...
CDD:212552	105	PRK	Bacteria:60,Environmental:4	cd11714, GINS_A_archaea, Alpha-helical domain of archaeal GINS complex proteins.  The GINS complex is involved in replication of archaeal and eukayotic genomes. The archaeal DNA replication system is a simplified version of that of the eukaryotes. Like its eukaryotic counterpart, the archaeal GINS complex is tetrameric, but instead of four different subunits (Sld5, Psf1, Psf2 and Psf3) it consists of two different proteins named Gins51 and Gins23. ...
CDD:212584	152	EUKprk	Bacteria:293,Environmental:6,Invertebrates:7,Plants:10,Primates:1,Vertebrates:3,nodiv:1	cd11715, THUMP_AdoMetMT, THUMP domain associated with S-adenosylmethionine-dependent methyltransferases.  Proteins of this family contain an N-terminal THUMP domain and a C-terminal S-adenosylmethionine-dependent methyltransferase domain. Members have been implicated in the modification of 23S RNA m2G2445, a highly conserved modification in bacteria and in the m2G6 modification of tRNA.  ...
CDD:212585	166	PRK	Bacteria:238,Environmental:2	cd11716, THUMP_ThiI, THUMP domain of thiamine biosynthesis protein ThiI.  ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop ...
CDD:212586	158	EUKprk	Bacteria:17,Environmental:1,Invertebrates:26,Plants:37,Primates:1,Vertebrates:3,nodiv:1	cd11717, THUMP_THUMPD1_like, THUMP domain-containing protein 1-like.  This family contains THUMP domain-only proteins including THUMP domain-containing protein 1 and Saccharomyces cerevisiae Tan1. Tan1 is non essential and has been shown to be required for the formation of the modified nucleoside N(4)-acetylcytidine (ac(4)C) in tRNA. To date, there is no functional information available ...
CDD:212587	145	PRK	Bacteria:11	cd11718, THUMP_SPOUT, THUMP domain associated with SPOUT RNA Methylases.  Members of this archaeal protein family are characterized by containing an N-terminal THUMP domain and a C-terminal SPOUT RNA methyltransferase domain. No functional information is available The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by ...
CDD:212594	1202	EUK	Invertebrates:10,Plants:3,Rodents:1,Vertebrates:3	cd11720, FANCI, Fanconi anemia I protein.  The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at ...
CDD:212595	1161	EUK	Invertebrates:11,Plants:3,Rodents:1,Vertebrates:3	cd11721, FANCD2, Fanconi anemia D2 protein.  The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA ...
CDD:212596	92	EUK	Invertebrates:13,Primates:1,Vertebrates:4,nodiv:1	cd11722, SOAR, STIM1 Orai1-activating region.  STIM1 (stromal interaction module 1) is a metazoan transmembrane protein located in the endoplasmic reticulum (ER) membrane, which functions as a sensor for ER calcium ion levels and activates store-operated Ca2+ influx channels (SOCs), such as the Orai1 Ca2+ channel located in the plasma membrane. STIM1 has an N-terminal Ca-binding EF-hand domain, which is located in the ER lumen. ...
CDD:212509	220	PRK	Bacteria:19	cd11723, YabN_N, N-terminal S-AdoMet dependent methylase domain of Bacillus subtilis YabN and related proteins.  This family contains proteins similar to Bacillus subtilis YabN, which is a fusion of an N-terminal TP-methylase and a C-terminal MazG-type nucleotide pyrophosphohydrolase domain. MazG-like NTP-PPases have been implicated in house-cleaning functions such as degrading abnormal (d)NTPs. TP-methylases use S-AdoMet (S-adenosyl-L-methionine or SAM) in the ...
CDD:212510	255	PRK	Bacteria:8	cd11724, TP_methylase_like, Uncharacterized subfamily of S-AdoMet dependent tetrapyrrole methylases.  TP-methylases use S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis, other members like Diphthine synthase and Ribosomal RNA small subunit methyltransferase I (RsmI) act on other substrates. The function of this subfamily is not known.
CDD:213033	126	miss	miss	cd11725, ADDz_Dnmt3, ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3).  Dnmt3 is a de novo DNA methyltransferase family that includes two active enzymes Dnmt3a and -3b and one regulatory factor Dnmt3l. The ADDz domain of Dnmt3 is located in the C-terminal region of Dnmt3, which is an active catalytic domain in Dnmt3a and -b, but lacks some residues for enzymatic activity in Dnmt3l. DNA methylation is an important epigenetic mechanism involved in ...
CDD:213034	127	EUK	Invertebrates:23,Mammals:1,Plants:10,Primates:1,Vertebrates:4,nodiv:1	cd11726, ADDz_ATRX, ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked).  ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific ...
CDD:212497	198	PRK	Bacteria:23	cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins, classical (c) SDRs.  Lin1944 protein from Listeria Innocua is a classical SDR, it contains a glycine-rich motif similar to the canonical motif of the SDR NAD(P)-binding site. However, the typical SDR active site residues are absent in this subgroup of proteins of undetermined function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann ...
CDD:213038	159	EUKprk	Bacteria:442,Environmental:2,Invertebrates:1,Plants:1,Vertebrates:1	cd11740, YajQ_like, Proteins similar to Escherichia coli YajQ.  In Pseudomonas syringae, YajQ functions as a host protein involved in the temporal control of bacteriophage Phi6 gene transcription. It has been shown to bind to the phage's major structural core protein P1, most likely activating transcription by acting indirectly on the RNA polymerase. YajQ may remain bound to the phage particles throughout ...
CDD:240666	108	EUK	Mammals:1,Plants:5,Rodents:2,Vertebrates:1	cd11741, TIN2_TBM, TRF-binding motif region of TRF-Interacting Nuclear factor 2.  The C-terminal region of TIN2 contains the TRF-binding motif (TBM), while the TIN2 N-terminal region acts in the modulation of TRF1 activity via the inhibition of tankyrase 1. TIN2 binding to TRF2 is primarily via the TRF binding motif (TBM) and the N-terminus, while the far C-terminal region interacts with lower affinity. The TIN2 TBM, but not the ...
CDD:213039	122	EUKprk	Bacteria:26,Plants:4	cd11743, Cthe_2751_like, Uncharacterized protein domain similar to Clostridium thermocellum 2751.  Cthe_2751 has been found to form homodimers. Based on structural similarity to other families, a role in processing nucleic acids was suggested, though interactions with DNA could not be demonstrated.
CDD:213372	124	EUK	Plants:13	cd11745, Yos9_DD, C-terminal dimerization domain (DD) of Saccharomyces cerevisiae Yos9 and related proteins.  Yos9 participates in the ER-associated protein degradation pathway that targets misfolded proteins for proteolysis. Yos9 is a component of the reductase degradation (HRD) ubiquitin-ligase complex, specifically part of the luminal submodule of the ligase. Yos9 scans proteins for specific oligosaccharide modifications, which are critical determinants of ...
CDD:213062	179	PRK	Bacteria:9	cd11746, GH94N_like, N-terminal domain of glycoside hydrolase family 94 and related domains.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an ...
CDD:213063	204	PRK	Bacteria:18	cd11747, GH94N_like_1, Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase and many other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain. This GH64N domain also occurs as a standalone domain in distantly related proteins ...
CDD:213064	294	EUKprk	Bacteria:11,Plants:1	cd11748, GH94N_NdvB_like, Glycoside hydrolase family 94 N-terminal-like domain of NdvB-like proteins.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from ...
CDD:213065	229	PRK	Bacteria:21	cd11749, GH94N_LBP_like, N-terminal-like domain of Paenibacillus sp. YM-1 Laminaribiose Phosphorylase and similar proteins.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes bacterial laminaribiose phosphorylase. This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Bacterial laminaribiose phosphorylase ...
CDD:213067	223	PRK	Bacteria:9	cd11751, GH94N_like_4, Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the ...
CDD:213069	336	EUKprk	Bacteria:82,Environmental:2,Invertebrates:1,nodiv:1	cd11753, GH94N_ChvB_NdvB_2_like, Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cyclic beta 1-2 glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the chromosomal chvB virulence gene). This second of two tandemly repeated GH94-N-terminal-like domains has not been characterized functionally. Some ...
CDD:213070	303	PRK	Bacteria:24	cd11754, GH94N_CBP_like, N-terminal domain of cellobiose phosphorylase (CBP) and similar proteins.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20) or cellobiose:phosphate alpha-D-glucosyltransferase, or CepA. This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Cellobiose ...
CDD:213071	300	PRK	Bacteria:24	cd11755, GH94N_ChBP_like, N-terminal domain of chitobiose phosphorylase (ChBP) and similar proteins.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes chitobiose phosphorylase (EC:2.4.1.-). This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Chitobiose phosphorylase catalyzes the reversible phosphate dependent ...
CDD:213072	284	PRK	Bacteria:37,Environmental:1,nodiv:1	cd11756, GH94N_ChvB_NdvB_1_like, First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains.  The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cyclic beta 1-2 glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the chromosomal chvB virulence gene). This first of two tandemly repeated GH94-N-terminal-like domains has not been characterized functionally. Some beta 1-2 glucan ...
CDD:212697	55	EUK	Invertebrates:5,Primates:1	cd11763, SH3_SNX9_like, Src Homology 3 domain of Sorting Nexin 9 and similar proteins.  Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. This subfamily consists of SH3 domain containing SNXs including ...
CDD:212698	54	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd11764, SH3_Eps8, Src Homology 3 domain of Epidermal growth factor receptor kinase substrate 8 and similar proteins.  This group is composed of Eps8 and Eps8-like proteins including Eps8-like 1-3, among others. These proteins contain N-terminal Phosphotyrosine-binding (PTB), central SH3, and C-terminal effector domains. Eps8 binds either Abi1 (also called E3b1) or Rab5 GTPase activating protein RN-tre through its SH3 ...
CDD:212700	53	EUK	Invertebrates:10,Primates:1,Vertebrates:1,nodiv:1	cd11766, SH3_Nck_2, Second Src Homology 3 domain of Nck adaptor proteins.  Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates ...
CDD:212701	56	EUK	Invertebrates:4,Plants:1,Primates:1	cd11767, SH3_Nck_3, Third Src Homology 3 domain of Nck adaptor proteins.  This group contains the third SH3 domain of Nck, the first SH3 domain of Caenorhabditis elegans Ced-2 (Cell death abnormality protein 2), and similar domains. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a ...
CDD:212702	54	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:1	cd11768, SH3_Tec_like, Src Homology 3 domain of Tec-like Protein Tyrosine Kinases.  The Tec (Tyrosine kinase expressed in hepatocellular carcinoma) subfamily is composed of Tec, Btk, Bmx (Etk), Itk (Tsk, Emt), Rlk (Txk), and similar proteins. They are cytoplasmic (or nonreceptor) tyr kinases containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Most Tec subfamily members ...
CDD:212703	57	EUK	Invertebrates:5,Primates:1,Vertebrates:1	cd11769, SH3_CSK, Src Homology 3 domain of C-terminal Src kinase.  CSK is a cytoplasmic (or nonreceptor) tyr kinase containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. They negatively regulate the activity of Src kinases that are anchored to the plasma membrane. To inhibit Src kinases, CSK is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor ...
CDD:212704	54	EUK	Invertebrates:6,Vertebrates:5	cd11770, SH3_Nephrocystin, Src Homology 3 domain of Nephrocystin (or Nephrocystin-1).  Nephrocystin contains an SH3 domain involved in signaling pathways that regulate cell adhesion and cytoskeletal organization. It is a protein that in humans is associated with juvenile nephronophthisis, an inherited kidney disease characterized by renal fibrosis that lead to chronic renal failure in children. It is localized in cell-cell junctions in renal duct ...
CDD:212705	60	EUK	Plants:13	cd11771, SH3_Pex13p_fungal, Src Homology 3 domain of fungal peroxisomal membrane protein Pex13p.  Pex13p, located in the peroxisomal membrane, contains two transmembrane regions and a C-terminal SH3 domain. It binds to the peroxisomal targeting type I (PTS1) receptor Pex5p and the docking factor Pex14p through its SH3 domain. It is essential for both PTS1 and PTS2 protein import pathways into the peroxisomal matrix. Pex13p binds Pex14p, which contains a PxxP motif, in ...
CDD:212706	53	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd11772, SH3_OSTF1, Src Homology 3 domain of metazoan osteoclast stimulating factor 1.  OSTF1, also named OSF or SH3P2, is a signaling protein containing SH3 and ankyrin-repeat domains. It acts through a Src-related pathway to enhance the formation of osteoclasts and bone resorption. It also acts as a negative regulator of cell motility. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity ...
CDD:212709	57	EUK	Plants:13	cd11775, SH3_Sla1p_3, Third Src Homology 3 domain of the fungal endocytic adaptor protein Sla1p.  Sla1p facilitates endocytosis by playing a role as an adaptor protein in coupling components of the actin cytoskeleton to the endocytic machinery. It interacts with Abp1p, Las17p and Pan1p, which are activator proteins of actin-related protein 2/3 (Arp2/3). Sla1p contains multiple domains including three SH3 domains, a SAM (sterile alpha motif) domain, and a Sla1 homology ...
CDD:212713	57	EUK	Invertebrates:5,Primates:1,Vertebrates:1	cd11779, SH3_Irsp53_BAIAP2L, Src Homology 3 domain of Insulin Receptor tyrosine kinase Substrate p53, Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2 (BAIAP2)-Like proteins, and similar proteins.  Proteins in this family include IRSp53, BAIAP2L1, BAIAP2L2, and similar proteins. They all contain an Inverse-Bin/Amphiphysin/Rvs (I-BAR) or IMD domain in addition to the SH3 domain. IRSp53, also known as BAIAP2, is a scaffolding ...
CDD:212714	55	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd11780, SH3_Sorbs_3, Third (or C-terminal) Src Homology 3 domain of Sorbin and SH3 domain containing (Sorbs) proteins and similar domains.  This family, also called the vinexin family, is composed predominantly of adaptor proteins containing one sorbin homology (SoHo) and three SH3 domains. Members include the third SH3 domains of Sorbs1 (or ponsin), Sorbs2 (or ArgBP2), Vinexin (or Sorbs3), and similar domains. They ...
CDD:212723	55	EUK	Invertebrates:7,Primates:1	cd11789, SH3_Nebulin_family_C, C-terminal Src Homology 3 domain of the Nebulin family of proteins.  Nebulin family proteins contain multiple nebulin repeats, and may contain an N-terminal LIM domain and/or a C-terminal SH3 domain. They have molecular weights ranging from 34 to 900 kD, depending on the number of nebulin repeats, and they all bind actin. They are involved in the regulation of actin filament architecture and function as stabilizers and ...
CDD:212725	59	EUK	Invertebrates:8	cd11791, SH3_UBASH3, Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing proteins, also called TULA (T cell Ubiquitin LigAnd) family of proteins.  UBASH3 or TULA proteins are also referred to as Suppressor of T cell receptor Signaling (STS) proteins. They contain an N-terminal UBA domain, a central SH3 domain, and a C-terminal histidine phosphatase domain. They bind c-Cbl through the SH3 domain and to ubiquitin via UBA. In some vertebrates, ...
CDD:212726	55	EUK	Invertebrates:8,Vertebrates:1,nodiv:1	cd11792, SH3_Fut8, Src homology 3 domain of Alpha1,6-fucosyltransferase (Fut8).  Fut8 catalyzes the alpha1,6-linkage of a fucose residue from a donor substrate to N-linked oligosaccharides on glycoproteins in a process called core fucosylation, which is crucial for growth factor receptor-mediated biological functions. Fut8-deficient mice show severe growth retardation, early death, and a pulmonary emphysema-like phenotype. Fut8 is also ...
CDD:212727	55	EUK	Invertebrates:2,Primates:1,Vertebrates:1,nodiv:1	cd11793, SH3_ephexin1_like, Src homology 3 domain of ephexin-1-like SH3 domain containing Rho guanine nucleotide exchange factors.  Members of this family contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and C-terminal SH3 domains. They include the Rho guanine nucleotide exchange factors ARHGEF5, ARHGEF16, ARHGEF19, ARHGEF26, ARHGEF27 (also called ephexin-1), and similar proteins, and are also called ...
CDD:212735	55	EUK	Invertebrates:4	cd11801, SH3_JIP1_like, Src homology 3 domain of JNK-interacting proteins 1 and 2, and similar domains.  JNK-interacting proteins (JIPs) function as scaffolding proteins for c-Jun N-terminal kinase (JNK) signaling pathways. They bind to components of Mitogen-activated protein kinase (MAPK) pathways such as JNK, MKK, and several MAP3Ks such as MLK and DLK. There are four JIPs (JIP1-4); all contain a JNK binding domain. JIP1 and JIP2 also contain SH3 and ...
CDD:212736	52	EUK	Invertebrates:9,Rodents:1	cd11802, SH3_Endophilin_B, Src homology 3 domain of Endophilin-B.  Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilins ...
CDD:212737	55	EUK	Invertebrates:10,Primates:1,Rodents:1,Vertebrates:3	cd11803, SH3_Endophilin_A, Src homology 3 domain of Endophilin-A.  Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms (A1, A2, and A3). Endophilin-A proteins are enriched in the brain and play multiple roles in ...
CDD:212739	53	EUK	Invertebrates:6,Plants:4,Primates:1,Rodents:1,Vertebrates:1	cd11805, SH3_GRB2_like_C, C-terminal Src homology 3 domain of Growth factor receptor-bound protein 2 (GRB2) and related proteins.  This family includes the adaptor protein GRB2 and related proteins including Drosophila melanogaster Downstream of receptor kinase (DRK), Caenorhabditis elegans Sex muscle abnormal protein 5 (Sem-5), GRB2-related adaptor protein (GRAP), GRAP2, and similar proteins. Family members contain an ...
CDD:212753	54	EUK	Invertebrates:3,Plants:4	cd11819, SH3_Cortactin_like, Src homology 3 domain of Cortactin and related proteins.  This subfamily includes cortactin, Abp1 (actin-binding protein 1), hematopoietic lineage cell-specific protein 1 (HS1), and similar proteins. These proteins are involved in regulating actin dynamics through direct or indirect interaction with the Arp2/3 complex, which is required to initiate actin polymerization. They all contain at least one C-terminal SH3 domain. ...
CDD:212755	53	EUK	Invertebrates:7,Primates:1,Vertebrates:3,nodiv:1	cd11821, SH3_ASAP, Src homology 3 domain of ArfGAP with SH3 domain, ankyrin repeat and PH domain containing proteins.  ASAPs are Arf GTPase activating proteins (GAPs) and they function in regulating cell growth, migration, and invasion. They contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. Vertebrates contain at least three ...
CDD:212771	53	EUK	Invertebrates:6,Plants:2,Vertebrates:1	cd11837, SH3_Intersectin_2, Second Src homology 3 domain (or SH3B) of Intersectin.  Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN ...
CDD:212773	58	EUK	Invertebrates:6,Plants:1,Primates:1	cd11839, SH3_Intersectin_4, Fourth Src homology 3 domain (or SH3D) of Intersectin.  Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ...
CDD:212779	52	EUK	Invertebrates:11,Primates:1,Rodents:1,Vertebrates:4	cd11845, SH3_Src_like, Src homology 3 domain of Src kinase-like Protein Tyrosine Kinases.  Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, Yes, and Brk. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal ...
CDD:212783	53	EUK	Invertebrates:6,Vertebrates:3	cd11849, SH3_SPIN90, Src homology 3 domain of SH3 protein interacting with Nck, 90 kDa (SPIN90).  SPIN90 is also called NCK interacting protein with SH3 domain (NCKIPSD), Dia-interacting protein (DIP), 54 kDa vimentin-interacting protein (VIP54), or WASP-interacting SH3-domain protein (WISH). It is an F-actin binding protein that regulates actin polymerization and endocytosis. It associates with the Arp2/3 complex near actin filaments and ...
CDD:212785	62	EUK	Invertebrates:5,Plants:1,Primates:1	cd11851, SH3_RIM-BP, Src homology 3 domains of Rab3-interacting molecules (RIMs) binding proteins.  RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their ...
CDD:212788	56	EUK	Plants:12	cd11854, SH3_Fus1p, Src homology 3 domain of yeast cell fusion protein Fus1p.  Fus1p is required at the cell surface for cell fusion during the mating response in yeast. It requires Bch1p and Bud7p, which are Chs5p-Arf1p binding proteins, for localization to the plasma membrane. It acts as a scaffold protein to assemble a cell surface complex which is involved in septum degradation and inhibition of the NOG pathway to promote cell fusion. The SH3 domain of Fus1p ...
CDD:212790	53	EUK	Invertebrates:13,Plants:1,Primates:1,nodiv:1	cd11856, SH3_p47phox_like, Src homology 3 domains of the p47phox subunit of NADPH oxidase and similar domains.  This family is composed of the tandem SH3 domains of p47phox subunit of NADPH oxidase and Nox Organizing protein 1 (NoxO1), the four SH3 domains of Tks4 (Tyr kinase substrate with four SH3 domains), the five SH3 domains of Tks5, the SH3 domain of obscurin, Myosin-I,  and similar domains. Most members of this group also ...
CDD:212791	55	EUK	Mammals:3,Vertebrates:6	cd11857, SH3_DBS, Src homology 3 domain of DBL's Big Sister (DBS), a guanine nucleotide exchange factor.  DBS, also called MCF2L (MCF2-transforming sequence-like protein) or OST, is a Rho GTPase guanine nucleotide exchange factor (RhoGEF), facilitating the exchange of GDP and GTP. It was originally isolated from a cDNA screen for sequences that cause malignant growth. It plays roles in regulating clathrin-mediated endocytosis and cell migration through ...
CDD:212792	55	EUK	Plants:18	cd11858, SH3_Myosin-I_fungi, Src homology 3 domain of Type I fungal Myosins.  Type I myosins (myosin-I) are actin-dependent motors in endocytic actin structures and actin patches. They play roles in membrane traffic in endocytic and secretory pathways, cell motility, and mechanosensing. Saccharomyces cerevisiae has two myosins-I, Myo3 and Myo5, which are involved in endocytosis and the polarization of the actin cytoskeleton. Myosin-I contains an N-terminal ...
CDD:212793	62	EUK	Invertebrates:10,Primates:1,Rodents:1	cd11859, SH3_ZO, Src homology 3 domain of the Tight junction proteins, Zonula occludens (ZO) proteins.  ZO proteins are scaffolding proteins that associate with each other and with other proteins of the tight junction, zonula adherens, and gap junctions. They play roles in regulating cytoskeletal dynamics at these cell junctions. They are considered members of the MAGUK (membrane-associated guanylate kinase) protein family, which is ...
CDD:212794	63	EUK	Invertebrates:7,Vertebrates:3	cd11860, SH3_DLG5, Src homology 3 domain of Disks Large homolog 5.  DLG5 is a multifunctional scaffold protein that is located at sites of cell-cell contact and is involved in the maintenance of cell shape and polarity. Mutations in the DLG5 gene are associated with Crohn's disease (CD) and inflammatory bowel disease (IBD). DLG5 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of ...
CDD:212795	61	EUK	Invertebrates:12,Plants:1,Primates:1,Rodents:1,Vertebrates:1	cd11861, SH3_DLG-like, Src Homology 3 domain of Disks large homolog proteins.  The DLG-like proteins are scaffolding proteins that cluster at synapses and are also called PSD (postsynaptic density)-95 proteins or SAPs (synapse-associated proteins). They play important roles in synaptic development and plasticity, cell polarity, migration and proliferation. They are members of the MAGUK (membrane-associated guanylate ...
CDD:212796	61	EUK	Invertebrates:17,Primates:1,Vertebrates:2,nodiv:1	cd11862, SH3_MPP, Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins.  The MPP/p55 subfamily of MAGUK (membrane-associated guanylate kinase) proteins includes at least eight vertebrate members (MPP1-7 and CASK), four Drosophila proteins (Stardust, Varicose, CASK and Skiff), and other similar proteins; they all contain one each of the core of three domains characteristic of MAGUK ...
CDD:212797	62	EUK	Invertebrates:14,Primates:1,Rodents:2	cd11863, SH3_CACNB, Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta.  Voltage-dependent calcium channels (Ca(V)s) are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. ...
CDD:212798	58	EUK	Invertebrates:16,Vertebrates:3,nodiv:1	cd11864, SH3_PEX13_eumet, Src Homology 3 domain of eumetazoan Peroxisomal biogenesis factor 13.  PEX13 is a peroxin and is required for protein import into the peroxisomal matrix and membrane. It is an integral membrane protein that is essential for the localization of PEX14 and the import of proteins containing the peroxisome matrix targeting signals, PTS1 and PTS2. Mutations of the PEX13 gene in humans lead to a wide range of peroxisome ...
CDD:212805	56	EUK	Invertebrates:7,Rodents:1,Vertebrates:1	cd11872, SH3_DOCK_AB, Src Homology 3 domain of Class A and B Dedicator of Cytokinesis proteins.  DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. They are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1, 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 ...
CDD:212806	53	EUK	Invertebrates:8,Vertebrates:2	cd11873, SH3_CD2AP-like_1, First Src Homology 3 domain (SH3A) of CD2-associated protein and similar proteins.  This subfamily is composed of the first SH3 domain (SH3A) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate ...
CDD:212807	53	EUK	Invertebrates:2,Primates:1,nodiv:1	cd11874, SH3_CD2AP-like_2, Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins.  This subfamily is composed of the second SH3 domain (SH3B) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also ...
CDD:212810	53	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:1	cd11877, SH3_PIX, Src Homology 3 domain of Pak Interactive eXchange factors.  PIX proteins are Rho guanine nucleotide exchange factors (GEFs), which activate small GTPases by exchanging bound GDP for free GTP. They act as GEFs for both Cdc42 and Rac 1, and have been implicated in cell motility, adhesion, neurite outgrowth, and cell polarity. Vertebrates contain two proteins from the PIX subfamily, alpha-PIX and beta-PIX. ...
CDD:212811	54	EUK	Plants:12	cd11878, SH3_Bem1p_1, First Src Homology 3 domain of Bud emergence protein 1 and similar domains.  Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 domain. Bem1p is a scaffolding protein that is critical for proper Cdc42p activation during bud formation in yeast. During budding and mating, Bem1p migrates to the plasma membrane where it ...
CDD:212815	54	EUK	Invertebrates:4,Plants:1,Primates:1,Rodents:1	cd11882, SH3_GRAF-like, Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase and similar proteins.  This subfamily is composed of Rho GTPase activating proteins (GAPs) with similarity to GRAF. Members contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. Although vertebrates harbor four Rho GAPs in the GRAF subfamily including GRAF, ...
CDD:212816	55	EUK	Plants:16	cd11883, SH3_Sdc25, Src Homology 3 domain of Sdc25/Cdc25 guanine nucleotide exchange factors.  This subfamily is composed of the Saccharomyces cerevisiae guanine nucleotide exchange factors (GEFs) Sdc25 and Cdc25, and similar proteins. These GEFs regulate Ras by stimulating the GDP/GTP exchange on Ras. Cdc25 is involved in the Ras/PKA pathway that plays an important role in the regulation of metabolism, stress responses, and proliferation, depending on available ...
CDD:212818	55	EUK	Mammals:1,Plants:3,Primates:1,Vertebrates:1	cd11885, SH3_SH3TC, Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains.  This subfamily is composed of vertebrate SH3TC proteins and hypothetical fungal proteins containing BAR and SH3 domains. Mammals contain two SH3TC proteins, SH3TC1 and SH3TC2. The function of SH3TC1 is unknown. SH3TC2 is localized in Schwann cells in the peripheral nervous system, where it interacts ...
CDD:212820	60	EUK	Plants:9	cd11887, SH3_Bbc1, Src Homology 3 domain of Bbc1 and similar domains.  This subfamily is composed of Saccharomyces cerevisiae Bbc1p, also called Mti1p (Myosin tail region-interacting protein), and similar proteins. Bbc1p interacts with and regulates type I myosins in yeast, Myo3p and Myo5p, which are involved in actin cytoskeletal reorganization. It also binds and inhibits Las17, a WASp family protein that functions as an activator of the Arp2/3 complex. Bbc1p contains ...
CDD:212844	55	EUK	Invertebrates:6,Rodents:1,Vertebrates:1	cd11911, SH3_CIP4-like, Src Homology 3 domain of Cdc42-Interacting Protein 4.  This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory ...
CDD:212845	55	EUK	Plants:22	cd11912, SH3_Bzz1_1, First Src Homology 3 domain of Bzz1 and similar domains.  Bzz1 (or Bzz1p) is a WASP/Las17-interacting protein involved in endocytosis and trafficking to the vacuole. It physically interacts with type I myosins and functions in the early steps of endocytosis. Together with other proteins, it induces membrane scission in yeast. Bzz1 contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), a central coiled-coil, and two C-terminal ...
CDD:212945	62	EUK	Invertebrates:9,Primates:1,Vertebrates:3,nodiv:1	cd12012, SH3_RIM-BP_2, Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins.  RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic ...
CDD:240527	420	EUKprk	Bacteria:33,Environmental:1,Invertebrates:1,Plants:1,Vertebrates:1	cd12082, MATE_like, Multidrug and toxic compound extrusion family and similar proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A ...
CDD:213373	48	EUK	Invertebrates:12,Primates:1,Vertebrates:4,nodiv:1	cd12083, DD_cGKI, Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I.  Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a ...
CDD:213043	37	EUK	Invertebrates:3,Mammals:1,Plants:3,Primates:1,Rodents:1	cd12084, DD_R_PKA, Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains.  cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits ...
CDD:213374	48	miss	miss	cd12085, DD_cGKI-alpha, Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha.  Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory ...
CDD:213052	38	EUK	Plants:5,Primates:1,Vertebrates:3	cd12087, TM_EGFR-like, Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases.  PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding ...
CDD:213058	119	PRK	Bacteria:23,Environmental:5	cd12089, Hef_ID, insert domain of Hef nuclease and similar archaeal proteins.  Archaeal Hef helicase/nuclease, originally identified in the hyperthermophilic archaeon Pyrococcus furiosus, contains an N-terminal SF2 helicase domain and an C-terminal XPF/Mus81-type nuclease domain. Hef has been shown to process flap- or fork-DNA structures, and that both helicase and nuclease domain independently recognize branched DNA, with a strong preference for ...
CDD:213059	120	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:7	cd12090, MDA5_ID, insert domain of MDA5 helicase and similar proteins.  MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) ...
CDD:213060	122	EUK	Invertebrates:19,Plants:48,Primates:1,Vertebrates:2	cd12091, FANCM_ID, insert domain of FANCM helicase and similar proteins.  FANCM and related proteins, like Mph1 and Fml1, are DNA junction-specific helicases/translocases that bind to and process perturbed replication forks and intermediates of homologous recombination. FANCM contains an N-terminal superfamily 2 helicase (SF2) domain, although FANCM, in contrast to other members of this family, does not exhibit DNA helicase ...
CDD:213044	44	EUK	Invertebrates:14	cd12097, DD_RI_PKA, Dimerization/Docking domain of the Type I Regulatory subunit of cAMP-dependent protein kinase.  cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation ...
CDD:213045	38	EUK	Plants:12	cd12098, DD_R_PKA_fungi, Dimerization/Docking domain of the Regulatory subunit of fungal cAMP-dependent protein kinase.  cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is ...
CDD:213046	39	EUK	Invertebrates:12,Rodents:1,Vertebrates:1,nodiv:1	cd12099, DD_RII_PKA, Dimerization/Docking domain of the Type II Regulatory subunit of cAMP-dependent protein kinase.  cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of ...
CDD:213047	39	EUK	Invertebrates:10,Primates:1,Vertebrates:4,nodiv:1	cd12100, DD_CABYR_SP17, Dimerization/Docking domain of the sperm fibrous sheath proteins, Calcium-Binding tYrosine-phosphorylation Regulated protein and Sperm Protein 17.  CABYR and SP17 are naturally located in human sperm fibrous sheath (FS). CABYR was originally isolated from spermatoza and was thought to be testis-specific, but has been recently been observed in lung and brain tumors. It is a polymorphic calcium binding ...
CDD:213031	121	PRK	Bacteria:85	cd12105, HmuY, Bacterial proteins similar to Porphyromonas gingivalis HmuY.  HmuY is a hemophore that scavenges heme from infected hosts and delivers it to the outer membrane receptor HmuR. Related but uncharacterized proteins do not appear to share the specific heme-binding site.
CDD:213982	113	EUKprk	Bacteria:256,Environmental:2,Invertebrates:11	cd12107, Hemerythrin, Hemerythrin.  Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in ...
CDD:213983	130	EUKprk	Bacteria:52,Invertebrates:2,Plants:17,Primates:1	cd12108, Hr-like, Hemerythrin-like domain.  Hemerythrin (Hr) like domains have the same four alpha helix bundle and a similar, but slightly different active site structure than hemerythrin. They are non-heme diiron binding proteins mainly found in bacteria and eukaryotes. Like Hr, they may be involved in oxygen transport or like human FBXL5 (F-box and leucine-rich repeat protein 5), a member of this group, play a role in ...
CDD:213984	158	EUKprk	Bacteria:15,Invertebrates:6,Primates:1,Vertebrates:3	cd12109, Hr_FBXL5, Hemerythrin-like domain of FBXL5-like proteins.  Human FBXL5 (F-box and leucine-rich repeat protein 5) protein plays a role in cellular iron homeostasis. It is part of an E3 ubiquitin ligase complex that targets the iron regulatory protein IRP2 for proteasomal degradation. The FBXL5's stability is regulated by iron concentration, with its iron- and oxygen-binding hemerythrin domain acting as a ...
CDD:213994	244	EUKprk	Bacteria:123,Invertebrates:3,Plants:6,nodiv:2	cd12110, PHP_HisPPase_Hisj_like, Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like.  Bacillus subtilis YtvP HisJ has strong histidinol phosphate phosphatase (HisPPase) activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases ...
CDD:213996	235	PRK	Bacteria:12	cd12112, PHP_HisPPase_Chlorobi_like, Polymerase and Histidinol Phosphatase domain of Chlorobi like.  The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. Chlorobi PHP is uncharacterized protein. HisPPase catalyzes the eighth step of histidine ...
CDD:213997	283	PRK	Bacteria:103,Environmental:3	cd12113, PHP_PolIIIA_DnaE3, Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3.  PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA ...
CDD:213322	476	PRK	Bacteria:20	cd12114, A_NRPS_TlmIV_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including Streptoalloteichus tallysomycin biosynthesis genes.  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large ...
CDD:213323	449	PRK	Bacteria:9	cd12115, A_NRPS_Sfm_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including Saframycin A gene cluster from Streptomyces lavendulae.  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large ...
CDD:213324	438	PRK	Bacteria:24	cd12116, A_NRPS_Ta1_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including salinosporamide A polyketide synthase.  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes ...
CDD:213325	474	PRK	Bacteria:28	cd12117, A_NRPS_Srf_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including Bacillus subtilis termination module Surfactin (SrfA-C).  The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large ...
CDD:213326	520	EUKprk	Bacteria:10,Plants:4	cd12118, ttLC_FACS_AEE21_like, Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis.  This family includes fatty acyl-CoA synthetases that can activate medium to long-chain fatty acids. These enzymes catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. ...
CDD:213327	517	EUKprk	Bacteria:21,Invertebrates:1	cd12119, ttLC_FACS_AlkK_like, Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles.  This family includes fatty acyl-CoA synthetases that can activate medium-chain to long-chain fatty acids. They catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The fatty ...
CDD:213377	96	EUK	Invertebrates:13,Plants:8,Rodents:1,Vertebrates:1	cd12121, MARK_C_like, C-terminal kinase associated domain 1 (KA1), a phospholipid binding domain, of microtubule affinity-regulating kinases, and similar domains.  Microtubule-associated protein/microtubule affinity regulating kinases (MARKs), also called partition-defective (Par-1) kinases, are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein ...
CDD:213378	132	EUK	Invertebrates:18,Plants:18,Primates:1,Rodents:1	cd12122, AMPKA_C, C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha catalytic subunit.  AMPK, a serine/threonine protein kinase (STK), catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It acts as a sensor for the energy status of the cell and is activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose ...
CDD:271279	185	PRK	Bacteria:21	cd12124, Pgbs, Protoglobins (Pgbs).  Pgbs are single-domain globins of yet unknown biological function. Included in this subfamily are Pgbs from the strictly anaerobic methanogen Methanosarcina acetivorans (MaPgb) and from the obligate aerobic hyperthermophile Aeropyrum pernix (ApPgb). MaPgb is a dimeric globin which in addition to the 3-on-3 helical sandwich contains an N-terminal extension. This extension, along with other Pgb-specific loops buries the heme ...
CDD:271280	159	EUKprk	Bacteria:9,Plants:5	cd12125, APC_alpha, Allophycocyanin alpha subunit of the phycobiliosome core.  Phycobiliosomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker ...
CDD:271281	163	EUKprk	Bacteria:8,Plants:4	cd12126, APC_beta, Allophycocyanin beta subunit of the phycobiliosome core.  Phycobiliosomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker ...
CDD:271283	170	EUKprk	Bacteria:9,Plants:4	cd12128, PBP_PBS-LCM, Phycobiliprotein-like domain of the phycobiliosome core-membrane linker polypeptide.  Phycobiliosomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae, they consist of a central core and radiating rods and function to harvest and channel light energy toward the photosynthetic reaction centers (RCs) within the membrane. They are comprised of phycobiliproteins or chromophorylated proteins (PBPs) maintained ...
CDD:271285	154	PRK	Bacteria:14	cd12130, Apl, Allophycocyanin-like globins.  Phycobiliosomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of ...
CDD:271286	128	EUKprk	Bacteria:49,Plants:5	cd12131, HGbI_like, Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins.  HGbI is a single-domain heme-containing protein isolated from Methylacidiphilum infernorum, an aerobic acidophilic and thermophlic methanotroph. M. infernorum grows optimally at pH 2.0 and 60C and its home is New Zealands Hell's Gate geothermal park. The physiological role of HGbI has yet to be determined. It has an extremely strong resistance to ...
CDD:271287	145	EUK	Invertebrates:5,Vertebrates:3	cd12137, GbX, Globin_X (GbX).  Zebrafish globin X (GbX) is expressed at low levels in neurons of the central nervous system, and appears to be associated with the sensory system. GbX is likely to be attached to the cell membrane via S-palmitoylation and N-myristoylation. It's unlikely to have a true respiratory function as it is membrane-associated. It has been suggested that it may protect the lipids in the cell membrane from oxidation or act as ...
CDD:213387	114	EUKprk	Bacteria:39,Environmental:2,Invertebrates:1,Plants:13	cd12144, SDH_N_domain, Saccharopine dehydrogenase N-terminal domain.  SDH N-terminal domain is named due to its appearance at the N-terminal of SDH in eukaryotes, but can be found C-terminal of the SDH-like domain in other enzymes, such as the bifunctional lysine ketoglutarate reductase/saccharopine dehydrogenase enzyme. SDH catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to ...
CDD:213388	94	EUK	Invertebrates:9,Plants:3,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd12145, Rev1_C, C-terminal domain of the Y-family polymerase Rev1.  Rev1 is a eukaryotic translesion synthesis (TLS) polymerase; TLS is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. ...
CDD:213389	181	EUK	Invertebrates:7,Primates:1,Vertebrates:4,nodiv:1	cd12146, STING_C, C-terminal domain of STING.  STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding ...
CDD:213390	552	EUK	Plants:10	cd12147, Cep3_C, C-terminal domain of the Cep3, a subunit of the yeast centromere-binding factor 3.  Cep3, together with Skp1, Ctf13, and Ndc10, forms the yeast centromere-binding factor 3 (CBF3) which initiates kinetochore assembly by binding to the CDEIII locus of centromeric DNA. Cep3 is comprised of two domains, the N-terminal DNA-binding module, a Zn2Cys6-cluster, C-terminal domain, which dimerizes and is believed to be involved in the recruitment of the ...
CDD:213391	410	EUK	Plants:154	cd12148, fungal_TF_MHR, fungal transcription factor regulatory middle homology region.  This domain is present in the large family of fungal zinc cluster transcription factors that contain an N-terminal GAL4-like C6 zinc binuclear cluster DNA-binding domain. Examples of members of this large fungal group are the following Saccharomyces cerevisiae transcription factors, GAL4, STB5, DAL81, CAT8, RDR1, HAL9, PUT3, PPR1, ASG1, RSF2, PIP2, as well as the C-terminal ...
CDD:213392	91	PRK	Synthetic:1,Viruses:16,nodiv:1	cd12149, Flavi_E_C, Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E.  The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The ...
CDD:213393	172	EUK	Invertebrates:11,Rodents:2,Vertebrates:3,nodiv:1	cd12150, talin-RS, rod-segment of the talin C-terminal domain.  The talin rod-segment characterize by this model interacts with its N-terminal FERM domain to mask its integrin-binding site and interferes with interactions between the FERM domain and the cellular membrane. Talin is a large and ubiquitous cytoskeletal protein concentrated at focal adhesion sites. It is involved in linking integrins to the actin cytoskeleton.
CDD:213394	282	EUKprk	Bacteria:133,Environmental:2,Invertebrates:21,Mammals:1,Plants:21,Vertebrates:4,nodiv:1	cd12151, F1-ATPase_gamma, mitochondrial ATP synthase gamma subunit.  The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of ...
CDD:213395	123	EUKprk	Bacteria:227,Environmental:2,Invertebrates:18,Mammals:1,Plants:22,Vertebrates:3,nodiv:2	cd12152, F1-ATPase_delta, mitochondrial ATP synthase delta subunit.  The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is ...
CDD:213396	45	EUK	Invertebrates:17,Mammals:1,Plants:17,Vertebrates:3,nodiv:1	cd12153, F1-ATPase_epsilon, eukaryotic mitochondrial ATP synthase epsilon subunit.  The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes, and in chloroplast thylakoid membranes. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits (only found in ...
CDD:240632	314	PRK	Bacteria:30	cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family.  Phosphoglycerate Dehydrogenase (PGDH) catalyzes the NAD-dependent conversion of 3-phosphoglycerate into 3-phosphohydroxypyruvate, which is the first step in serine biosynthesis. Over-expression of PGDH has been implicated as supporting proliferation of certain breast cancers, while PGDH deficiency is linked to defects in mammalian central nervous system development. PGDH is a ...
CDD:240633	301	EUKprk	Bacteria:63,Plants:9	cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase.  Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the NADP-dependent reduction of hydroxyphenylpyruvates, hydroxypyruvate, or pyruvate to its respective lactate. HPPR acts as a dimer and is related to D-isomer-specific 2-hydroxyacid dehydrogenases, a superfamily that includes groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine ...
CDD:240634	318	PRK	Bacteria:13	cd12157, PTDH, Thermostable Phosphite Dehydrogenase.  Phosphite dehydrogenase (PTDH), a member of the D-specific 2-hydroxyacid dehydrogenase family, catalyzes the NAD-dependent formation of phosphate from phosphite (hydrogen phosphonate). PTDH has been suggested as a potential enzyme for cofactor regeneration systems. The D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine ...
CDD:240635	343	PRK	Bacteria:62	cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains.  D-Erythronate-4-phosphate Dehydrogenase (E. coli gene PdxB), a D-specific 2-hydroxyacid dehydrogenase family member, catalyzes the NAD-dependent oxidation of erythronate-4-phosphate, which is followed by transamination to form 4-hydroxy-L-threonine-4-phosphate within the de novo biosynthesis pathway of vitamin B6. D-Erythronate-4-phosphate dehydrogenase has the common ...
CDD:240636	303	EUKprk	Bacteria:21,Plants:1	cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate ...
CDD:240638	315	PRK	Bacteria:22	cd12161, GDH_like_1, Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family.  This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, aka Hydroxypyruvate Reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a ...
CDD:240639	307	EUKprk	Bacteria:95,Environmental:1,Invertebrates:1,nodiv:1	cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240640	334	EUK	Plants:15	cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine ...
CDD:240641	306	EUKprk	Bacteria:85,Environmental:1,Plants:1,nodiv:1	cd12164, GDH_like_2, Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family.  This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid ...
CDD:240642	314	PRK	Bacteria:27,nodiv:1	cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, ...
CDD:240643	300	EUKprk	Bacteria:30,Plants:1	cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate ...
CDD:240644	330	PRK	Bacteria:30,nodiv:1	cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, ...
CDD:240645	321	EUK	Plants:31	cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like dehydrogenases.  D-Mandelate dehydrogenase (D-ManDH), identified as an enzyme that interconverts benzoylformate and D-mandelate, is a D-2-hydroxyacid dehydrogenase family member that catalyzes the conversion of c3-branched 2-ketoacids. D-ManDH exhibits broad substrate specificities for 2-ketoacids with large hydrophobic side chains, particularly those with C3-branched side chains. 2-hydroxyacid dehydrogenases ...
CDD:240646	308	EUKprk	Bacteria:46,Environmental:1,Plants:10	cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.  Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, ...
CDD:240647	294	PRK	Bacteria:10	cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, ...
CDD:240648	310	PRK	Bacteria:36	cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid dehydrogenases.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, ...
CDD:240649	306	PRK	Bacteria:64,nodiv:1	cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains.  Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase ...
CDD:240650	304	EUKprk	Bacteria:116,Environmental:1,Invertebrates:9,Plants:6,Vertebrates:2,nodiv:1	cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains.  Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in ...
CDD:240651	305	EUKprk	Bacteria:42,Invertebrates:2,Plants:3	cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains.  Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific ...
CDD:240652	311	EUKprk	Bacteria:34,Plants:4	cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240653	304	EUKprk	Bacteria:23,Invertebrates:3,Plants:3	cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains.  Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis ...
CDD:240654	321	PRK	Bacteria:11	cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240655	317	PRK	Bacteria:20	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240656	306	PRK	Bacteria:14	cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240657	308	PRK	Bacteria:11	cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains.  2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate ...
CDD:240658	295	PRK	Bacteria:22,nodiv:1	cd12181, ceo_syn, N(5)-(carboxyethyl)ornithine synthase.  N(5)-(carboxyethyl)ornithine synthase (ceo_syn) catalyzes the NADP-dependent conversion of N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine + pyruvate. Ornithine plays a key role in the urea cycle, which in mammals is used in arginine biosynthesis, and is a precursor in polyamine synthesis. ceo_syn is related to the NAD-dependent L-alanine dehydrogenases. Like formate dehydrogenase and related ...
CDD:240659	328	EUKprk	Bacteria:69,Invertebrates:7,Plants:12,nodiv:1	cd12183, LDH_like_2, D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains.  D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2-domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins ...
CDD:240660	330	PRK	Bacteria:16	cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic domains.  (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. HGDH is a member of the D-2-hydroxyacid NAD(+)-dependent dehydrogenase family; these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ ...
CDD:240661	322	PRK	Bacteria:19	cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and (R)-2-Hydroxyglutarate Dehydrogenase-like proteins, NAD-binding and catalytic domains.  This group contains various putative dehydrogenases related to D-lactate dehydrogenase (LDH), (R)-2-hydroxyglutarate dehydrogenase (HGDH), and related enzymes, members of the 2-hydroxyacid dehydrogenases family. LDH catalyzes the interconversion of pyruvate and lactate, and HGDH catalyzes the NAD-dependent reduction of ...
CDD:240662	329	PRK	Bacteria:39	cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains.  D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenases family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate ...
CDD:240663	329	PRK	Bacteria:14	cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains.  D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins are NAD-dependent members ...
CDD:240664	351	EUKprk	Bacteria:12,Invertebrates:4,Plants:7	cd12188, SDH, Saccharopine Dehydrogenase NAD-binding and catalytic domains.  Saccharopine Dehydrogenase (SDH) catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to alpha-ketoglutarate and lysine, in the alpha-aminoadipate pathway of L-lysine biosynthesis. SHD is structurally related to formate dehydrogenase and similar enzymes, having a 2-domain structure in which a Rossmann-fold NAD(P)-binding ...
CDD:240665	433	EUKprk	Bacteria:2,Invertebrates:17,Plants:14,Primates:1,Vertebrates:3	cd12189, LKR_SDH_like, bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase enzyme.  Bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase protein is a pair of enzymes linked on a single polypeptide chain that catalyze the initial, consecutive steps of lysine degradation. These proteins are related to the 2-domain saccharopine dehydrogenases. Along with formate dehydrogenase ...
CDD:213397	159	PRK	Bacteria:42	cd12190, Bacova_04320_like, Uncharacterized proteins similar to Bacteroides ovatus 4320.  This model characterized a family of proteins conserved in Bacteroidetes, similar to B. ovatus ATCC 8483 reading frame 04320. Structurally, the protein resembles members of the SRPBCC domain superfamily (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC).
CDD:213398	90	EUK	Plants:30	cd12191, gal11_coact, gall11 coactivator domain.  Gall11/MED15 acts in the general regulation of GAL structural genes and is required for full expression for several genes in this pathway, including GALs 1,7, and 10 in Saccharomyces cerevisiae. GAL11 function is dependent on GCN4 functionality and binds GCN4 in a degenerate manner with multiple orientations found at the GCN4-Gal11 interface.
CDD:213399	40	EUK	Plants:24,Primates:1,Vertebrates:3	cd12192, GCN4_cent, GCN4 central activation domain-like acidic activation domain.  GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region.
CDD:269833	54	EUK	Plants:37	cd12193, bZIP_GCN4, Basic leucine zipper (bZIP) domain of General control protein GCN4: a DNA-binding and dimerization domain.  GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain. In amino acid-deprived cells, GCN4 is up-regulated leading to ...
CDD:213379	122	EUK	Plants:20	cd12194, Kcc4p_like_C, C-terminal kinase associated domain 1 (KA1), a phospholipid binding domain, of Kcc4p and similar proteins.  This subfamily is composed of three Saccharomyces cerevisiae proteins, Kcc4p, Gin4p, and Hsl1p, as well as similar serine/threonine protein kinases (STKs). They catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. Kcc4p, Gin4p, and Hsl1p are septin-associated proteins that are involved in ...
CDD:213380	116	EUK	Plants:23	cd12195, CIPK_C, C-terminal regulatory domain of Calcineurin B-Like (CBL)-interacting protein kinases.  CIPKs are serine/threonine protein kinases (STKs), catalyzing the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They comprise a unique family in higher plants of proteins that interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of ...
CDD:213383	96	EUK	Invertebrates:15,Primates:1,Vertebrates:2,nodiv:1	cd12198, MELK_C, C-terminal kinase associated domain 1 (KA1) of Maternal embryonic leucine zipper kinase.  MELK, also called protein kinase 38 (PK38) or pEg3 kinase, is a cell cycle-regulated serine/threonine protein kinase (STK) that catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It is phosphorylated and maximally active during mitosis and is involved in regulating cell ...
CDD:213401	66	EUK	Invertebrates:4,Primates:1,Rodents:1,Vertebrates:4	cd12202, CASP8AP2, Caspase 8-associated protein 2 myb-like domain.  This domain is the SANT/myb-like domain of Caspase 8-associated protein 2 (CASP8AP2) / GON-4 like proteins. CASP8AP2 (aka Flice-Associated Huge Protein (FLASH)) is implicated in numerous gene regulatory roles including roles in embryogenesis, oncogenesis, down-regulation of replication-dependent histone genes, regulation of Caspase 8 activity at the ...
CDD:213402	66	EUK	Invertebrates:2,Plants:10	cd12203, GT1, GT1, myb-like, SANT family.  GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb ...
CDD:213176	48	PRK	Bacteria:27	cd12204, CBD_like, Cellulose-binding domain, chitinase and related proteins.  This group contains proteins related to the cellulose-binding domain of Erwinia chrysanthemi endoglucanase Z (EGZ) and Serratia marcescens chitinase B (ChiB). Gram negative plant parasite Erwinia chrysanthemi produces a variety of depolymerizing enzymes to metabolize pectin and cellulose on the host plant. Cellulase EGZ has a modular structure, with N-terminal catalytic domain linked to a ...
CDD:213344	382	EUK	Invertebrates:11,Rodents:1	cd12205, RasGAP_plexin, Ras-GTPase Activating Domain of plexins.  Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Ligand binding activates signal transduction pathways controlling axon guidance in the nervous system and other developmental processes, including cell migration and morphogenesis, immune function, and tumor progression. Plexins are divided into four types (A-D) according ...
CDD:213345	359	EUK	Invertebrates:4,Plants:15	cd12206, RasGAP_IQGAP_related, Ras-GTPase Activating Domain of proteins related to IQGAPs.  RasGAP: Ras-GTPase Activating Domain. RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence ...
CDD:213403	150	EUKprk	Bacteria:64,Environmental:1,Plants:11	cd12208, septicolysin_like, putative septicolysin, cholesterol-dependent cytolysin family and related proteins.  This group contains some members identified as septicolysin. While septolysin is poorly characterized, it has been identified as a a cholesterol-dependent cytolysin, and acts to facilitate the infection of certain pathogenic bacteria to cells. Cholesterol-dependent cytolysins are pore-forming toxins that aid in bacterial ...
CDD:213405	113	EUK	Plants:111,Primates:1,Rodents:1	cd12212, Fis1, Mitochondria Fission Protein Fis1, cytosolic domain.  Fis1, along with Dnm1 and Mdv1, is an essential protein in mediating mitochondrial fission. Dnm1 and Fis1 are highly conserved, with a common mechanism in disparate species. In mutants of these proteins, mitochondrial fission is impaired, resulting in networks of undivided mitochondria. The Fis1 N-terminus is cytosolic and tethered to the mitochondrial outer membrane via a ...
CDD:213406	112	EUKprk	Bacteria:2,Invertebrates:1,Plants:10,nodiv:1	cd12213, ABD, Alpha-Mannosidase Binding Domain of Atg19/34.  These proteins are related to the Alpha-mannosidase (Ams1) Binding Domain of Atg19/Atg34, a key component in the targeting pathway that directs alpha-mannosidase and aminopeptidase I to the vacuole, either through cytoplasm-to-vacuole trafficking or via autophagy in starvation conditions. Autophagy in a eukaryotic mechanism in which cytoplasm is enclosed in ...
CDD:213177	45	EUKprk	Bacteria:24,Plants:1	cd12214, ChiA1_BD, chitin-binding domain of Chi A1-like proteins.  This group contains proteins related to the chitin binding domain of chitinase A1 (ChiA1) of Bacillus circulans WL-12. Glycosidase ChiA1 hydrolyzes chitin and is comprised of several domains: the C-terminal chitin binding domain, an N-terminal and catalytic domain, and 2 fibronectin type III-like domains. Chitinases function in invertebrates in the degradation of old exoskeletons, in ...
CDD:213178	42	EUKprk	Bacteria:105,Plants:8	cd12215, ChiC_BD, Chitin-binding domain of chitinase C.  Chitin-binding domain of chitinase C (ChiC) of Streptomyces griseus and related proteins. Chitinase C is a family 19 chitinase, and consists of a N-terminal chitin binding domain and a C-terminal chitin-catalytic domain that effects degradation. Chitinases function in invertebrates in the degradation of old exoskeletons, in fungi to utilize chitin in cell walls, and in bacteria which use chitin as ...
CDD:213409	217	PRK	Bacteria:3	cd12216, Csn2_like, CRISPR/Cas system-associated protein Csn2.  Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against ...
CDD:213410	343	PRK	Bacteria:8,nodiv:1	cd12217, Stu0660_Csn2, Stu0660-like CRISPR/Cas system-associated protein Csn2.  Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. This family of Csn2 proteins includes Stu0660, the proteins are larger than other (canonical) Csn2 proteins as they have an additional ...
CDD:213411	219	PRK	Bacteria:15,nodiv:2	cd12218, Csn2, CRISPR/Cas system-associated protein Csn2.  Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells ...
CDD:240618	89	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd12219, UBL_TBK1_like, Ubiquitin-Like Domain Of Human Tbk1 and similar proteins.  This family contains ubiquitin-like domain (UBL) found in TANK-binding kinase 1 (TBK1) and similar proteins. TBK1 regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. In addition to the central UBL, these proteins have an N-terminal kinase domain and a C-terminal elongated helical domain. The ...
CDD:240669	84	EUK	Invertebrates:10,Plants:9,Vertebrates:3,nodiv:1	cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins.  This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and ...
CDD:240670	74	EUK	Invertebrates:12,Plants:4	cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins.  This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p ...
CDD:240671	77	EUK	Invertebrates:2,Plants:4	cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins.  This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs ...
CDD:240672	78	EUK	Invertebrates:4,Plants:17,Vertebrates:3	cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins.  This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA ...
CDD:240673	77	EUK	Invertebrates:8,Primates:1	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins.  This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or ...
CDD:240676	82	EUK	Invertebrates:22,Plants:12,Vertebrates:3,nodiv:1	cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins.  The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly ...
CDD:240677	77	EUK	Invertebrates:8,Plants:5	cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins.  This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed ...
CDD:240678	89	EUK	Invertebrates:15,Plants:20,Vertebrates:1,nodiv:1	cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins.  This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly ...
CDD:240681	83	EUK	Invertebrates:18,Plants:11,Vertebrates:3	cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins.  This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, ...
CDD:240682	91	EUK	Invertebrates:14,Plants:9,Vertebrates:3,nodiv:1	cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins.  This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing ...
CDD:240683	93	EUK	Invertebrates:6,Plants:4,Vertebrates:3,nodiv:1	cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins.  This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. ...
CDD:240684	73	EUK	Invertebrates:14,Plants:2,Vertebrates:3,nodiv:1	cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins.  This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as ...
CDD:240685	82	EUK	Invertebrates:10,Plants:6,Primates:1,Vertebrates:2	cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins.  This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs ...
CDD:240686	78	EUK	Invertebrates:20,Plants:13,Vertebrates:2,nodiv:1	cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins.  This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric ...
CDD:240687	77	EUK	Invertebrates:19,Plants:12,Vertebrates:2	cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins.  This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been ...
CDD:240688	73	EUK	Invertebrates:6,Vertebrates:3	cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins.  This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions ...
CDD:240689	71	EUK	Invertebrates:11,Plants:5,Primates:1	cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family.  This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs ...
CDD:240690	79	EUK	Plants:1,Primates:1	cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family.  This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein ...
CDD:240691	79	EUK	Invertebrates:7,Plants:10,nodiv:1	cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins.  This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as ...
CDD:240692	78	EUKprk	Invertebrates:16,Plants:14,Primates:1,Viruses:1	cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family.  This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs ...
CDD:240693	72	EUK	Invertebrates:13,Plants:9,Primates:1,nodiv:1	cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family.  This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) ...
CDD:240695	78	EUK	Invertebrates:15,Primates:1,Vertebrates:2	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins.  This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA ...
CDD:240696	82	EUK	Invertebrates:11	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins.  This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, ...
CDD:240697	72	EUK	Invertebrates:7,Plants:1,Primates:1,Vertebrates:1	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins.  This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and ...
CDD:240698	71	PRK	Bacteria:108,Environmental:1	cd12252, RRM_DbpA, RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases.  This subfamily corresponds to the C-terminal RRM homology domain of dbpA proteins implicated in ribosome biogenesis. They bind with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92), which is part of the ribosomal A-site. The majority of dbpA proteins contain two N-terminal ATPase catalytic domains and a ...
CDD:240700	73	EUK	Invertebrates:26,Plants:6,Primates:1,Vertebrates:2,nodiv:1	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins.  The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, ...
CDD:240701	73	EUK	Invertebrates:3,Vertebrates:2,nodiv:1	cd12255, RRM1_LKAP, RNA recognition motif 1 in Limkain-b1 (LKAP) and similar proteins.  This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve ...
CDD:240702	89	EUK	Invertebrates:4	cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins.  This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common ...
CDD:240703	72	EUK	Invertebrates:14,Plants:10,Primates:1,Vertebrates:1	cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins.  This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs ...
CDD:240704	72	EUK	Invertebrates:5,Vertebrates:3,nodiv:1	cd12258, RRM2_RBM26_like, RNA recognition motif 2 of vertebrate RNA-binding protein 26 (RBM26) and similar proteins.  This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play ...
CDD:240705	76	EUK	Invertebrates:11,Plants:1,Vertebrates:1	cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins.  This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex ...
CDD:240706	85	EUK	Invertebrates:6,Vertebrates:2	cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins.  This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine ...
CDD:240707	73	EUK	Plants:17	cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in RNA-binding protein MRN1 and similar proteins.  This subfamily corresponds to the RRM1 and RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four ...
CDD:240709	98	EUK	Invertebrates:20,Plants:13,Vertebrates:3,nodiv:1	cd12263, RRM_ABT1_like, RNA recognition motif found in activator of basal transcription 1 (ABT1) and similar proteins.  This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 ...
CDD:240710	121	EUK	Invertebrates:11,Plants:3,Vertebrates:3	cd12264, RRM_AKAP17A, RNA recognition motif found in A-kinase anchor protein 17A (AKAP-17A) and similar proteins.  This subfamily corresponds to the RRM domain of AKAP-17A, also termed 721P, or splicing factor, arginine/serine-rich 17A (SFRS17A). It was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor. It has been suggested that AKAP-17A is an alternative splicing ...
CDD:240711	86	EUK	Plants:12	cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins.  This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative ...
CDD:240712	107	EUK	Plants:7	cd12266, RRM_like_XS, RNA recognition motif-like XS domain found in plants.  This XS (named after rice gene X and SGS3) domain is a single-stranded RNA-binding domain (RBD) and possesses a unique version of a RNA recognition motif (RRM) fold. It is conserved in a family of plant proteins including gene X and SGS3. Although its function is still unknown, the plant SGS3 proteins are thought to be involved in post-transcriptional gene silencing (PTGS) pathways. In ...
CDD:240716	74	EUK	Invertebrates:5,Vertebrates:3	cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins.  This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein ...
CDD:240722	71	EUK	Invertebrates:3,Plants:15	cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins.  This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some ...
CDD:240723	86	EUK	Invertebrates:5,Plants:7	cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins.  This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some ...
CDD:240724	84	EUK	Invertebrates:22,Plants:21,Vertebrates:2,nodiv:1	cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins.  This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed ...
CDD:240726	81	EUK	Invertebrates:4,Plants:5,Primates:1	cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins.  This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and ...
CDD:240727	92	EUK	Invertebrates:17,Plants:12,Vertebrates:3,nodiv:1	cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins.  This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding ...
CDD:240728	91	EUK	Invertebrates:3	cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins.  This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein ...
CDD:240729	73	EUK	Invertebrates:14,Plants:8,Primates:1,nodiv:1	cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins.  This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or ...
CDD:240730	73	EUK	Invertebrates:7,Plants:6,Vertebrates:3	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins.  This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is ...
CDD:240731	85	EUK	Invertebrates:8,Plants:18,Vertebrates:2	cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins.  This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding ...
CDD:240732	92	EUK	Invertebrates:10,Vertebrates:3	cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane protein Man1 (Man1) and similar proteins.  This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions ...
CDD:240733	102	EUK	Invertebrates:8,Plants:7,Primates:1	cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins.  This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small ...
CDD:240735	93	EUK	Invertebrates:8,Plants:1,Vertebrates:4	cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins.  This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including ...
CDD:240736	80	EUK	Invertebrates:11,Vertebrates:2,nodiv:1	cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins.  This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ...
CDD:240737	72	EUK	Invertebrates:10,Plants:11,Primates:1,Vertebrates:1,nodiv:1	cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins.  This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts ...
CDD:240738	75	EUK	Invertebrates:5,Plants:2	cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins.  This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In ...
CDD:240739	96	EUK	Plants:13	cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins.  This subfamily corresponds to the RRM of Rrp7p which is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains an N-terminal RNA recognition motif (RRM), ...
CDD:240740	102	EUK	Invertebrates:14,Vertebrates:4,nodiv:1	cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins.  This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct ...
CDD:240742	71	EUK	Plants:18	cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins.  This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome ...
CDD:240743	78	EUK	Plants:8	cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins.  This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome ...
CDD:240744	78	EUK	Invertebrates:1,Plants:2	cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins.  This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during ...
CDD:240745	71	EUK	Plants:3	cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins.  This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome ...
CDD:240746	82	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:4	cd12300, RRM1_PAR14, RNA recognition motif 1 in vertebrate poly [ADP-ribose] polymerase 14 (PARP-14).  This subfamily corresponds to the RRM1 of PARP-14, also termed aggressive lymphoma protein 2, a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. It is expressed in B lymphocytes and interacts with the IL-4-induced transcription factor Stat6. It plays a fundamental role in the regulation of ...
CDD:240747	74	EUK	Invertebrates:4,Primates:1	cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins.  This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding ...
CDD:240748	110	EUK	Invertebrates:2,Plants:9	cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins.  This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and ...
CDD:240749	86	EUK	Plants:8	cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins.  This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, ...
CDD:240750	93	EUK	Invertebrates:10,Primates:1,nodiv:1	cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases.  This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic ...
CDD:240751	75	EUK	Invertebrates:7,Vertebrates:3,nodiv:1	cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins.  This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which ...
CDD:240752	73	EUK	Invertebrates:10,Plants:14,Vertebrates:1	cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins.  This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. ...
CDD:240753	74	EUK	Invertebrates:18,Plants:10,Vertebrates:3	cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins.  This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and ...
CDD:240754	79	EUK	Invertebrates:7,Primates:1,nodiv:1	cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end) protein family.  This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It ...
CDD:240756	72	EUK	Invertebrates:6,Plants:3	cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family.  This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 ...
CDD:240759	84	EUK	Invertebrates:15,Plants:7,nodiv:1	cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins.  This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of ...
CDD:240761	77	EUK	Invertebrates:6,Plants:5	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins.  This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain ...
CDD:240762	74	EUK	Invertebrates:4,Plants:7	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1).  This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a ...
CDD:240763	72	EUK	Invertebrates:6,Plants:3	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1).  This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a ...
CDD:240764	82	EUK	Invertebrates:9,Plants:3,Vertebrates:3	cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins.  This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA ...
CDD:240766	76	EUK	Invertebrates:4,Plants:5	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1).  This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. ...
CDD:240768	71	EUK	Invertebrates:10,Plants:1,Primates:1,Vertebrates:2	cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins.  This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral ...
CDD:240770	88	EUK	Invertebrates:16,Plants:12,Vertebrates:1	cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins.  This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other ...
CDD:240771	72	EUK	Invertebrates:8,Plants:7,Primates:1,Rodents:1	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins.  This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant ...
CDD:240774	73	EUK	Invertebrates:8,Primates:1,Vertebrates:1	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily.  This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced ...
CDD:240778	71	EUK	Invertebrates:12,Primates:1	cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family.  This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a ...
CDD:240779	80	EUK	Invertebrates:4,Vertebrates:1	cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family.  This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a ...
CDD:240780	74	EUK	Invertebrates:21,Plants:12,Vertebrates:3	cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins.  This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is ...
CDD:240781	83	EUK	Invertebrates:3,Plants:1	cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins.  This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the ...
CDD:240785	71	EUK	Invertebrates:8,Plants:11,Primates:1	cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins.  This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and ...
CDD:240787	68	EUK	Invertebrates:13,Primates:1,Vertebrates:2,nodiv:1	cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins.  This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein ...
CDD:240789	66	EUK	Invertebrates:10,Primates:1,Vertebrates:1	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins.  This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a ...
CDD:240790	81	EUK	Invertebrates:8,Plants:8	cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins.  This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the ...
CDD:240791	80	EUK	Invertebrates:1,Plants:5	cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins.  This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the ...
CDD:240792	72	EUK	Plants:8	cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins.  This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. ...
CDD:240793	73	EUK	Invertebrates:16,Plants:11,Vertebrates:3,nodiv:1	cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins.  This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 ...
CDD:240795	74	EUK	Invertebrates:9,Vertebrates:2,nodiv:1	cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins.  This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and ...
CDD:240797	77	EUK	Invertebrates:1	cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins.  This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the ...
CDD:240798	72	EUK	Invertebrates:8,Plants:5,Primates:1	cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR.  This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are ...
CDD:240800	73	EUK	Invertebrates:7,Plants:3,nodiv:1	cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1.  This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte ...
CDD:240801	80	EUK	Invertebrates:10,Plants:1,Vertebrates:1	cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins.  This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. .
CDD:240805	76	EUK	Invertebrates:6,Primates:1	cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins.  This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs ...
CDD:240806	78	EUK	Invertebrates:10,Plants:10	cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins.  This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number ...
CDD:240807	77	EUK	Invertebrates:12,Plants:9,Primates:1,nodiv:1	cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA.  This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation ...
CDD:240808	73	EUK	Invertebrates:7,Plants:5,Primates:1	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins.  This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and ...
CDD:240809	78	EUK	Invertebrates:12,Plants:3,Primates:1	cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins.  This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing ...
CDD:240811	73	EUK	Invertebrates:18,Plants:12,Vertebrates:1	cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins.  This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in ...
CDD:240814	75	EUK	Invertebrates:6,Plants:2,Vertebrates:3,nodiv:1	cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins.  This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 ...
CDD:240817	77	EUK	Invertebrates:15,Plants:2,Vertebrates:3	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins.  This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in ...
CDD:240818	76	EUK	Invertebrates:5,Plants:10,Primates:1	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins.  This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the ...
CDD:240819	73	EUK	Invertebrates:15,Plants:9,Primates:1,Vertebrates:1	cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins.  This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a ...
CDD:240820	85	EUK	Invertebrates:13,Plants:5,Primates:1	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins.  This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal ...
CDD:240824	80	EUK	Invertebrates:17,Plants:13,Primates:1,Vertebrates:4,nodiv:1	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins.  This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA ...
CDD:240825	77	EUK	Invertebrates:6,Plants:5,Primates:1,Vertebrates:2	cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins.  This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization ...
CDD:240826	80	EUK	Invertebrates:1,Plants:1,Vertebrates:1	cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins.  This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by ...
CDD:240827	79	EUK	Invertebrates:2,Plants:2,Primates:1	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins.  This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA ...
CDD:240828	80	EUK	Invertebrates:5,Plants:9,Primates:1,Vertebrates:3	cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins.  This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has ...
CDD:240829	83	EUK	Invertebrates:20,Plants:11,Vertebrates:3	cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins.  This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress ...
CDD:240830	76	EUK	Invertebrates:13,Plants:4,Primates:1,Vertebrates:3	cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins.  This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the ...
CDD:240833	72	EUK	Invertebrates:5,Plants:4,Primates:1	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins.  This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and ...
CDD:240835	77	EUK	Invertebrates:8,Plants:3,Primates:1,nodiv:1	cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins.  This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the ...
CDD:240836	92	EUK	Invertebrates:4	cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins.  This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and ...
CDD:240837	72	EUK	Invertebrates:12,Vertebrates:2,nodiv:1	cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins.  This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is ...
CDD:240840	91	EUK	Invertebrates:14,Plants:7,Vertebrates:3,nodiv:1	cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins.  This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an ...
CDD:240841	73	EUK	Invertebrates:6,Plants:2	cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins.  This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related ...
CDD:240844	75	EUK	Invertebrates:8,Plants:5,Primates:1	cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins.  This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all ...
CDD:240845	78	EUKprk	Bacteria:18,Plants:1	cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins.  This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. .
CDD:240846	74	EUK	Invertebrates:3,Plants:6	cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins.  This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences ...
CDD:240854	77	EUK	Invertebrates:20,Plants:15,Vertebrates:1	cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins.  This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal ...
CDD:240856	93	EUK	Plants:16	cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins.  This subfamily corresponds to the RRM2 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). .
CDD:240857	89	EUK	Invertebrates:16,Plants:10,Vertebrates:3,nodiv:1	cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.  This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast ...
CDD:240858	80	EUK	Invertebrates:7,Primates:1,Rodents:1,nodiv:1	cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE.  This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. ...
CDD:240859	79	EUK	Invertebrates:6,Plants:7,Vertebrates:2	cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins.  This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the ...
CDD:240860	76	EUK	Invertebrates:5,Plants:2	cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins.  This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of ...
CDD:240861	82	EUK	Invertebrates:13,Plants:1,Vertebrates:1	cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins.  This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the ...
CDD:240862	98	EUK	Invertebrates:7,Plants:2	cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins.  This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of ...
CDD:240863	74	EUK	Invertebrates:10,Primates:1	cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family.  This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and ...
CDD:240864	75	EUK	Invertebrates:7,Plants:12,Primates:1	cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family.  This subfamily corresponds to the RRM of  Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is ...
CDD:240865	80	EUK	Plants:5	cd12419, RRM_Ssp2_like, RNA recognition motif in yeast sporulation-specific protein 2 (Ssp2) and similar protein.  This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall ...
CDD:240866	79	EUK	Invertebrates:6,Plants:7,Primates:1	cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins.  This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and ...
CDD:240867	74	EUK	Invertebrates:12,Plants:4,Primates:1,Rodents:1	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins.  This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), ...
CDD:240868	85	EUK	Invertebrates:10,Plants:4,Rodents:1	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins.  This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), ...
CDD:240869	74	EUK	Invertebrates:11,Primates:1	cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins.  This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and ...
CDD:240870	71	EUK	Invertebrates:15,Plants:1,Primates:1	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins.  This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 ...
CDD:240871	76	EUK	Invertebrates:3,nodiv:1	cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins.  This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also ...
CDD:240873	84	EUK	Invertebrates:12,nodiv:1	cd12427, RRM4_hnRNPL_like, RNA recognition motif 4 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins.  This subfamily corresponds to the RRM4 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation ...
CDD:240874	65	EUK	Invertebrates:11,Plants:3,Primates:1,Vertebrates:2	cd12428, RRM_PARN, RNA recognition motif in poly(A)-specific ribonuclease PARN and similar proteins.  The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine ...
CDD:240875	74	EUK	Invertebrates:11,Plants:10,Vertebrates:3	cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17.  The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important ...
CDD:240876	76	EUK	Invertebrates:12,Plants:2,Primates:1,Vertebrates:1,nodiv:1	cd12430, RRM_LARP4_5_like, RNA recognition motif in La-related protein 4 (LARP4), La-related protein 5 (LARP5 or LARP4B) and similar proteins.  This subfamily corresponds to the RRM of LARP4 and LARP5. LARP4 is a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP5 is a cytosolic protein that co-sediments ...
CDD:240877	80	EUK	Invertebrates:14,Vertebrates:3	cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins.  This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has ...
CDD:240878	90	EUK	Invertebrates:18,Plants:16,Vertebrates:1,nodiv:1	cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins.  This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural ...
CDD:240879	86	EUK	Invertebrates:2,Plants:16	cd12433, RRM_Yme2p_like, RNA recognition motif in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins.  This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA ...
CDD:240880	75	EUK	Invertebrates:10,Plants:10,Primates:1,nodiv:1	cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins.  This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic ...
CDD:240882	76	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:5	cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the matrin 3 family of nuclear proteins.  This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that ...
CDD:240883	82	EUK	Invertebrates:1,Plants:6	cd12437, RRM_BRAP2_like, RNA recognition motif in BRCA1-associated protein (BRAP2) and similar proteins.  This subfamily corresponds to the RRM domain of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to ...
CDD:240884	98	EUK	Invertebrates:17,Plants:11,Vertebrates:3	cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins.  This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ...
CDD:240885	79	EUK	Invertebrates:11,Primates:1,Vertebrates:2,nodiv:1	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins.  This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains ...
CDD:240887	73	EUK	Invertebrates:16,Plants:13	cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins.  This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a ...
CDD:240888	100	EUK	Invertebrates:8,Plants:3,Vertebrates:3	cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48 (RBM48) and similar proteins.  This subfamily corresponds to the RRM of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). .
CDD:240892	84	EUK	Invertebrates:19,Plants:13,Vertebrates:3,nodiv:1	cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins.  This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding ...
CDD:240900	80	EUK	Plants:5	cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins.  This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and ...
CDD:240901	88	EUK	Invertebrates:15,Plants:23,Primates:1,Vertebrates:1	cd12455, RRM_like_Smg4_UPF3, RNA recognition motif-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins.  This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed ...
CDD:240943	73	EUKprk	Bacteria:21,Invertebrates:1,Plants:1	cd12499, RRM_EcCsdA_like, RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins.  This subgroup corresponds to the C-terminal RRM homology domain of E. coli CsdA, also termed ATP-dependent RNA helicase deaD, or translation factor W2, a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. CsdA may be involved in translation ...
CDD:240945	73	EUKprk	Bacteria:16,Invertebrates:2,Plants:1	cd12501, RRM_EcDbpA_like, RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins.  This subgroup corresponds to the C-terminal RRM homology domain of dbpA. E. coli dbpA is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity for RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' ...
CDD:240952	80	EUK	Invertebrates:8,Plants:3,Primates:1,Vertebrates:1	cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins.  This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 ...
CDD:240954	74	EUK	Invertebrates:3,Vertebrates:1	cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding protein RBM12, RBM12B and similar proteins.  This subfamily corresponds to the RRM1 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative ...
CDD:240968	77	EUK	Invertebrates:4,Plants:5	cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins.  This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell ...
CDD:240970	71	EUK	Plants:5	cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins.  This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein ...
CDD:240982	104	EUK	Invertebrates:12,Mammals:1,Plants:3,Vertebrates:2	cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35).  This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and ...
CDD:240984	105	EUK	Invertebrates:10,Plants:3,Vertebrates:3,nodiv:1	cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins.  This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif ...
CDD:240985	76	EUK	Invertebrates:7,Plants:1,Vertebrates:2	cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins.  This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from ...
CDD:240986	78	EUK	Invertebrates:6,Vertebrates:1	cd12542, RRM2_LARP7, RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins.  This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ...
CDD:240990	77	EUK	Invertebrates:3,Mammals:1,Vertebrates:4	cd12546, RRM_RBM43, RNA recognition motif in vertebrate RNA-binding protein 43 (RBM43).  This subgroup corresponds to the RRM of RBM43, a putative RNA-binding protein containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although its biological function remains unclear, RBM43 shows high sequence homology to poly [ADP-ribose] polymerase 10 (PARP-10), which is a novel oncoprotein ...
CDD:240991	71	EUK	Invertebrates:3,Primates:1,Vertebrates:3	cd12547, RRM1_2_PAR10, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase 10 (PARP-10) and similar proteins.  This subgroup corresponds to the RRM1 and RRM2 of PARP-10, a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to the PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting ...
CDD:241009	76	EUK	Invertebrates:2,Plants:5	cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins.  This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar ...
CDD:241054	84	EUK	Invertebrates:9,Vertebrates:3	cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43).  This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding ...
CDD:241056	82	EUK	Invertebrates:2,Vertebrates:1	cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43).  This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding ...
CDD:241091	96	EUK	Invertebrates:10,Plants:7,Vertebrates:3	cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins.  This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD ...
CDD:241096	79	EUK	Invertebrates:12,Primates:1,Rodents:1	cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family.  This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons ...
CDD:241113	105	EUK	Invertebrates:1,Plants:8	cd12669, RRM1_Nop12p_like, RNA recognition motif 1 in yeast nucleolar protein 12 (Nop12p) and similar proteins.  This subgroup corresponds to the RRM1 of Nop12p which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not ...
CDD:241124	75	EUK	Invertebrates:12,Plants:7,Primates:1,Vertebrates:2	cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins.  This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA ...
CDD:241125	69	EUK	Invertebrates:11,Vertebrates:3	cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins.  This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely ...
CDD:241162	84	EUK	Invertebrates:12,Vertebrates:3	cd12718, RRM_BRAP2, RNA recognition motif in BRCA1-associated protein (BRAP2).  This subgroup corresponds to the RRM of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS ...
CDD:241165	86	EUK	Plants:8	cd12721, RRM_Nup53p_fungi, RNA recognition motif in yeast nucleoporin Nup53p and similar proteins.  This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an ...
CDD:240614	455	EUK	Plants:23	cd12794, Hsm3_like, Hsm3 is a  yeast Proteasome chaperone of the 19S regulatory particle and related proteins.  This group contains proteins related to the Hsm3 protein (Yeast Proteasome Interacting Protein) of Saccharomyces cerevisiae. S. cerevisiae Hsm3 is a chaperone of regulatory particles involved in proteasome assembly. The 26S Proteasome is a large, 2.5 MDa complex comprised of at least 33 subunits, and relies on chaperones to facilitate correct assembly. The ...
CDD:240613	114	EUK	Mammals:3,Primates:3,Rodents:4,Vertebrates:1	cd12795, FILIA_N_like, FILIA-N KH-like domain.  This group contains the N-terminal atypical KH domain of FILIA and related domains. FILIA is expressed in oocytes and embryo, and contains an atypical KH domain at the N-terminus with an N-terminal extension that interacts with RNA. RNA-binding may mediate RNA transcript regulation in oogenesis and embryogenesis. FILIA-N differs from typical KH domains by forming a stable dimer in ...
CDD:240609	114	EUK	Invertebrates:1,Plants:6	cd12796, LbR_Ice_bind, Ice-binding protein, left-handed beta-roll.  The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix.
CDD:213998	132	EUK	Plants:13	cd12798, Alt_A1, Alternaria alternata allergen Alt a 1.  Alt a 1 defines a new homologous protein family with unknown function exclusively found in fungi. The unique structure of Alt a 1 contains intramolecular disulfide bonds that are conserved among the Alt a 1 homologs.  Residues reported to be IgE antibody-binding epitopes are exposed through dimerization via a conserved disulfide bond and hydrophobic and polar interactions. Further mechanistic structure/function ...
CDD:214000	77	PRK	Bacteria:8	cd12801, HopAB_KID, Kinase-interacting domains of the HopAB family of Type III Effector proteins.  HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen. AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular ...
CDD:214003	45	EUK	Invertebrates:3,Primates:1,Vertebrates:1	cd12804, AKAP10_AKB, PKA-binding (AKB) domain of A Kinase Anchor Protein 10.  AKAPs coordinate the specificity of PKA signaling by facilitating the localization of the kinase to subcellular sites through their binding to regulatory (R) subunits of PKA. AKAP-10, also called PRKA10 or Dual-specific AKAP 2 (D-AKAP2), is a multisubunit protein containing two regulator of G protein signaling (RGS)-like domains and a PKA-binding (AKB) domain. ...
CDD:214004	85	EUK	Plants:7	cd12805, Allergen_V_VI, Group V, VI major allergens from grass, including Phlp 5, Phlp 6, Pha a 5 and Lol p 5.  This family contains major allergens from various grass pollen, including Phl p 5 and Phl p 6 (timothy grass), Lol p 5 (rye grass) and Pha a 5 (canary grass). They induce allergic rhinitis and bronchial asthma in millions of allergic patients worldwide. These group V and group VI grass-pollen allergens belong to a new class of protease-resistant ...
CDD:214006	315	EUKprk	Bacteria:9,Plants:1	cd12807, Esterase_713, Novel bacterial esterase 713 that cleaves esters on halogenated cyclic compounds.  This family contains proteins similar to a novel bacterial esterase (esterase 713) with the alpha/beta hydrolase fold that cleaves esters on halogenated cyclic compounds. This Alcaligenes esterase, however, does not contain the GXSXXG pentapeptide around the active site serine residue as seen in other esterase families. This enzyme is active as a ...
CDD:214007	309	EUKprk	Bacteria:21,Plants:1	cd12808, Esterase_713_like-1, Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds.  This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible ...
CDD:214008	280	EUKprk	Bacteria:12,Plants:20	cd12809, Esterase_713_like-2, Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds.  This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible ...
CDD:214009	328	EUKprk	Bacteria:35,Plants:2	cd12810, Esterase_713_like-3, Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds.  This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible ...
CDD:240611	111	EUKprk	Bacteria:10,Environmental:1,Invertebrates:1,Plants:1	cd12819, LbR_vir_like, Cell adhesion-like domain, left-handed beta-roll.  This group contains proteins of unknown function related to characterized cell surface adhesion proteins with a left-handed beta-roll, like the UspA1 Head And Neck Domain and YadA of Yersinia. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend ...
CDD:240612	126	PRK	Bacteria:84	cd12820, LbR_YadA-like, YadA-like, left-handed beta-roll.  This group contains the collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins, including Moraxella catarrhalis UspA-like proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the ...
CDD:213355	285	EUKprk	Bacteria:24,Plants:1	cd12821, EcCorA_ZntB-like, Escherichia coli CorA-Salmonella typhimurium ZntB_like family.  A family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of this family are found in all three kingdoms of life. It is a functionally diverse family, including the Mg2+ transporters Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ...
CDD:213356	289	EUKprk	Bacteria:89,Environmental:2,Invertebrates:1,Plants:4	cd12822, TmCorA-like, Thermotoga maritima CorA-like family.  This family belongs to the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the Thermotoga maritima CorA_like family are found in all three kingdoms of life. It is a functionally diverse family, in addition to the CorA Co2+ transporter from the hyperthermophilic Thermotoga ...
CDD:213357	323	EUK	Invertebrates:10,Plants:41,Primates:1,Vertebrates:3	cd12823, Mrs2_Mfm1p-like, Saccharomyces cerevisiae inner mitochondrial membrane Mg2+ transporters Mfm1p and Mrs2p-like family.  A eukaryotic subfamily belonging to the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This functionally diverse subfamily ...
CDD:213359	287	PRK	Bacteria:7	cd12825, EcCorA-like, Escherichia coli Mg2+ transporter CorA_like subfamily.  A bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB_like(EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Mg2+ transporters Escherichia coli, Salmonella typhimurium, and Helicobacter pylori CorAs (which can also transport Co2+, ...
CDD:213360	281	PRK	Bacteria:42	cd12826, EcCorA_ZntB-like_u1, uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family.  A uncharacterized subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. The EcCorA-ZntB_like family includes the Mg2+ transporters Escherichia coli and Salmonella ...
CDD:213361	289	PRK	Bacteria:155,nodiv:3	cd12827, EcCorA_ZntB-like_u2, uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family.  A uncharacterized subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes.The EcCorA-ZntB-like family includes the Mg2+ transporters Escherichia coli and ...
CDD:213362	294	PRK	Bacteria:189	cd12828, TmCorA-like_1, Thermotoga maritima CorA_like subfamily.  This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of this subfamily are found in all three kingdoms of life. It is functionally diverse subfamily, in addition to the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, it ...
CDD:213363	305	EUK	Invertebrates:12,Plants:22	cd12829, Alr1p-like, Saccharomyces cerevisiae Alr1p-like subfamily.  This eukaryotic subfamily belongs to the Thermotoga maritima CorA (TmCorA)-family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes three Saccharomyces cerevisiae members: two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ...
CDD:213364	292	PRK	Bacteria:85	cd12830, MtCorA-like, Mycobacterium tuberculosis CorA-like subfamily.  This bacterial subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Mg2+ transporter Mycobacterium tuberculosis CorA (which also transports Co2+). Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of ...
CDD:213365	287	PRK	Bacteria:29	cd12831, TmCorA-like_u2, Uncharacterized bacterial subfamily of the Thermotoga maritima CorA-like family.  This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the TmCorA-like family are found in all three kingdoms of life. It is a functionally diverse family which includes the CorA Co2+ transporter ...
CDD:213366	287	EUKprk	Bacteria:15,Environmental:1,Invertebrates:3	cd12832, TmCorA-like_u3, Uncharacterized subfamily of the Thermotoga maritima CorA-like family.  This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the TmCorA-like family are found in all three kingdoms of life. It is a functionally diverse family which includes ...
CDD:213367	290	PRK	Bacteria:78	cd12833, ZntB-like_1, Salmonella typhimurium Zn2+ transporter ZntB-like subgroup.  A bacterial subgroup belonging to the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). Structures of ...
CDD:213368	290	PRK	Bacteria:30	cd12834, ZntB_u1, Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily.  The MIT superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. The ZntB-like subfamily includes the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella ...
CDD:213369	287	PRK	Bacteria:17,Environmental:1	cd12835, EcCorA-like_1, Escherichia coli Mg2+ transporter CorA_like subgroup.  A bacterial subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Mg2+ transporters Escherichia coli CorA and Salmonella typhimurium CorA (which can also transport Co2+, ...
CDD:213370	288	PRK	Bacteria:15	cd12836, HpCorA-like, Mg2+ transporter Helicobacter pylori CorA-like subgroup.  A bacterial subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Mg2+ transporter Helicobacter pylori CorAs (which can also transport Co2+, and Ni2+); CorA plays an important role in ...
CDD:213371	298	PRK	Bacteria:52,nodiv:1	cd12837, EcCorA-like_u1, uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily.  A uncharacterized subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. The EcCorA_ZntB-like family includes the Mg2+ transporters Escherichia coli and Salmonella ...
CDD:240608	105	PRK	Bacteria:28	cd12843, Bvu_2165_C_like, The C-terminal domain of uncharacterized bacterial proteins.  This family contains the C-terminal domain of uncharacterized hypothetical proteins from bacteria, including Bacteroides vulgatus Bvu_2165. The structure of Bvu_2165 is dimeric, with an extensive binding interface.
CDD:240607	98	PRK	Bacteria:36	cd12869, MqsR, Motility quorum-sensing regulator (MqsR).  This family includes domains similar to the motility quorum-sensing regulator MqsR, a toxin that is highly upregulated in persisters (dormant cells found in biofilms that are a source of antibiotic resistance). MqsR pairs with its antitoxin MqsA, forming a unique family of toxin:antitoxin (TA) systems. MqsR has been found to be structurally homologous to the bacterial ribonuclease (RelE) toxins; however, its ...
CDD:240606	66	PRK	Bacteria:39,Environmental:1	cd12870, MqsA, antitoxin MqsA for MqsR toxin.  This family includes domains similar to the antitoxin MqsA that binds motility quorum-sensing regulator MqsR, a toxin that is highly upregulated in persisters (dormant cells found in biofilms that are a source of antibiotic resistance), thus forming a unique toxin:antitoxin (TA) pair. MqsA neutralizes MsqR toxicity. It binds its own promoter as well as those of genes important for E. coli physiology, ...
CDD:214015	231	PRK	Bacteria:37	cd12871, Bacuni_01323_like, Uncharacterized protein conserved in Bacteroidetes.  A well-conserved family of 16-stranded beta barrels resembling outer membrane porins. The interior of the barrels is mostly occupied by an insert with partially helical structure.
CDD:240452	149	EUK	Invertebrates:23,Plants:33,Vertebrates:3,nodiv:1	cd12872, SPRY_Ash2, SPRY domain in Ash2.  This SPRY domain is found at the C-terminus of Ash2 (absent, small, or homeotic discs 2) -like proteins, core components of all mixed-lineage leukemia (MLL) family histone methyltransferases. Ash2 is a member of the trithorax group of transcriptional regulators of the Hox genes. Recent studies show that the SPRY domain of Ash2 mediates the interaction with RbBP5 and has an important role ...
CDD:240453	155	EUK	Invertebrates:20,Plants:8,Vertebrates:2	cd12873, SPRY_DDX1, SPRY domain associated with DEAD box gene DDX1.  This SPRY domain is associated with the DEAD box gene, DDX1, an RNA-dependent ATPase involved in HIV-1 Rev function and virus replication. It is suggested that DDX1 acts as a cellular cofactor by promoting oligomerization of Rev on the Rev response element (RRE). DDX1 RNA is overexpressed in breast cancer, data showing a strong and independent association between poor ...
CDD:240456	187	EUK	Invertebrates:15,Vertebrates:4,nodiv:1	cd12876, SPRY_SOCS3, SPRY domain in the suppressor of cytokine signaling 3 (SOCS3) family.  The SPRY domain-containing SOCS box protein family (SPSB1-4, also known as SSB-1 to -4) is composed of a central SPRY protein interaction domain and a C-terminal SOCS box. All four SPSB proteins interact with c-Met, the hepatocyte growth factor receptor, but SOCS3 regulates cellular response to a variety of cytokines such as leukemia inhibitory ...
CDD:240457	151	EUK	Invertebrates:9,Vertebrates:2	cd12877, SPRY1_RyR, SPRY domain 1 (SPRY1) of ryanodine receptor (RyR).  This SPRY domain is the first of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the cytoplasmic ...
CDD:240458	133	EUK	Invertebrates:3,Vertebrates:1	cd12878, SPRY2_RyR, SPRY domain 2 (SPRY2) of ryanodine receptor (RyR).  This SPRY domain (SPRY2) is the second of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the ...
CDD:240459	151	EUK	Invertebrates:4,Vertebrates:2	cd12879, SPRY3_RyR, SPRY domain 3 (SPRY3) of ryanodine receptor (RyR).  This SPRY domain (SPRY3) is the third of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the ...
CDD:240460	160	EUK	Invertebrates:19,Plants:2,Primates:1,Vertebrates:3,nodiv:1	cd12880, SPRYD7, SPRY domain-containing protein 7.  This family contains SPRY domain-containing protein 7 (also known as SPRY domain-containing protein 7 or CLL deletion region gene 6 protein homolog or CLLD6 or chronic lymphocytic leukemia deletion region gene 6 protein homolog). In humans, CLLD6 is highly expressed in heart, skeletal muscle, and testis as well as cancer cell lines. It also has cross-species ...
CDD:240461	160	EUK	Invertebrates:7,Plants:3,Vertebrates:3,nodiv:1	cd12881, SPRY_HERC1, SPRY domain in HERC1.  This SPRY domain is found in the HERC1, a large protein related to chromosome condensation regulator RCC1. It is widely expressed in many tissues, playing an important role in intracellular membrane trafficking in the cytoplasm as well as Golgi apparatus. HERC1 also interacts with tuberous sclerosis 2 (TSC2, tuberin), which suppresses cell growth, and results in the destabilization of ...
CDD:240462	128	EUK	Invertebrates:4,Plants:5,Vertebrates:3,nodiv:1	cd12882, SPRY_RNF123, SPRY domain at N-terminus of ring finger protein 123.  This SPRY domain is found at the N-terminus of RING finger protein 123 domain (also known as E3 ubiquitin-protein ligase RNF123). The ring finger domain motif is present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. RNF123 displays E3 ubiquitin ligase activity toward the ...
CDD:240463	121	EUK	Invertebrates:11,Primates:1,Vertebrates:2	cd12883, SPRY_RING, SPRY domain at N-terminus of Really Interesting New Gene (RING) finger domain.  This SPRY domain is found at the N-terminus of RING finger domains which are present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. RING-finger domain is a type of Zn-finger that binds two Zn atoms and is identified in proteins with a wide range of functions such ...
CDD:240464	176	EUK	Invertebrates:22,Plants:1,Primates:1,Vertebrates:4,nodiv:1	cd12884, SPRY_hnRNP, SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1 (also known as HNRPUL1 ) which is a major constituent of nuclear matrix or scaffold and binds directly to DNA sequences through ...
CDD:240465	132	EUK	Invertebrates:26,Plants:39,Primates:1,Vertebrates:1	cd12885, SPRY_RanBP_like, SPRY domain in Ran binding proteins, SSH4, HECT E3 and SPRYD3.  This family includes SPRY domains found in Ran binding proteins (RBP or RanBPM) 9 and 10, SSH4 (suppressor of SHR3 null mutation protein 4), SPRY domain-containing protein 3 (SPRYD3) as well as HECT, a C-terminal catalytic domain of a subclass of ubiquitin-protein ligase (E3). RanBP9 and RanBP10 act as androgen receptor (AR) ...
CDD:240466	128	PRK	Bacteria:12	cd12886, SPRY_like, SPRY domain-like in bacteria.  This family contains SPRY-like domains that are found only in bacterial and are mostly uncharacterized. SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 eukaryotic protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA ...
CDD:240467	161	EUK	Invertebrates:17,Primates:1,Rodents:1,Vertebrates:5	cd12887, SPRY_NHR_like, SPRY domain in neuralized homology repeat.  This family contains the neuralized homology repeat 1 (NHR1) domain similar to the SPRY domain (known to mediate specific protein-protein interactions) at the C-terminus of a conserved region within eukaryotic neuralized and neuralized-like proteins. In Drosophila, the neuralized protein (Neur) belongs to a group of ubiquitin ligases and is required in a ...
CDD:240468	171	EUK	Mammals:2,Primates:2,Rodents:2,Vertebrates:3	cd12888, SPRY_PRY_TRIM7_like, PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several tripartite motif-containing (TRIM) proteins, including TRIM7 (also referred to as glycogenin-interacting protein, RING finger protein 90 or ...
CDD:240469	172	EUK	Invertebrates:14,Primates:1,Vertebrates:2,nodiv:1	cd12889, SPRY_PRY_TRIM67_9, PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM9 proteins. TRIM9 protein is expressed mainly in the cerebral cortex, and functions as an E3 ubiquitin ligase. It has been shown that TRIM9 is localized to the neurons in the normal human brain ...
CDD:240471	169	EUK	Mammals:2,Primates:1,Rodents:2,Vertebrates:14	cd12891, SPRY_PRY_C-IV_2, PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM14-like, TRIM16-like, TRIM25-like, TRIM47-like and RNF135 and stonustoxin.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class IV TRIM proteins, including  TRIM14, TRIM16 and TRIM25, TRIM47 as well as RING finger protein RNF135 and ...
CDD:240473	171	EUK	Primates:1,Vertebrates:7	cd12893, SPRY_PRY_TRIM35, PRY/SPRY domain in tripartite motif-containing protein 35 (TRIM35).  This PRY/SPRY domain is found at the C-terminus of the overall domain architecture of tripartite motif 35, TRIM35 (also known as hemopoietic lineage switch protein), which includes a RING finger domain (RING) and a B-box motif (BBOX). TRIM35 may play a role as a tumor suppressor and is implicated in the cell death mechanism.
CDD:240477	186	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:8	cd12897, SPRY_PRY_TRIM50_62_72, PRY/SPRY domain in tripartite motif-binding (TRIM) proteins TRIM50, TRIM62 and TRIM72.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several TRIM proteins, including TRIM72, TRIM62 and TRIM50. TRIM72 (also known as MG53) has been shown to perform a critical function in membrane repair following acute muscle injury by ...
CDD:240480	173	EUK	Mammals:9,Primates:7,Rodents:5,Vertebrates:2	cd12900, SPRY_PRY_Btn_TRIMs, PRY/SPRY domain in butyrophilins and butyrophilins-like proteins, pyrin, as well as tripartite motif-containing proteins (TRIM4, 5, 6, 11, 21, 22, 27, 30, 34, 38, 58, 60, 68, 75).  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of pyrin, several tripartite motif-containing proteins (TRIMs), as well as butyrophilin (Btns) and ...
CDD:240485	176	EUK	Primates:1,Vertebrates:6	cd12905, SPRY_PRY_TRIM_Bty_69_NF7, PRY/SPRY domain in tripartite motif-containing protein 69 (TRIM69), Bloodthirsty (bty) and NF7.  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM69 and TRIM proteins NF7 and bloodthirsty (bty). TRIM69 is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, ...
CDD:240486	174	EUK	Invertebrates:12,Primates:1,Vertebrates:2	cd12906, SPRY_SOCS1-2-4, SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4).  The SPRY domain-containing SOCS box protein family (SPSB1-4, also known as SSB-1 to -4) is composed of a central SPRY protein interaction domain and a C-terminal SOCS box. All four SPSB proteins interact with c-Met, the hepatocyte growth factor receptor, but only SPSB1, SPSB2, and SPSB4 interact with prostate apoptosis ...
CDD:240488	171	EUK	Invertebrates:6,Primates:1,Vertebrates:5	cd12908, SPRYD3, SPRY domain-containing protein 3.  This family contains SPRY domain-containing protein 3 (SPRYD3). In humans, it is highly expressed in most tissues, including brain, kidney, heart, intestine, skeletal muscle, and testis. It also has cross-species conservation, suggesting that it is likely to carry out important cellular processes.
CDD:240489	153	EUK	Invertebrates:12,Plants:15,Primates:1,Vertebrates:2	cd12909, SPRY_RanBP9_10, SPRY domain in Ran binding proteins 9 and 10.  This family includes SPRY domain in Ran binding protein (RBP or RanBPM) 9 and 10, and similar proteins. RanBP9 (also known as RanBPM), a binding partner of Ran, is a small Ras-like GTPase that exerts multiple functions via interactions with various proteins. RanBP9 and RanBP10 also act as androgen receptor (AR) coactivators. Both consist of the N-terminal ...
CDD:240490	191	EUK	Plants:24	cd12910, SPRY_SSH4_like, SPRY domain in SSH4 and similar proteins.  This family includes SPRY domain in SSH4 (suppressor of SHR3 null mutation protein 4) and similar proteins. SSH4 is a component of the endosome-vacuole trafficking pathway that regulates nutrient transport and may be involved in processes determining whether plasma membrane proteins are degraded or routed to the plasma membrane. The SPRY domain in SSH4 may be involved in cargo recognition, either ...
CDD:240599	133	EUKprk	Bacteria:39,Plants:14	cd12916, VKOR_1, Vitamin K epoxide reductase family in bacteria and plants.  This family includes vitamin K epoxide reductase (VKOR) present in bacteria and plant. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of ...
CDD:240600	140	EUK	Invertebrates:28,Plants:3,Primates:5,Rodents:3,Vertebrates:2	cd12917, VKOR_euk, Vitamin K epoxide reductase family in eukaryotes, excluding plants.  This family includes vitamin K epoxide reductase (VKOR) present in bacteria and plant. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues ...
CDD:240601	126	EUKprk	Bacteria:26,Invertebrates:2	cd12918, VKOR_arc, Vitamin K epoxide reductase family in archaea and some bacteria.  This family includes vitamin K epoxide reductase (VKOR) mostly present in archaea and some bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood ...
CDD:240603	134	PRK	Bacteria:12	cd12920, VKOR_3, Vitamin K epoxide reductase family in bacteria.  This family includes vitamin K epoxide reductase (VKOR) present in proteobacteria and spirochetes. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain ...
CDD:240604	128	PRK	Bacteria:42	cd12921, VKOR_4, Vitamin K epoxide reductase (VKOR) family in bacteria.  This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active ...
CDD:240605	133	PRK	Bacteria:57	cd12922, VKOR_5, Vitamin K epoxide reductase family in bacteria.  This family includes vitamin K epoxide reductase (VKOR) mostly present in actinobacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an ...
CDD:214016	152	EUK	Invertebrates:14,Primates:1,Rodents:1,Vertebrates:1	cd12923, iSH2_PI3K_IA_R, Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits.  PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle ...
CDD:240571	97	PRK	Bacteria:140	cd12927, MMP_TTHA0227_like, Minimal MMP-like domain found in Thermus thermophilus TTHA0227, Acidothermus cellulolyticus ACEL2062 and similar proteins.  The family includes hypothetical proteins from bacteria that contain a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets.These proteins may belong to a superfamily of bacterial zinc metallo-peptidases, which is characterized by a conserved HExxHxxGxxD (x could be any amino acid) ...
CDD:260087	81	EUK	Invertebrates:7,Plants:11,Primates:1	cd12930, GAT_SF, GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins.  The GAT (GGA and Tom1) domain superfamily includes GGAs found in eukaryotes, Tom1-like proteins from metazoa, and LAS seventeen-binding protein 5 (Lsb5p)-like proteins from fungi. GGAs, also termed Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a ...
CDD:240579	90	EUK	Invertebrates:7,nodiv:1	cd12931, eNOPS_SF, NOPS domain, including C-terminal helical extension region, in the p54nrb/PSF/PSP1 family.  All members in this family contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRM1 and RRM2), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain with a long helical C-terminal ...
CDD:240576	118	EUK	Invertebrates:13,Plants:30,Vertebrates:1	cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins.  This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the ...
CDD:240597	114	EUK	Invertebrates:12,Plants:14,Primates:1,nodiv:1	cd12933, eIF3G, eIF3G domain found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins.  eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3. eIF3 is a large multi-subunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. ...
CDD:240585	37	EUK	Invertebrates:29,Primates:1,Vertebrates:1,nodiv:2	cd12934, LEM, LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins.  The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular ...
CDD:240596	36	EUKprk	Bacteria:6,Invertebrates:4,Plants:42,Primates:1,Vertebrates:3	cd12935, LEM_like, LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins.  LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, ...
CDD:240594	86	EUK	Invertebrates:18,Plants:16,nodiv:1	cd12937, GUCT_RH7_like, RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar proteins.  This subfamily corresponds to the  Gu C-terminal (GUCT) domain of RH7 and similar proteins. RH7, also termed plant RNA helicase 75 (PRH75), is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains ...
CDD:240595	74	EUKprk	Bacteria:5,Plants:8	cd12938, GUCT_Hera, RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins.  This subfamily corresponds to the  Gu C-terminal (GUCT)-like domain of Hera and similar proteins. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a ...
CDD:240587	42	EUK	Invertebrates:3,Mammals:1,Primates:1,Vertebrates:3	cd12940, LEM_LAP2_LEMD1, LEM (Lap2/Emerin/Man1) domain found in lamina-associated polypeptide 2 (LAP2), LEM domain-containing protein 1 (LEMP-1) and similar proteins.  This CD corresponds to the LEM domain of LAP2, LEMP-1 and similar proteins. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and ...
CDD:240580	100	EUK	Invertebrates:13	cd12945, NOPS_NONA_like, NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species.  The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, ...
CDD:240577	128	miss	miss	cd12950, RRP7_Rrp7p, RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins.  This CD corresponds to the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly. Rrp7p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain.
CDD:240578	129	miss	miss	cd12951, RRP7_Rrp7A, RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins.  The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or ...
CDD:240572	117	miss	miss	cd12952, MMP_ACEL2062, Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein.  The subfamily includes an uncharacterized protein from Acidothermus cellulolyticus (ACEL2062) and its homologs from bacteria. Although its biological role remains unclear, ACEL2062 contains a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets and a HExxHxxGxxD/S (x could be any amino acid) motif. It ...
CDD:240573	112	miss	miss	cd12953, MMP_TTHA0227, Minimal MMP-like domain found in Thermus thermophilus hypothetical protein TTHA0227 and similar proteins.  The subfamily includes an uncharacterized protein from Thermus thermophilus (TTHA0227) and its homologs from bacteria. Although its biological role remains unclear, TTHA0227 contains a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets and a HExxH (x could be any amino acid) motif. It may belong to a ...
CDD:240574	99	miss	miss	cd12954, MMP_TTHA0227_like_1, Minimal MMP-like domain found in a group of hypothetical proteins from alphaproteobacteria and actinobacteria.  The subfamily includes some uncharacterized bacterial proteins which show high sequence similarity with Thermus thermophilus hypothetical protein TTHA0227. However, they do not contain the conserved HExxH (x could be any amino acid) motif. They may not have any zinc metallo-peptidase activity.
CDD:240562	93	PRK	Bacteria:14	cd12956, CBM_SusE-F_like, carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins.  This group includes five starch-specific CBMs (carbohydrate-binding modules) of SusE and SusF, two cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are ...
CDD:214022	226	EUK	Invertebrates:13,Plants:3,Primates:1,Vertebrates:3,nodiv:1	cd12959, MMACHC-like, Methylmalonic aciduria and homocystinuria type C protein and similar proteins.  MMACHC, also called CblC, is involved in the intracellular processing of vitamin B12 by catalyzing two reactions: the reductive decyanation of cyanocobalamin in the presence of a flavoprotein oxidoreductase and the dealkylation of alkylcobalamins through the nucleophilic displacement of the alkyl group by glutathione. ...
CDD:240575	36	EUK	Invertebrates:10	cd12960, Spider_toxin, Spider neurotoxins including agatoxin, purotoxin and ctenitoxin.  This domain family contains spider toxins that include the omega-Aga-IVB, a P-type calcium channel antagonist from venom of the funnel web spider, Agelenopsis aperta, as well as purotoxin-1 (PT1), a spider peptide venom of the Central Asian spider Geolycosa sp., which specifically exerts inhibitory action on P2X3 purinoreceptors at nanomolar concentrations. These spider ...
CDD:240568	95	PRK	Bacteria:36	cd12962, X25_BaPul_like, X25 domain of Bacillus acidopullulyticus pullulanase and similar proteins.  Pullulanase (EC 3.2.1.41) cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. BaPul is used industrially in the production of high fructose corn syrup, high maltose content syrups and low calorie and ''light'' beers.  Pullulanases, in addition to the catalytic domain, ...
CDD:240563	110	PRK	Bacteria:15	cd12964, CBM-Fa, carbohydrate-binding module Fa from Bacteroides thetaiotaomicron SusE, and similar CBMs.  CBM-Fa is the first of three starch-specific CBM (carbohydrate-binding modules) of SusF, a cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. The precise mechanistic role of SusF in starch metabolism is unclear. SusF has an N-terminal domain which may belong to the immunoglobulin ...
CDD:240564	98	PRK	Bacteria:26	cd12965, CBM-Eb_CBM-Fb, carbohydrate-binding modules Eb and Fb from SusE and SusF, respectively, and similar CBMs.  Included in this subgroup are CBM-Eb and CBM-Fb, starch-specific carbohydrate-binding modules of SusE and SusF, cell surface lipoproteins within the Sus (Starch-utilization system)system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are ...
CDD:240565	98	PRK	Bacteria:5	cd12966, CBM-Ec_CBM-Fc, carbohydrate-binding modules Ec and Fc from SusE and SusF, respectively, and similar CBMs.  Included in this subgroup are CBM-Ec and CBM-Fc, starch-specific carbohydrate-binding modules of SusE and SusF, cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are ...
CDD:240566	91	PRK	Bacteria:30	cd12967, CBM_SusE-F_like_u1, Uncharacterized subgroup of the CBM-SusE-F_like superfamily.  The CBM SusE-F_like superfamily includes starch-specific CBMs (carbohydrate-binding modules) of SusE and SusF, two cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are unclear. Both ...
CDD:240556	76	EUK	Invertebrates:2,Primates:1,Rodents:1	cd13112, POLO_box, Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases.  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single ...
CDD:240557	112	EUK	Invertebrates:15,Mammals:1,Plants:2,Vertebrates:3,nodiv:1	cd13114, POLO_box_Plk4_1, First (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak).  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a ...
CDD:240558	108	EUK	Invertebrates:3,Primates:1	cd13115, POLO_box_Plk4_2, Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak).  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), ...
CDD:240559	81	EUK	Invertebrates:7,Plants:1,Vertebrates:1	cd13116, POLO_box_Plk4_3, C-terminal (third) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak).  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single ...
CDD:240560	81	EUK	Invertebrates:42,Plants:38,Primates:2,Rodents:1,Vertebrates:3,nodiv:1	cd13117, POLO_box_2, Second polo-box domain (PBD) of polo-like kinases Plk1, Plk2, Plk3, and Plk5.  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein ...
CDD:240561	91	EUK	Invertebrates:15,Mammals:4,Plants:23,Primates:2,Rodents:1,Vertebrates:2	cd13118, POLO_box_1, First polo-box domain (PBD) of polo-like kinases Plk1, Plk2, Plk3, and Plk5.  The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein ...
CDD:240524	115	PRK	Bacteria:2	cd13119, BF2867_like, Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins.  Two structurally similar domains with low sequence similarity form a protein that may have a role in cell adhesion. This family also includes BF1858 and overlaps with DUF3988.
CDD:240525	156	PRK	Bacteria:31,Environmental:1	cd13120, BF2867_like_N, N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins.  Two structurally similar domains with low sequence similarity in a tandem repeat arrangement form a protein that may have a role in cell adhesion. This family overlaps with DUF3988.
CDD:240526	138	PRK	Bacteria:23,Environmental:1	cd13121, BF2867_like_C, C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins.  Two structurally similar domains with low sequence similarity  in a tandem repeat arrangement form a protein that may have a role in cell adhesion. This family overlaps with DUF3988.
CDD:240555	50	EUK	Invertebrates:8,Primates:1,Vertebrates:4	cd13122, MSL2_CXC, DNA-binding cysteine-rich domain of male-specific lethal 2 and related proteins.  The CXC domain of Drosophila melanogaster MSL2 forms a Zn(3)Cys(9) cluster and is involved in recruiting members of the dosage compensation complex (DCC) to sites on the X chromosome.
CDD:240528	420	PRK	Bacteria:225,Environmental:7	cd13123, MATE_MurJ_like, MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins.  Escherichia coli MurJ (MviN) has been identified as essential for murein biosynthesis. It has been suggested that MurJ functions as the peptidoglycan lipid II flippase which is involved in translocation of lipid-anchored peptidoglycan precursors across the cytoplasmic membrane, though results obtained in Bacillus subtilis seem to ...
CDD:240529	434	PRK	Bacteria:112	cd13124, MATE_SpoVB_like, Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins.  The integral membrane protein SpoVB has been implicated in the biosynthesis of the peptidoglycan component of the spore cortex in Bacillus subtilis. This model represents a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Proteins from the MATE family are involved in exporting metabolites across the cell ...
CDD:240530	409	PRK	Bacteria:41	cd13125, MATE_like_10, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  This family might function as a translocase for lipopolysaccharides, such as O-antigen. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of ...
CDD:240531	396	PRK	Bacteria:17	cd13126, MATE_like_11, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  This family might function as a translocase for lipopolysaccharides, such as O-antigen. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of ...
CDD:240532	406	PRK	Bacteria:161,Environmental:1	cd13127, MATE_tuaB_like, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  This family might function as a translocase for lipopolysaccharides and participate in the biosynthesis of cell wall components such as teichuronic acid. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria ...
CDD:240533	402	PRK	Bacteria:76	cd13128, MATE_Wzx_like, Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins.  Escherichia coli Wzx and related proteins from other gram-negative bacteria are thought to act as flippases, assisting in the membrane translocation of lipopolysaccharides including those containing O-antigens. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR).
CDD:240535	441	EUK	Plants:7	cd13130, MATE_rft1, Rft1-like subfamily of the multidrug and toxic compound extrusion family (MATE).  This eukaryotic family may function as a transporter, shuttling phospholipids, lipopolysaccharides or oligosaccharides from cytoplasmic to the lumenal side of the endoplasmic reticulum. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has ...
CDD:240536	435	PRK	Bacteria:39,nodiv:1	cd13131, MATE_NorM_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Vibrio cholerae NorM and functions most likely as a multidrug efflux pump, removing xenobiotics from the ...
CDD:240537	436	EUK	Invertebrates:8,Plants:16,Primates:1,Rodents:1,Vertebrates:1	cd13132, MATE_eukaryotic, Eukaryotic members of the multidrug and toxic compound extrusion (MATE) family.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease ...
CDD:240538	438	EUKprk	Bacteria:63,Environmental:1,Plants:1	cd13133, MATE_like_7, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240539	438	PRK	Bacteria:70	cd13134, MATE_like_8, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240540	429	PRK	Bacteria:8	cd13135, MATE_like_9, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240541	424	EUKprk	Bacteria:49,Plants:8	cd13136, MATE_DinF_like, DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins.  Escherichia coli DinF is a membrane protein that has been found to protect cells against oxidative stress and bile salts. The expression of DinF is regulated as part of the SOS system. It may act by detoxifying oxidizing molecules that have the potential to damage DNA. Some member of this family have been reported to ...
CDD:240542	432	PRK	Bacteria:90,Environmental:2	cd13137, MATE_NorM_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240543	431	EUKprk	Bacteria:101,Plants:1	cd13138, MATE_yoeA_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240544	448	PRK	Bacteria:16	cd13139, MATE_like_14, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240545	435	EUKprk	Bacteria:44,Plants:2	cd13140, MATE_like_1, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members ...
CDD:240546	443	PRK	Bacteria:8	cd13141, MATE_like_13, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240547	444	PRK	Bacteria:29	cd13142, MATE_like_12, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240548	426	PRK	Bacteria:67	cd13143, MATE_MepA_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Streptococcus aureus MepA and Vibrio vulnificus VmrA and functions most likely as a multidrug efflux pump.
CDD:240549	434	PRK	Bacteria:18	cd13144, MATE_like_4, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240550	440	PRK	Bacteria:14,Environmental:1	cd13145, MATE_like_5, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240552	441	PRK	Bacteria:27	cd13147, MATE_MJ0709_like, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins, similar to Methanocaldococcus jannaschii MJ0709.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240553	441	PRK	Bacteria:13,Environmental:1	cd13148, MATE_like_3, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240554	434	PRK	Bacteria:6	cd13149, MATE_like_2, Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins.  The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.
CDD:240523	198	EUK	Invertebrates:15,Primates:1,Vertebrates:2	cd13150, DAXX_histone_binding, Histone binding domain of the death-domain associated protein (DAXX).  DAXX is a nuclear protein that modulates transcription of various genes and is involved in cell death and/or the suppression of growth. DAXX is also a histone chaperone conserved in Metazoa that acts specifically on histone H3.3. This alignment models a functional domain of DAXX that interacts with the histone H3.3-H4 dimer, and in ...
CDD:240516	57	EUK	Invertebrates:21,Vertebrates:3,nodiv:1	cd13152, KOW_GPKOW_A, KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat A.  GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far ...
CDD:240517	51	EUK	Invertebrates:8,Plants:9,Vertebrates:1	cd13153, KOW_GPKOW_B, KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B.  GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far ...
CDD:240518	129	EUK	Invertebrates:14,Plants:18,Primates:1,Vertebrates:3	cd13154, KOW_Mtr4, KOW_Mtr4 is an inserted domain in Mtr4 globular domain.  Mtr4 is a conserved helicase with a core DExH region that cooperates with the eukaryotic nuclear exosome in RNA processing and degradation. KOW_Mtr4 motif might be involved in presenting RNA substrates to the helicase core. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential ...
CDD:240519	54	EUK	Invertebrates:28,Plants:12,Vertebrates:3,nodiv:1	cd13155, KOW_KIN17, KOW_Kin17 is a RNA-binding motif.  KOW domain of the KIN17protein contributes to the RNA-binding properties of the whole protein. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KIN17 is ...
CDD:240520	152	EUK	Invertebrates:33,Plants:20,Rodents:2,Vertebrates:3,nodiv:1	cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6.  RPL6 contains KOW motif that has an extra ribosomal role as an oncogenic. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. .
CDD:269979	129	EUK	Invertebrates:4,Primates:1,Rodents:1,Vertebrates:2	cd13157, PTB_tensin-related, Tensin-related Phosphotyrosine-binding (PTB) domain.  Tensin plays critical roles in renal function, muscle regeneration, and cell migration. It binds to actin filaments and interacts with the cytoplasmic tails of beta-integrin via its PTB domain, allowing tensin to link actin filaments to integrin receptors. Tensin functions as a platform for assembly and disassembly of signaling complexes at ...
CDD:269980	135	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:5	cd13158, PTB_APPL, Adaptor protein containing PH domain, PTB domain, and Leucine zipper motif (APPL; also called DCC-interacting protein (DIP)-13alpha) Phosphotyrosine-binding (PTB) domain.  APPL interacts with oncoprotein serine/threonine kinase AKT2, tumor suppressor protein DCC (deleted in colorectal cancer), Rab5, GIPC (GAIP-interacting protein, C terminus), human follicle-stimulating hormone receptor (FSHR), and the ...
CDD:269981	123	EUK	Invertebrates:13,Mammals:1,Primates:1,Vertebrates:2	cd13159, PTB_LDLRAP-mammal-like, Low Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) in mammals and similar proteins Phosphotyrosine-binding (PTB) PH-like fold.  The null mutations in the LDL receptor adaptor protein 1 (LDLRAP1) gene, which serves as an adaptor for LDLR endocytosis in the liver, causes autosomal recessive hypercholesterolemia (ARH). LDLRAP1 contains a single PTB domain. PTB domains have a common ...
CDD:269982	125	EUK	Invertebrates:8	cd13160, PTB_LDLRAP_insect-like, Low Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) in insects and similar proteins Phosphotyrosine-binding (PTB) PH-like fold.  The null mutations in the LDL receptor adaptor protein 1 (LDLRAP1) gene, which serves as an adaptor for LDLR endocytosis in the liver, causes autosomal recessive hypercholesterolemia (ARH). LDLRAP1 contains a single PTB domain. PTB domains have a common PH-like fold and are found in various ...
CDD:269983	120	EUK	Invertebrates:3	cd13161, PTB_TK_HMTK, Tyrosine-specific kinase/HM-motif TK (TM/HMTK) Phosphotyrosine-binding (PTB) PH-like fold.  TK kinases catalyzes the transfer of the terminal phosphate of ATP to a specific tyrosine residue on its target protein. TK kinases play significant roles in development and cell division. Tyrosine-protein kinases can be divided into two subfamilies: receptor tyrosine kinases, which have an intracellular tyrosine kinase domain, a transmembrane ...
CDD:269984	131	EUK	Invertebrates:4,Vertebrates:5	cd13162, PTB_RGS12, Regulator of G-protein signaling 12 Phosphotyrosine-binding (PTB) PH-like fold.  RGS12 functions as a GTPase-activating protein and a transcriptional repressor. It is thought to play a role in tumorigenesis. RGS12 specifically interacts with guanine nucleotide-binding protein G(i), alpha-1 subunit and guanine nucleotide-binding protein G(k) subunit alpha. RGS proteins are multi-functional, GTPase-accelerating proteins that ...
CDD:269989	125	miss	miss	cd13168, PTB_LOC417372, uncharacterized protein LOC417372 Phosphotyrosine-binding (PTB) PH-like fold.  The function of LOC417372 and its related proteins are unknown to date. Members here contain a N-terminal RUN domain, followed by a PDZ domain, and a C-terminal PTB domain. The RUN domain is involved in Ras-like GTPase signaling. The PDZ domain (also called DHR/Dlg homologous region or GLGF after its conserved sequence motif) binds C-terminal polypeptides, internal ...
CDD:269991	111	EUK	Invertebrates:22,Plants:36,Vertebrates:3	cd13170, RanBD_NUP50, Nucleoporin 50 Ran-binding domain.  NUP50 acts as a cofactor for the importin-alpha:importin-beta heterodimer, which allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. It is thought to function primarily at the terminal stages of nuclear protein import to coordinate import complex disassembly and importin recycling. NUP50 is composed of a N-terminal NUP50 domain which binds ...
CDD:269997	117	EUK	Invertebrates:4,Primates:1,Vertebrates:2	cd13176, RanBD_RanBP2-like, Ran-binding protein 2, Ran binding domains.  RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates ...
CDD:270000	136	EUK	Invertebrates:18,Plants:14,Primates:1,Vertebrates:3	cd13179, RanBD_RanBP1, Ran-binding domain.  RanBP1 interacts specifically with GTP-charged Ran. RanBP1 does not activate GTPase activity of Ran, but does markedly increase GTP hydrolysis by the RanGTPase-activating protein (RanGAP1). In both mammalian cells and in yeast, RanBP1 acts as a negative regulator of Regulator of chromosome condensation 1 (RCC1) by inhibiting RCC1-stimulated guanine nucleotide release from Ran. In ...
CDD:270001	113	EUK	Invertebrates:23,Plants:3,Vertebrates:2	cd13180, RanBD_RanBP3, Ran-binding protein 3 Ran-binding domain.  RanBP3, a Ran-interacting nuclear protein, unlike the related proteins RanBP1 and RanBP2, which promote disassembly of the export complex in the cytosol, acts as a CRM1 cofactor, enhancing nuclear export signal (NES) export by stabilizing the export complex in the nucleus. CRM1/Exportin1 is responsible for exporting many proteins and ribonucleoproteins from the nucleus to ...
CDD:270003	116	EUK	Invertebrates:11,Plants:21,Primates:1,Vertebrates:2	cd13182, EVH1-like_Dcp1, Decapping enzyme EVH1-like domain.  Dcp1 is a small protein containing an EVH1 domain. The Dcp1-Dcp2 complex plays a critical step in mRNA degradation with the removal of the 50 cap structure. Dcp1 stimulates the activity of Dcp2 by promoting and/or stabilizing the closed complex. The interface of Dcp1 and Dcp2 is not fully conserved and in higher eukaryotes it requires an additional factor. The ...
CDD:270005	94	EUK	Invertebrates:11,Vertebrates:3	cd13184, FERM_C_4_1_family, Protein 4.1 family FERM domain C-lobe.  The protein 4.1 family includes four well-defined members: erythroid protein 4.1 (4.1R), the bestknown and characterized member, 4.1G (general), 4.1N (neuronal), and 4.1 B (brain). The less well understood 4.1O/FRMD3 is not a true member of this family and is not included in this hierarchy. Besides three highly conserved domains, FERM, SAB (spectrin and actin binding domain) and ...
CDD:270006	107	EUK	Invertebrates:13,Rodents:1,Vertebrates:2	cd13185, FERM_C_FRMD1_FRMD6, FERM domain containing 1 and 6 proteins FERM domain C-lobe.  FRMD6 (also called willin and hEx/human expanded) is localized throughout the cytoplasm or along the plasma membrane The Drosophilla protein Ex is a regulator of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway, a signaling pathway that plays a pivotal role in organ size control and is tumor suppression by restricting proliferation and promoting ...
CDD:270007	92	EUK	Invertebrates:13,Rodents:1,Vertebrates:3	cd13186, FERM_C_NBL4_NBL5, Novel band 4.1-like protein 4 and 5 FERM (NBL4 and 5) domain C-lobe.  NBL4 (also called Erythrocyte protein band 4.1-like 4; Epb4 1l4) plays a role the beta-catenin/Tcf signaling pathway and is thought to be involved in establishing the cell polarity or proliferation. NBL4 may be also involved in adhesion, in cell motility and/or in cell-to-cell communication. No role for NBL5 has been proposed to date. Both ...
CDD:270008	103	EUK	Invertebrates:6,Primates:1,Vertebrates:3	cd13187, FERM_C_PTPH13, Protein tyrosine phosphatase non-receptor 13 (PTPH13) FERM domain C-lobe.  There are many functions of PTPN13 (also called PTPL1, PTP-BAS, hPTP1E, FAP1, or PTPL1). Mice lacking PTPN13 activity have abnormal regulation of signal transducer and activator of transcription signaling in their T cells, mild impairment of motor nerve repair, and a significant reduction in the growth of retinal glia cultures. It also ...
CDD:270009	91	EUK	Invertebrates:14,Vertebrates:3	cd13188, FERM_C_PTPN14_PTPN21, Protein tyrosine phosphatase non-receptor proteins 14 and 21 (PTPN14 and 21) FERM domain.  This CD contains PTP members: pez/PTPN14 and PTPN21. A number of mutations in Pez have been shown to be associated with breast and colorectal cancer. The PTPN protein family belong to larger family of PTPs. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, ...
CDD:270010	95	EUK	Invertebrates:7,Primates:1,Vertebrates:2	cd13189, FERM_C_PTPN4_PTPN3_like, Protein tyrosine phosphatase non-receptor proteins 3 and 4 (PTPN4 and PTPN3) FERM domain C-lobe.  PTPN4 (also called PTPMEG, protein tyrosine phosphatase, megakaryocyte) is a cytoplasmic protein-tyrosine phosphatase (PTP) thought to play a role in cerebellar function. PTPMEG-knockout mice have impaired memory formation and cerebellar long-term depression. PTPN3/PTPH1 is a membrane-associated PTP that is ...
CDD:270011	111	EUK	Invertebrates:15,Primates:1,Rodents:1,Vertebrates:5,nodiv:1	cd13190, FERM_C_FAK1, Focal Adhesion Kinase 1 and 2 FERM domain C-lobe.  FAK1 (also called FRNK/Focal adhesion kinase-related nonkinase; p125FAK/pp125FAK;PTK2/Protein-tyrosine kinase 2 protein tyrosine kinase 2 (PTK2) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. It has been implicated in diverse cellular roles including cell locomotion, mitogen response and cell survival. The ...
CDD:270012	113	EUK	Invertebrates:9,Vertebrates:2	cd13191, FERM_C_FRMD4A_FRMD4B, FERM domain-containing protein 4A and 4B (FRMD4A and 4B) FERM domain C-lobe.  FRMD4A is part of the Par-3/FRMD4A/cytohesin-1 complex that activates Arf6, a central player in actin cytoskeleton dynamics and membrane trafficking, during junctional remodeling and epithelial polarization. The Par-3/Par-6/aPKC/Cdc42 complex regulates the conversion of primordial adherens junctions (AJs) into belt-like AJs and the ...
CDD:270014	122	EUK	Invertebrates:4,Plants:1,Vertebrates:2	cd13193, FERM_C_FARP1-like, FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins FERM domain.  Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FRMD7(FERM domain containing 7). FARP1 and FARP2 are members of the Dbl family guanine nucleotide exchange factors ...
CDD:270015	97	EUK	Invertebrates:19,Primates:1,Rodents:1,Vertebrates:3,nodiv:1	cd13194, FERM_C_ERM, ERM family FERM domain C-lobe/F3.  The ERM family includes ezrin, radixin, moesin and merlin. They are composed of a N-terminal FERM (ERM) domain (also called N-ERMAD (N-terminal ERM association domain)), a coiled coil region (CRR), and a C-terminal domain CERMAD (C-terminal ERM association domain) which has an F-actin-binding site (ABD). Two actin-binding sites have been identified in the middle ...
CDD:270016	111	EUK	Invertebrates:13,Primates:1,Vertebrates:3	cd13195, FERM_C_MYLIP_IDOL, The E3 ubiquitin ligase myosin regulatory light chain-interacting protein (MYLIP; also called inducible degrader of the LDL receptor, IDOL) FERM domain C-lobe.  MYLIP/IDOL is a regulator of the LDL receptor (LDLR) pathway via the nuclear receptor liver X receptor (LXR). In response to cellular cholesterol loading, the activation of LXR leads to the induction of MYLIP expression. MYLIP stimulates ...
CDD:270017	111	EUK	Invertebrates:3,Mammals:1,Primates:1,Vertebrates:6	cd13196, FERM_C_JAK, Janus kinase (JAK) FERM domain C-lobe.  JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, ...
CDD:270019	99	EUK	Invertebrates:20,Mammals:1,Primates:1,Vertebrates:4	cd13198, FERM_C1_MyoVII, Myosin VII (MyoVII/Myo7) FERM domain C-lobe, repeat 1.  MyoVII, a MyTH-FERM myosin, is an actin-based motor protein essential for a variety of biological processes in the actin cytoskeleton function. Mutations in MyoVII leads to problems in sensory perception: deafness and blindness in humans (Usher Syndrome), retinal defects and deafness in mice (shaker 1), and aberrant auditory and vestibular ...
CDD:270020	96	EUK	Invertebrates:4,Mammals:1,Vertebrates:1	cd13199, FERM_C2_MyoVII, Myosin VII (MyoVII, Myo7) FERM domain C-lobe, repeat 2.  MyoVII, a MyTH-FERM myosin, is an actin-based motor protein essential for a variety of biological processes in the actin cytoskeleton function. Mutations in MyoVII leads to problems in sensory perception: deafness and blindness in humans (Usher Syndrome), retinal defects and deafness in mice (shaker 1), and aberrant auditory and vestibular function in ...
CDD:270022	101	EUK	Invertebrates:10,Mammals:1,Primates:1,Vertebrates:4	cd13201, FERM_C_MyoXV, Myosin XV (MyoXV/Myo15) FERM domain C-lobe.  MyoXV, a MyTH-FERM myosin, are actin-based motor proteins essential for a variety of biological processes in actin cytoskeleton function. Specifically MyoXV functions in the actin organization in hair cells of the organ of Corti. Mutations in Human MyoXVa causes non-syndromic deafness, DFNB3 and the mouse shaker-2 mutation. MyoXV consists of a N-terminal ...
CDD:270027	105	EUK	Invertebrates:17,Mammals:1,Primates:1,Vertebrates:4,nodiv:1	cd13207, PX-FERM_C_SNX, sorting nexin family Phox FERM-like domain C-lobe.  Sorting nexins function in regulating recycling from endosomes to the cell surface. SNX17, SNX27, and SNX31 contain a N-terminal PX domain, a FERM-like domain, and a unique C-terminal region. All three proteins are able to bind the Ras GTPase through their FERM-like domains. The PX domain of SNXs binds PIs and targets the protein to ...
CDD:270030	98	EUK	Invertebrates:12,Primates:3,Vertebrates:4,nodiv:1	cd13210, PH-GRAM_MTMR6-like, Myotubularian (MTM) related (MTMR) 7 and 8 proteins Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  MTMR6, MTMR7, and MRMR8 are all member of the myotubularin dual specificity protein phosphatase gene family. They bind to phosphoinositide lipids through its PH-GRAM domain. These proteins also interact with each other as well as MTMR9. They ...
CDD:270031	97	EUK	Invertebrates:12,Mammals:1,Primates:1,Vertebrates:4	cd13211, PH-GRAM_MTMR9, Myotubularian (MTM) related 9 protein (MTMR9) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  MTMR9 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Gly residue instead of a conserved Cys residue in the dsPTPase catalytic loop which ...
CDD:270033	119	EUK	Invertebrates:8,Vertebrates:3	cd13213, PH-GRAM_MTMR14, Myotubularian (MTM) related 14 protein (MTMR14) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  MTMR14 is a member of the myotubularin protein phosphatase gene family. MTMR14 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. MTMR14 plays a role in the ...
CDD:270034	102	EUK	Invertebrates:24,Plants:24,Primates:1,Vertebrates:3,nodiv:1	cd13214, PH-GRAM_WBP2, WW binding protein 2 (WB2) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  WBP2 plays a number of roles including: acting as a tyrosine kinase substrate, activation of estrogen receptor alpha (ERalpha)/progesterone receptor (PR) transcription, and playing a role in breast cancer. WBP2 contain a N-terminal PH-GRAM domain and a C-terminal ...
CDD:270035	114	EUK	Invertebrates:2,Plants:24	cd13215, PH-GRAM1_AGT26, Autophagy-related protein 26/Sterol 3-beta-glucosyltransferase Pleckstrin homology (PH) domain, repeat 1.  ATG26 (also called UGT51/UDP-glycosyltransferase 51), a member of the glycosyltransferase 28 family, resulting in the biosynthesis of sterol glucoside. ATG26 in decane metabolism and autophagy. There are 32 known autophagy-related (ATG) proteins, 17 are components of the core autophagic machinery essential for all ...
CDD:270036	93	EUK	Plants:16	cd13216, PH-GRAM2_AGT26, Autophagy-related protein 26/Sterol 3-beta-glucosyltransferase Pleckstrin homology (PH) domain, repeat 2.  ATG26 (also called UGT51/UDP-glycosyltransferase 51), a member of the glycosyltransferase 28 family, resulting in the biosynthesis of sterol glucoside. ATG26 in decane metabolism and autophagy. There are 32 known autophagy-related (ATG) proteins, 17 are components of the core autophagic machinery essential for all autophagy-related ...
CDD:270038	96	EUK	Invertebrates:13,Mammals:2,Primates:1,Vertebrates:4	cd13218, PH-GRAM2_TCB1D8_TCB1D9_family, TCB1D8 and TCB1D9 family Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2.  TBC1D8, TBC1D8B, TBC1D9 and TBC1D9B may act as a GTPase-activating proteins for Rab family protein(s). They all contain an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second ...
CDD:270040	94	EUK	Invertebrates:24,Plants:27,Primates:1,Rodents:1,Vertebrates:6,nodiv:1	cd13220, PH-GRAM_GRAMDC, GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  The GRAMDC proteins are membrane proteins. Nothing is known about its function. Members include: GRAMDC1A, GRAMDC1B, GRAMDC1C, GRAMDC2, GRAMDC3, GRAMDC4, and GRAMDC-like proteins. All of the members, except for GRAMDC4 are included in this ...
CDD:270041	104	EUK	Invertebrates:7,Mammals:1,Primates:1,Rodents:1,Vertebrates:2	cd13221, PH-GRAM_GRAMDC4, GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  GRAMDC4 is a membrane protein. Nothing is known about its function. Paralogs include: GRAMDC1A, GRAMDC1B, GRAMDC1C, GRAMDC2, GRAMDC3, and GRAMDC-like proteins. It contains a single PH-GRAM domain at its N-terminus. The GRAM domain is found in ...
CDD:270042	109	EUK	Plants:6	cd13222, PH-GRAM_GEM, GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain.  GEM interacts with CDT1, a pre-replication complex component that is involved in DNA replication, and with TTG1 (Transparent Testa GLABRA 1), a transcriptional regulator of epidermal cell fate. GEM controls the level of histone H3K9 methylation at the promoters of the GLABRA 2 and CAPRICE (CPC) genes, which ...
CDD:270043	100	EUK	Invertebrates:15,Mammals:1,Primates:1,Vertebrates:3	cd13223, PH-GRAM_MTM-like, Myotubularian 1 and related proteins Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase.  MTM1, MTMR1, and MTMR2 are members of the myotubularin protein phosphatase gene family. They contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. In addition MTMR1 (Myotubularian related 1 ...
CDD:270045	95	PRK	Bacteria:30	cd13225, PH-like_bacteria, Pleckstrin homology (PH)-like domains in bacteria (PHb).  Pleckstrin homology (PH) domains were first identified in eukaryotic proteins. Recently PH-like domains have been identified in bacteria as well. These PHb form dome-shaped oligomeric rings with a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. It is now thought that the PH domain ...
CDD:270046	128	EUK	Invertebrates:7,Rodents:1,Vertebrates:2,nodiv:1	cd13226, PH-like_Eap45_GLUE, Eap45 GLUE (GRAM-like ubiquitin-binding in Eap45) Pleckstrin homology-like domain.  ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Human/yeast ESCRT-I consists of Tsg101/Vps23, Vps28/Vps28, and a Vps37 homolog/Vps37. Human/yeast ESCRT-II is composed of EAP20/Vps25, EAP30/Vps22, and EAP45/Vps36. Yeast ESCRT-III consists Vps2, Vps20, Vps24, and Snf7 ...
CDD:270047	128	EUK	Plants:15	cd13227, PH-like_Vps36_GLUE, Vps36 GLUE (GRAM-like ubiquitin-binding in Eap45) Pleckstrin homology-like domain.  ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Yeast/human ESCRT-I consists of Vps23/Tsg101, Vps28/Vps28, and Vps37/Vps37 homolog. Yeast/human ESCRT-II is composed of Vps25/EAP20, Vps22/EAP30, and Vps36/EAP45. Yeast ESCRT-III consists Vps2, Vps20, Vps24, and Snf7 subunits. In contrast, there are three human ...
CDD:270048	120	EUK	Invertebrates:17,Plants:23,Vertebrates:3	cd13228, PHear_NECAP, NECAP (adaptin-ear-binding coat-associated protein) Plextrin Homology (PH) fold with ear-like function (PHear) domain.  NECAPs are alpha-ear-binding proteins that enrich on clathrin-coated vesicles (CCVs). NECAP 1 is expressed in brain and non-neuronal tissues and cells while NECAP 2 is ubiquitously expressed. The PH-like domain of NECAPs is a protein-binding interface that mimics the FxDxF motif binding properties ...
CDD:270049	93	EUK	Invertebrates:16,Mammals:1,Plants:22,Vertebrates:3	cd13229, PH_TFIIH, Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain.  The transcription factor II H (TFIIH) is one of the general transcription factors (GTFs) known to be a target of the transactivation domain (TAD) of p53. Human TFIIH and its homologous yeast counterpart (factor b) are composed of ten subunits that can be divided into two groups, the core TFIIH (XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, ...
CDD:270050	137	EUK	Invertebrates:25,Plants:22,Primates:1,Vertebrates:3	cd13230, PH1_SSRP1-like, Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 1.  SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively. The middle ...
CDD:270051	100	EUK	Invertebrates:7,Plants:12	cd13231, PH2_SSRP1-like, Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 2.  SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively.The middle domain of the Pob3 subunit ...
CDD:270053	110	EUK	Invertebrates:11,Mammals:1,Plants:1,Primates:1,Rodents:1,Vertebrates:6	cd13233, PH_ARHGAP9-like, Beta-spectrin pleckstrin homology (PH) domain.  ARHGAP family genes encode Rho/Rac/Cdc42-like GTPase activating proteins with RhoGAP domain. The ARHGAP members here all have a PH domain upstream of their C-terminal RhoGAP domain. Some have additional N-terminal SH3 and WW domains. The members here include: ARHGAP9, ARHGAP12, ARHGAP15, and ARHGAP27. ARHGAP27 and ARHGAP12 shared the ...
CDD:270055	98	EUK	Invertebrates:5	cd13235, PH2_FARP1-like, FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 2.  Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc finger FYVE domain-containing protein 24). They are members of the Dbl family guanine ...
CDD:270056	105	EUK	Invertebrates:1,Mammals:2,Primates:2,Rodents:1,Vertebrates:6	cd13236, PH2_FGD1-4, FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus.  In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is ...
CDD:270057	91	EUK	Invertebrates:5,Vertebrates:2	cd13237, PH2_FGD5_FGD6, FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus.  FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. The specific function of FGD6 is unknown. In general, FGDs have a RhoGEF (DH) domain, followed by a PH ...
CDD:270061	140	EUK	Invertebrates:13,Primates:1,Vertebrates:3	cd13241, PH2_Kalirin_Trio_p63RhoGEF, p63RhoGEF pleckstrin homology (PH) domain, repeat 2.  The guanine nucleotide exchange factor p63RhoGEF is an effector of the heterotrimeric G protein, Galphaq and linking Galphaq-coupled receptors (GPCRs) to the activation of RhoA. The Dbl(DH) and PH domains of p63RhoGEF interact with the effector-binding site and the C-terminal region of Galphaq and appear to relieve autoinhibition of the catalytic ...
CDD:270062	136	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd13242, PH_puratrophin-1, Puratrophin-1 pleckstrin homology (PH) domain.  Puratrophin-1 (also called Purkinje cell atrophy-associated protein 1 or PLEKHG4/Pleckstrin homology domain-containing family G member 4) contains a spectrin repeat, a RhoGEF (DH) domain, and a PH domain. It is thought to function in intracellular signaling and cytoskeleton dynamics at the Golgi. Puratrophin-1 is expressed in kidney, Leydig cells in the testis, ...
CDD:270063	147	EUK	Invertebrates:11,Primates:1,Vertebrates:1	cd13243, PH_PLEKHG1_G2_G3, Pleckstrin homology domain-containing family G members 1, 2, and 3 pleckstrin homology (PH) domain.  PLEKHG1 (also called ARHGEF41), PLEKHG2 (also called ARHGEF42 or CLG/common-site lymphoma/leukemia guanine nucleotide exchange factor2), and PLEKHG3 (also called ARHGEF43) have RhoGEF DH/double-homology domains in tandem with a PH domain which is involved in phospholipid binding. They function as a guanine ...
CDD:270064	100	EUK	Invertebrates:17,Primates:1,Vertebrates:1	cd13244, PH_PLEKHG5_G6, Pleckstrin homology domain-containing family G member 5 and 6 pleckstrin homology (PH) domain.  PLEKHG5 has a RhoGEF DH/double-homology domain in tandem with a PH domain which is involved in phospholipid binding. PLEKHG5 activates the nuclear factor kappa B (NFKB1) signaling pathway. Mutations in PLEKHG5 are associated with autosomal recessive distal spinal muscular atrophy. PLEKHG6 (also called MyoGEF) has no ...
CDD:270065	128	EUK	Invertebrates:10,Vertebrates:3	cd13245, PH_PLEKHG7, Pleckstrin homology domain-containing family G member 7 pleckstrin homology (PH) domain.  PLEKHG7 has a RhoGEF DH/double-homology domain in tandem with a PH domain which is involved in phospholipid binding. PLEKHG7 is proposed to functions as a guanine nucleotide exchange factor (GEF) and is involved in the regulation of Rho protein signal transduction. PH domains have diverse functions, but in general are involved in ...
CDD:270066	148	EUK	Plants:31	cd13246, PH_Scd1, Shape and Conjugation Deficiency 1 Pleckstrin homology (PH) domain.  Fission yeast Scd1 is an exchange factor for Cdc42 and an effector of Ras1, the homolog of the human H-Ras. Scd2/Bem1 mediates Cdc42 activation by binding to Scd1/Cdc24 and to Cdc42. Ras1 regulates Scd1/Cdc24/Ral1, which is a putative guanine nucleotide exchange factor for Cdc42, a member of the Rho family of Ras-like proteins. Cdc42 then activates the Shk1/Orb2 protein kinase. ...
CDD:270067	125	EUK	Invertebrates:3	cd13247, BAR-PH_APPL, Adaptor protein containing PH domain, PTB domain, and Leucine zipper motif Bin1/amphiphysin/Rvs167 (BAR)-Pleckstrin homology (PH) domain.  APPL (also called DCC-interacting protein (DIP)-13alpha) interacts with oncoprotein serine/threonine kinase AKT2, tumor suppressor protein DCC (deleted in colorectal cancer), Rab5, GIPC (GAIP-interacting protein, C terminus), human follicle-stimulating hormone receptor (FSHR), and the adiponectin ...
CDD:270068	104	EUK	Invertebrates:11,Primates:1,Vertebrates:3	cd13248, PH_PEPP1_2_3, Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain.  PEPP1 (also called PLEKHA4/PH domain-containing family A member 4 and RHOXF1/Rhox homeobox family member 1), and related homologs PEPP2 (also called PLEKHA5/PH domain-containing family A member 5) and PEPP3 (also called PLEKHA6/PH domain-containing family A member 6), have PH domains that interact specifically with ...
CDD:270069	111	EUK	Invertebrates:1,Mammals:1,Primates:1,Vertebrates:6	cd13249, PH_rhotekin2, Anillin Pleckstrin homology (PH) domain.  Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin homology domain-containing family K) is an actin binding protein involved in cytokinesis. It interacts with GTP-bound Rho proteins and results in the inhibition of their GTPase activity. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Anillin proteins have a ...
CDD:270070	98	EUK	Invertebrates:14,Plants:12,Primates:1,Vertebrates:1	cd13250, PH_ACAP, ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain.  ACAP (also called centaurin beta) functions both as a Rab35 effector and as an Arf6-GTPase-activating protein (GAP) by which it controls actin remodeling and membrane trafficking. ACAP contain an NH2-terminal bin/amphiphysin/Rvs (BAR) domain, a phospholipid-binding domain, a PH domain, a GAP domain, and four ankyrin ...
CDD:270071	108	EUK	Invertebrates:6,Vertebrates:1	cd13251, PH_ASAP, ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain.  ASAPs (ASAP1, ASAP2, and ASAP3) function as an Arf-specific GAPs, participates in rhodopsin trafficking, is associated with tumor cell metastasis, modulates phagocytosis, promotes cell proliferation, facilitates vesicle budding, Golgi exocytosis, and regulates vesicle coat assembly via a Bin/Amphiphysin/Rvs domain. ASAPs contain an NH2-terminal ...
CDD:270072	109	EUK	Invertebrates:2,Primates:1,Vertebrates:4	cd13252, PH1_ADAP, ArfGAP with dual PH domains Pleckstrin homology (PH) domain, repeat 1.  ADAP (also called centaurin alpha) is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following ...
CDD:270073	94	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:1	cd13253, PH1_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1.  ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol ...
CDD:270078	123	EUK	Invertebrates:11,Primates:1,Vertebrates:3	cd13258, PH_PLEKHJ1, Pleckstrin homology domain containing, family J member 1 Pleckstrin homology (PH) domain.  PLEKHJ1 (also called GNRPX2/Guanine nucleotide-releasing protein x ). It contains a single PH domain. Very little information is known about PLEKHJ1. PLEKHJ1 has been shown to interact with IKBKG (inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma) and KRT33B (keratin 33B). PH domains have diverse ...
CDD:270080	103	EUK	Invertebrates:2	cd13260, PH_RASA1, RAS p21 protein activator (GTPase activating protein) 1 Pleckstrin homology (PH) domain.  RASA1 (also called RasGap1 or p120) is a member of the RasGAP family of GTPase-activating proteins. RASA1 contains N-terminal SH2-SH3-SH2 domains, followed by two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Splice variants lack the N-terminal domains. It is a cytosolic vertebrate protein that acts as a suppressor of RAS via its C-terminal ...
CDD:270082	125	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:4	cd13262, PH_RasSynGAP-like, Synaptic Ras-GTPase activating protein family Pleckstrin homology (PH) domain.  The RasSynGAP family is composed of members: DAB2IP, nGAP, and SynGAP. Neuronal growth-associated proteins (nGAPs) are growth cone markers found in multiple types of neurons. There are many nGAPs including Cap1 (Adenylate cyclase-associated protein 1), Capzb (Capping protein (actin filament) muscle Z-line, beta), Clptm1 ...
CDD:270085	108	EUK	Invertebrates:6,Mammals:1,Rodents:1,Vertebrates:3	cd13265, PH_evt, Evectin Pleckstrin homology (PH) domain.  There are 2 members of the evectin family (also called pleckstrin homology domain containing, family B): evt-1 (also called PLEKHB1) and evt-2 (also called PLEKHB2). evt-1 is specific to the nervous system, where it is expressed in photoreceptors and myelinating glia. evt-2 is widely expressed in both neural and nonneural tissues. Evectins possess a single N-terminal PH ...
CDD:270087	126	EUK	Invertebrates:5,Primates:1,Vertebrates:3	cd13267, PH_DOCK-D, Dedicator of cytokinesis-D subfamily Pleckstrin homology (PH) domain.  DOCK-D subfamily (also called Zizimin subfamily) consists of Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2. DOCK-D has a N-terminal DUF3398 domain, a PH-like domain, a Dock Homology Region 1, DHR1 (also called CZH1), a C2 domain, and a C-terminal DHR2 domain (also called CZH2). Zizimin1 is enriched in the brain, lung, and kidney; zizimin2 ...
CDD:270090	114	EUK	Invertebrates:4,Primates:1,Vertebrates:4	cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and 2 Pleckstrin homology (PH) domain, C-terminal repeat.  The binding of TAPP1 (also called PLEKHA1/pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1) and TAPP2 (also called PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4, 5)P3, function as negative regulators of insulin and PI3K signalling pathways (i.e. ...
CDD:270092	110	EUK	Invertebrates:6,Primates:1,Vertebrates:6	cd13273, PH_SWAP-70, Switch-associated protein-70 Pleckstrin homology (PH) domain.  SWAP-70 (also called Differentially expressed in FDCP 6/DEF-6 or IRF4-binding protein) functions in cellular signal transduction pathways (in conjunction with Rac), regulates cell motility through actin rearrangement, and contributes to the transformation and invasion activity of mouse embryo fibroblasts. Metazoan SWAP-70 is found in B lymphocytes, mast ...
CDD:270094	104	EUK	Invertebrates:11	cd13275, PH_M-RIP, Myosin phosphatase-RhoA Interacting Protein Pleckstrin homology (PH) domain.  M-RIP is proposed to play a role in myosin phosphatase regulation by RhoA. M-RIP contains 2 PH domains followed by a Rho binding domain (Rho-BD), and a C-terminal myosin binding subunit (MBS) binding domain (MBS-BD). The amino terminus of M-RIP with its adjacent PH domains and polyproline motifs mediates binding to both actin and Galpha. M-RIP brings RhoA and MBS ...
CDD:270095	106	EUK	Invertebrates:4,Plants:9	cd13276, PH_AtPH1, Arabidopsis thaliana Pleckstrin homolog (PH) 1 (AtPH1) PH domain.  AtPH1 is expressed in all plant tissue and is proposed to be the plant homolog of human pleckstrin. Pleckstrin consists of two PH domains separated by a linker region, while AtPH has a single PH domain with a short N-terminal extension. AtPH1 binds PtdIns3P specifically and is thought to be an adaptor molecule since it has no obvious catalytic functions. PH domains ...
CDD:270096	111	EUK	Plants:18	cd13277, PH_Bem3, Bud emergence protein 3 (Bem3) Pleckstrin homology (PH) domain.  Bud emergence in Saccharomyces cerevisiae involves cell cycle-regulated reorganizations of cortical cytoskeletal elements and requires the action of the Rho-type GTPase Cdc42. Bem3 contains a RhoGAP domain and a PH domain. Though Bem3 and Bem2 both contain a RhoGAP, but only Bem3 is able to stimulate the hydrolysis of GTP on Cdc42. Bem3 is thought to be the GAP for Cdc42. PH domains ...
CDD:241432	139	EUK	Plants:25	cd13278, PH_Bud4, Bud4 Pleckstrin homology (PH) domain.  Bud4 is an anillin-like yeast protein involved in the formation and the disassembly of the double ring structure formed by the septins during cytokinesis. Bud4 acts with Bud3 and and in parallel with septin phosphorylation by the p21-activated kinase Cla4 and the septin-dependent kinase Gin4. Bud4 is regulated by the cyclin-dependent protein kinase Cdk1, the master regulator of cell cycle progression. Bud4 ...
CDD:270097	92	EUK	Plants:21	cd13279, PH_Cla4_Ste20, Pleckstrin homology (PH) domain.  Budding yeast contain two main p21-activated kinases (PAKs), Cla4 and Ste20. The yeast Ste20 protein kinase is involved in pheromone response, though the function of Ste20 mammalian homologs is unknown. Cla4 is involved in budding and cytokinesis and interacts with Cdc42, a GTPase required for polarized cell growth as is Pak. Cla4 and Ste20 kinases share a function in localizing cell growth with respect to the ...
CDD:270098	105	EUK	Plants:17	cd13280, PH_SIP3, Snf1p-interacting protein 3 Pleckstrin homology (PH) domain.  SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. SIP3 contain an N-terminal Bin/Amphiphysin/Rvs (BAR) domain followed by a PH domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. PH domains have diverse functions, ...
CDD:270099	139	EUK	Invertebrates:7,Primates:1,Vertebrates:1	cd13281, PH_PLEKHD1, Pleckstrin homology (PH) domain containing, family D (with coiled-coil domains) member 1 PH domain.  Human PLEKHD1 (also called UPF0639, pleckstrin homology domain containing, family D (with M protein repeats) member 1) is a single transcript and contains a single PH domain. PLEKHD1 is conserved in human, chimpanzee, , dog, cow, mouse, chicken, zebrafish, and Caenorhabditis elegans. PH domains have diverse ...
CDD:241436	96	EUK	Invertebrates:10,Primates:1,Vertebrates:2	cd13282, PH1_PLEKHH1_PLEKHH2, Pleckstrin homology (PH) domain containing, family H (with MyTH4 domain) members 1 and 2 (PLEKHH1) PH domain, repeat 1.  PLEKHH1 and PLEKHH2 (also called PLEKHH1L) are thought to function in phospholipid binding and signal transduction. There are 3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3. There are many isoforms, the longest of which contain a FERM domain, a MyTH4 domain, two PH domains, a ...
CDD:270100	100	EUK	Invertebrates:12,Vertebrates:3	cd13283, PH_GPBP, Goodpasture antigen binding protein Pleckstrin homology (PH) domain.  The GPBP (also called Collagen type IV alpha-3-binding protein/hCERT; START domain-containing protein 11/StARD11; StAR-related lipid transfer protein 11) is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen, which is commonly known as the goodpasture antigen. Its splice variant the ceramide transporter (CERT) mediates ...
CDD:270101	99	EUK	Invertebrates:13,Primates:1,Vertebrates:1	cd13284, PH_OSBP_ORP4, Human Oxysterol binding protein and OSBP-related protein 4 Pleckstrin homology (PH) domain.  Human OSBP is proposed to function is sterol-dependent regulation of ERK dephosphorylation and sphingomyelin synthesis as well as modulation of insulin signaling and hepatic lipogenesis. It contains a N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. OSBPs and ...
CDD:270104	123	EUK	Invertebrates:7,Mammals:1,Primates:1,Rodents:2,Vertebrates:3	cd13287, PH_ORP3_ORP6_ORP7, Human Oxysterol binding protein related proteins 3, 6, and 7 Pleckstrin homology (PH) domain.  Human ORP3 is proposed to function in regulating the cell-matrix and cell-cell adhesion. A proposed specific function for Human ORP6 was not found at present. Human ORP7is proposed to function in negatively regulating the Golgi soluble NSF attachment protein receptor (SNARE) of 28kDa (GS28) ...
CDD:270105	120	EUK	Invertebrates:14,Mammals:1,Primates:1,Vertebrates:3	cd13288, PH_Ses, Sesquipedalian family Pleckstrin homology (PH) domain.  The sesquipedalian family has 2 mammalian members: Ses1 and Ses2, which are also callled 7 kDa inositol polyphosphate phosphatase-interacting protein 1 and 2. They play a role in endocytic trafficking and are required for receptor recycling from endosomes, both to the trans-Golgi network and the plasma membrane. Members of this family form homodimers and ...
CDD:241443	90	EUK	Plants:15	cd13289, PH_Osh3p_yeast, Yeast oxysterol binding protein homolog 3 Pleckstrin homology (PH) domain.  Yeast Osh3p is proposed to function in sterol transport and regulation of nuclear fusion during mating and of pseudohyphal growth as well as sphingolipid metabolism. Osh3 contains a N-GOLD (Golgi dynamics) domain, a PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. GOLD domains are thought to mediate protein-protein ...
CDD:270106	107	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd13291, PH_ORP10_ORP11, Human Oxysterol binding protein (OSBP) related proteins 10 and 11 (ORP10 and ORP11) Pleckstrin homology (PH) domain.  Human ORP10 is involvedt in intracellular transport or organelle positioning and is proposed to function as a regulator of cellular lipid metabolism. Human ORP11 localizes at the Golgi-late endosome interface and is thought to form a dimer with ORP9 functioning as an intracellular lipid sensor or ...
CDD:241446	103	EUK	Plants:11	cd13292, PH_Osh1p_Osh2p_yeast, Yeast oxysterol binding protein homologs 1 and 2 Pleckstrin homology (PH) domain.  Yeast Osh1p is proposed to function in postsynthetic sterol regulation, piecemeal microautophagy of the nucleus, and cell polarity establishment. Yeast Osh2p is proposed to function in sterol metabolism and cell polarity establishment. Both Osh1p and Osh2p contain 3 N-terminal ankyrin repeats, a PH domain, a FFAT motif (two phenylalanines in an acidic ...
CDD:241447	88	EUK	Invertebrates:7	cd13293, PH_CpORP2-like, Cryptosporidium-like Oxysterol binding protein related protein 2 Pleckstrin homology (PH) domain.  There are 2 types of ORPs found in Cryptosporidium: CpORP1 and CpORP2. Cryptosporium differs from other apicomplexans like Plasmodium, Toxoplasma, and Eimeria which possess only a single long-type ORP consisting of an N-terminal PH domain followed by a C-terminal ligand binding (LB) domain. CpORP2 is like this, but CpORP1 differs and has a ...
CDD:270107	126	EUK	Invertebrates:9,Primates:1,Vertebrates:2	cd13295, PH_EFA6, Exchange Factor for ARF6 Pleckstrin homology (PH) domain.  EFA6 (also called PSD/pleckstrin and Sec7 domain containing) is an guanine nucleotide exchange factor for ADP ribosylation factor 6 (ARF6), which is involved in membrane recycling. EFA6 has four structurally related polypeptides: EFA6A, EFA6B, EFA6C and EFA6D. It consists of a N-terminal proline rich region (PR), a SEC7 domain, a PH domain, a PR, a coiled-coil ...
CDD:270110	106	EUK	Plants:17	cd13298, PH1_PH_fungal, Fungal proteins Pleckstrin homology (PH) domain, repeat 1.  The functions of these fungal proteins are unknown, but they all contain 2 PH domains. This cd represents the first PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is ...
CDD:270111	102	EUK	Plants:6	cd13299, PH2_PH_fungal, Fungal proteins Pleckstrin homology (PH) domain, repeat 2.  The functions of these fungal proteins are unknown, but they all contain 2 PH domains. This cd represents the second PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is ...
CDD:241457	139	EUK	Plants:6	cd13303, PH1_Rtt106, Histone chaperone RTT106, regulator of Ty1 transposition protein 106 Pleckstrin homology (PH) domain.  Rtt106 is a histone chaperone. The binding of Rtt106 to H3K56-acetylated (H3-H4)2 tetramers contributes to nucleosome assembly in terms of DNA replication, gene silencing and maintenance of genomic stability. Rtt106 contains an N-terminal homodimerization domain and two C-terminal pleckstrin-homology (PH) domains (PH1 and PH2). The N-terminal ...
CDD:270118	113	EUK	Invertebrates:6,Vertebrates:2	cd13308, PH_3BP2, SH3 domain-binding protein 2 Pleckstrin homology (PH) domain.  SH3BP2 (the gene that encodes the adaptor protein 3BP2), HD, ITU, IT10C3, and ADD1 are located near the Huntington's Disease Gene on Human Chromosome 4pl6.3. SH3BP2 lies in a region that is often missing in individuals with Wolf-Hirschhorn syndrome (WHS). Gain of function mutations in SH3BP2 causes enhanced B-cell antigen receptor (BCR)-mediated activation of nuclear ...
CDD:270119	103	EUK	Invertebrates:7,Primates:1,Vertebrates:2	cd13309, PH_SKIP, SifA and kinesin-interacting protein Pleckstrin homology (PH) domain.  SKIP (also called PLEKHM2/Pleckstrin homology domain-containing family M member 2) is a soluble cytosolic protein that contains a RUN domain and a PH domain separated by a unstructured linker region. SKIP is a target of the Salmonella effector protein SifA and the SifA-SKIP complex regulates kinesin-1 on the bacterial vacuole. The PH domain of SKIP ...
CDD:270120	116	EUK	Invertebrates:15,Primates:1,Vertebrates:3	cd13310, PH_RalGPS1_2, Ral GEF with PH domain and SH3 binding motif 1 and 2 Pleckstrin homology (PH) domain.  RalGPS1 (also called Ral GEF with PH domain and SH3 binding motif 1;RALGEF2/ Ral guanine nucleotide exchange factor 2; RalA exchange factor RalGPS1; Ral guanine nucleotide exchange factor RalGPS1A2; ras-specific guanine nucleotide-releasing factor RalGPS1) and RalGPS2 (also called Ral GEF with PH domain and SH3 binding motif 2; ...
CDD:270121	110	EUK	Plants:19	cd13311, PH_Slm1, Slm1 Pleckstrin homology (PH) domain.  Slm1 is a component of the target of rapamycin complex 2 (TORC2) signaling pathway. It plays a role in the regulation of actin organization and is a target of sphingolipid signaling during the heat shock response. Slm1 contains a single PH domain that binds PtdIns(4,5)P2, PtdIns(4)P, and dihydrosphingosine 1-phosphate (DHS-1P). Slm1 possesses two binding sites for anionic lipids. The non-canonical binding site ...
CDD:270122	103	EUK	Mammals:1,Primates:2,Rodents:4,Vertebrates:3	cd13312, PH_USP37_like, Ubiquitin carboxyl-terminal hydrolase 37 Pleckstrin homology-like domain.  Members here include USP37, USP29, and USP26. All of these contain a single PH domain. USP37 (also called ubiquitin carboxyl-terminal hydrolase 37, ubiquitin thiolesterase 37, deubiquitinating enzyme 37, and tmp_locus_50) is a deubiquitinase that antagonizes the anaphase-promoting complex (APC/C) during G1/S transition by mediating ...
CDD:270124	105	EUK	Invertebrates:12,Plants:13,Primates:1,Vertebrates:3	cd13314, PH_Rpn13, Regulatory Particle Non-ATPase 13 Pleckstrin homology-like domain.  Targeted protein degradation is performed to a great extent by the ubiquitin-proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. Rpn13(also called ADRM1/ARM1) is one of the two major ubiquitin receptors of the proteasome, the other being S5a/Rpn10 ...
CDD:270125	141	EUK	Plants:21	cd13315, PH_Sec3, Sec 3 Pleckstrin homology-like domain.  The Sec3 subunit of the exocyst, a complex involved in polarized exocytosis, bind phospholipids and GTPase Cdc42 and therefore functions as a coincidence detector at the plasma membrane. Unlike most PH domains, Sec3 contains an additional alpha-helix at its N-terminus and two beta-strands at its C-terminus that mediate dimerization through domain swapping. PH domains have diverse functions, but in general are ...
CDD:270126	97	EUK	Plants:8	cd13316, PH_Boi, Boi family Pleckstrin homology domain.  Yeast Boi proteins Boi1 and Boi2 are functionally redundant and important for cell growth with Boi mutants displaying defects in bud formation and in the maintenance of cell polarity.They appear to be linked to Rho-type GTPase, Cdc42 and Rho3. Boi1 and Boi2 display two-hybrid interactions with the GTP-bound ("active") form of Cdc42, while Rho3 can suppress of the lethality caused by deletion of Boi1 and Boi2. ...
CDD:270128	128	EUK	Invertebrates:14,Primates:1,Vertebrates:3	cd13318, PH_IQSEC, IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain.  The IQSEC (also called BRAG/Brefeldin A-resistant Arf-gunanine nucleotide exchange factor) family are a subset of Arf GEFs that have been shown to activate Arf6, which acts in the endocytic pathway to control the trafficking of a subset of cargo proteins including integrins and have key roles in the function and organization of distinct ...
CDD:270129	97	EUK	Invertebrates:10,Mammals:1,Primates:1,Rodents:3,Vertebrates:4	cd13319, PH_RARhoGAP, RA and RhoGAP domain-containing protein Pleckstrin homology PH domain.  RARhoGAP (also called Rho GTPase-activating protein 20 and ARHGAP20 ) is thought to function in rearrangements of the cytoskeleton and cell signaling events that occur during spermatogenesis. RARhoGAP was also shown to be activated by Rap1 and to induce inactivation of Rho, resulting in the neurite outgrowth. Recent findings ...
CDD:270134	114	EUK	Invertebrates:8	cd13325, PH_unc89, unc89 pleckstrin homology (PH) domain.  unc89 is a myofibrillar protein. unc89-B the largest isoform is composed of 53 immunoglobulin (Ig) domains, 2 Fn3 domains, a triplet of SH3, DH and PH domains at its N-terminus, and 2 protein kinase domains (PK1 and PK2) at its C-terminus. unc-89 mutants display disorganization of muscle A-bands, and usually lack M-lines. The COOH-terminal region of obscurin, the human homolog of unc89, interacts via ...
CDD:270135	91	EUK	Invertebrates:6	cd13326, PH_CNK_insect-like, Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain.  CNK family members function as protein scaffolds, regulating the activity and the subcellular localization of RAS activated RAF. There is a single CNK protein present in Drosophila and Caenorhabditis elegans in contrast to mammals which have 3 CNK proteins (CNK1, CNK2, and CNK3). All of the CNK members contain a sterile a motif (SAM), a ...
CDD:270138	109	EUK	Invertebrates:16,Primates:1,Vertebrates:4	cd13329, PH_RhoGEF, Rho guanine nucleotide exchange factor Pleckstrin homology domain.  RhoGEFs belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. The members here all contain Dbl homology (DH)-PH domains. In addition some members contain N-terminal C1 (Protein kinase C conserved region 1) domains, PDZ (also ...
CDD:270145	113	EUK	Primates:1	cd13337, PX-FERM_C_SNX17, sorting nexin 17 Phox FERM-like domain C-lobe.  SNX17 is a beta1-integrin-tail-binding protein that interacts with the free kindlin-binding site in endosomes to stabilize beta1 integrins, resulting in their recycling to the cell surface where they can be reused. SNX17 contains a N-terminal PX domain, a FERM-like domain, and a unique C-terminal region. SNX17 binds Ras GTPase through its FERM-like domains. The PX domain of SNXs binds PIs and ...
CDD:270146	102	miss	miss	cd13338, PX-FERM_C_SNX27, sorting nexin family Phox FERM-like domain C-lobe.  SNX27 is localized to early endosomes and known to regulate the intracellular trafficking of ion channels and receptors. SNX27 contain a N-terminal PDZ domain, a PX domain, and a FERM-like domain. SNX27 regulates trafficking of a PAK interacting exchange factor-G protein-coupled receptor kinase interacting protein complex via its PDZ domain interaction. Sorting nexin 27 interacts with multidrug ...
CDD:270161	97	EUK	Invertebrates:1	cd13354, PH-GRAM2_TCB1D9_TCB1D9B, TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2.  TBC1D9 and TCB1D9B may act as a GTPase-activating proteins for Rab family protein(s). TBC1D9 and TCB1D9B contain two N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second repeat of the PH-GRAM ...
CDD:270166	126	EUK	Invertebrates:8,Vertebrates:2	cd13359, PH_ELMO1_CED-12, Engulfment and cell motility protein 1 pleckstrin homology (PH) domain.  DOCK2 (Dedicator of cytokinesis 2), a hematopoietic cell-specific, atypical GEF, controls lymphocyte migration through Rac activation. A DOCK2-ELMO1 complex s necessary for DOCK2-mediated Rac signaling. DOCK2 contains a SH3 domain at its N-terminus, followed by a lipid binding DHR1 domain, and a Rac-binding DHR2 domain at its C-terminus. ELMO1, a ...
CDD:241514	118	EUK	Plants:38	cd13360, PH_PLC_fungal, Fungal Phospholipase C (PLC) pleckstrin homology (PH) domain.  Fungal PLC have mostly been characterized in the yeast Saccharomyces cerevisiae via deletion studies which resulted in a pleiotropic phenotype, with defects in growth, carbon source utilization, and sensitivity to osmotic stress and high temperature. Unlike Saccharomyces several other fungi including Neurospora crassa, Cryphonectria parasitica , and Magnaporthe oryzae (Mo) have ...
CDD:270167	127	EUK	Invertebrates:13,Primates:1,Rodents:1,Vertebrates:5	cd13361, PH_PLC_beta, Phospholipase C-beta (PLC-beta) pleckstrin homology (PH) domain.  PLC-beta (PLCbeta) is regulated by heterotrimeric G protein-coupled receptors through their C2 domain and long C-terminal extension which forms an autoinhibitory helix. There are four isoforms: PLC-beta1-4. The PH domain of PLC-beta2 and PLC-beta3 plays a dual role, much like PLC-delta1, by binding to the plasma membrane, as well as the ...
CDD:270168	121	EUK	Invertebrates:9,Rodents:1,Vertebrates:3	cd13362, PH_PLC_gamma, Phospholipase C-gamma (PLC-gamma) pleckstrin homology (PH) domain.  PLC-gamma (PLCgamma) is activated by receptor and non-receptor tyrosine kinases due to the presence of its SH2 and SH3 domains. There are two main isoforms of PLC-gamma expressed in human specimens, PLC-gamma1 and PLC-gamma2. PLC-gamma consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves internal to ...
CDD:270169	117	EUK	Primates:1,Vertebrates:6	cd13363, PH_PLC_delta, Phospholipase C-delta (PLC-delta) pleckstrin homology (PH) domain.  The PLC-delta (PLCdelta) consists of three family members, delta 1, 2, and 3. PLC-delta1 is the most well studied. PLC-delta is activated by high calcium levels generated by other PLC family members, and functions as a calcium amplifier within the cell. PLC-delta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, ...
CDD:270170	109	EUK	Invertebrates:7,Primates:1,Vertebrates:1	cd13364, PH_PLC_eta, Phospholipase C-eta (PLC-eta) pleckstrin homology (PH) domain.  PLC-eta (PLCeta) consists of two enzymes, PLCeta1 and PLCeta2. They hydrolyze phosphatidylinositol 4,5-bisphosphate, are more sensitive to Ca2+ than other PLC isozymes, and involved in PKC activation in the brain and neuroendocrine systems. PLC-eta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves by a ...
CDD:270171	115	EUK	Invertebrates:8,Plants:17	cd13365, PH_PLC_plant-like, Plant-like Phospholipase C (PLC) pleckstrin homology (PH) domain.  PLC-gamma (PLCgamma) was the second class of PLC discovered. PLC-gamma consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves internal to which is a PH domain split by two SH2 domains and a single SH3 domain, and a C-terminal C2 domain. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, ...
CDD:241528	129	EUK	Invertebrates:2	cd13377, PH_SynGAP_2, Synaptic Ras-GTPase activating protein Pleckstrin homology (PH) domain.  SynGAP is a member of the RasSynGAP family along with DOC-2/DAB2-interacting protein (DAB2IP) and neuronal growth-associated protein (nGAP/RASAL2). SynGAP, a neuronal Ras-GAP, has been shown display both Ras-GAP activity and Ras-related protein (Rap)-GAP activity. Saccharomyces cerevisiae Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras inactivator) and RASAL ...
CDD:270187	124	EUK	Invertebrates:7,Primates:1	cd13389, PH1_FGD5_FGD6, FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 Pleckstrin Homology (PH) domain.  FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. The specific function of FGD6 is unknown. In general, FGDs have a RhoGEF (DH) domain, followed by a PH domain, a FYVE ...
CDD:240521	597	EUK	Invertebrates:6,Plants:42,Primates:1,Vertebrates:2	cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.  This family of eukaryotic proteins includes Saccharomyces cerevisiae Ydl063c and Chaetomium thermophilum Syo1, which mediate the co-import of two ribosomal proteins, Rpl5 and Rpl11 (which both interact with 5S rRNA) into the nucleus. Import precedes their association with rRNA and subsequent ribosome assembly in the nucleolus. The primary structure of syo1 is ...
CDD:240449	206	EUKprk	Bacteria:25,Plants:43	cd13426, Peptidase_G1, Peptidases of the G1 family, including scytalidoglutamic peptidase and aspergillopepsin.  Some members of this family had been classified earlier as carboxyl peptidases insensitive to pepstatin, and the family has also been called the eqolisin family, due to the fact that the conserved catalytic dyad of the family consists of a glutamate (E) and glutamine (Q) residue. The family is found in fungi and bacteria.
CDD:240450	204	EUKprk	Bacteria:9,Plants:1	cd13427, YncM_like, Uncharacterized proteins similar to Bacillus subtilis YncM.  Members of this family share close structural similarity with peptidases of the Peptidase_G1 family and may be homologous. They do not appear to share the peptidases' active site, though a bound sulfate ion in the single available structure suggests a functional site at a matching location.
CDD:259832	162	PRK	Bacteria:14	cd13428, UreI_AmiS, UreI/Amis family, proton-gated urea channel and putative amide transporters.  This subfamily includes UreI proton-gated urea channels as well as putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, leading to buffering of the periplasm. This action is ...
CDD:259833	165	PRK	Bacteria:12	cd13429, UreI_AmiS_like_2, UreI/AmiS family, subgroup 2. Putative transporters related to proton-gated urea channel and putative amide transporters.  This subfamily includes putative UreI proton-gated urea channels and putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, ...
CDD:240446	95	PRK	Bacteria:18	cd13431, LDT_IgD_like_1, IgD-like repeat domain of mycobacterial L,D-transpeptidases.  Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase ...
CDD:240447	99	PRK	Bacteria:62	cd13432, LDT_IgD_like_2, IgD-like repeat domain of mycobacterial L,D-transpeptidases.  Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase ...
CDD:240441	54	EUK	Invertebrates:25,Mammals:8,Plants:2,Primates:3,Rodents:4,Vertebrates:7,nodiv:1	cd13433, Na_channel_gate, Inactivation gate of the voltage-gated sodium channel alpha subunits.  This region is part of the intracellular linker between domains III and IV of the alpha subunits of voltage-gated sodium channels. It is responsible for fast inactivation of the channel and essential for proper physiological function.
CDD:259812	108	EUKprk	Bacteria:5,Invertebrates:9,Plants:1,Primates:1,Vertebrates:1	cd13434, SPFH_SLPs, Stomatin-like proteins (slipins) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes proteins similar to stomatin, podocin, and other members of the stomatin-like protein family (SLPs or slipins). The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster ...
CDD:259815	222	EUKprk	Invertebrates:3,Plants:8,Viruses:1	cd13437, SPFH_alloslipin, Alloslipin, a subgroup of the stomatin-like proteins (slipins) familyfamily; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in some eukaryotes and viruses. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of ...
CDD:259816	215	PRK	Bacteria:56	cd13438, SPFH_eoslipins_u2, Uncharacterized prokaryotic subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily.  This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to ...
CDD:240442	106	PRK	Bacteria:4	cd13439, CamS_repeat, Repeat domain of CamS sex pheromone cAM373 precursor and related proteins.  This  family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. cAM373 ...
CDD:240443	115	PRK	Bacteria:68,nodiv:1	cd13440, CamS_repeat_2, C-terminal repeat domain of CamS sex pheromone cAM373 precursor.  This  family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. ...
CDD:240444	204	PRK	Bacteria:29,nodiv:2	cd13441, CamS_repeat_1, N-terminal repeat domain of CamS sex pheromone cAM373 precursor.  This  family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. ...
CDD:259835	129	PRK	Bacteria:30	cd13442, CDI_toxin_Bp1026b_like, Mg-dependent tRNAse of the contact-dependent growth inhibition (CDI) system of Burkholderia pseudomallei 1026b, and related proteins.  CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface ...
CDD:259837	143	PRK	Bacteria:23,nodiv:1	cd13444, CDI_toxin_EC869_like, Zn-dependent DNAse of the contact-dependent growth inhibition (CDI) system of Escherichia coli EC869, and related proteins.  CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring bacteria. This model represents the C-terminal toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface ...
CDD:259838	157	PRK	Bacteria:30	cd13445, CDI_inhibitor_EC869_like, Inhibitor of the contact-dependent growth inhibition (CDI) system of Escherichia coli EC869, and related proteins.  CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring bacteria. This model represents the inhibitor of the CdiA effector protein from Escherichia coli EC869 (which is a DNAse). CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a ...
CDD:259825	97	EUK	Invertebrates:10,Primates:1,Vertebrates:3	cd13516, HHD_CCM2, harmonin-homology domain (harmonin_N_like domain) of malcavernin (CCM2).  CCM2 (also called malcavernin; C7orf22/chromosome 7 open reading frame 22; OSM) along with CCM1 and CCM3 constitutes a set of proteins which when mutated are responsible for cerebral cavernous malformations, an autosomal dominant neurovascular disease characterized by cerebral hemorrhages and vascular malformations in the central nervous system. ...
CDD:270235	223	PRK	Bacteria:18	cd13517, PBP2_ModA3_like, Substrate binding domain of molybdate binding protein-like (ModA3), a member of the type 2 periplasmic binding fold superfamily.  This subfamily contains molybdate binding protein-like (ModA3) domain of an ABC-type transporter. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA ...
CDD:270236	260	PRK	Bacteria:18	cd13518, PBP2_Fe3_thiamine_like, Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily.  The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living ...
CDD:270237	227	PRK	Bacteria:17	cd13519, PBP2_PEB3_AcfC, Ligand-binding domain of a glycoprotein adhesion and an accessory colonization factor, a member of the type 2 periplasmic binding fold superfamily.  PEB3 is a glycoprotein adhesion from Campylobacter jejuni whose structure suggests a functional role in transport, and resembles PEB1a, an Asp/Glu transporter and an adhesin. The overall structure of PEB3 is a dimer and is similar to that of other type 2 periplasmic transport proteins such as ...
CDD:270238	285	PRK	Bacteria:62,Environmental:1	cd13520, PBP2_TAXI_TRAP, Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold.  This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two ...
CDD:270239	483	PRK	Bacteria:5	cd13521, PBP2_AlgQ_like, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold.  This family represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria and related proteins. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the ...
CDD:270240	368	PRK	Bacteria:5	cd13522, PBP2_ABC_oligosaccharides, The periplasmic-binding component of ABC transport systems specific for maltose and related oligosaccharides; possess type 2 periplasmic binding fold.  This family represents the periplasmic binding component of ABC transport systems involved in uptake of oligosaccharides including maltose, trehalose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised ...
CDD:270241	268	PRK	Bacteria:5	cd13523, PBP2_polyamines, The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding proteins that function as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly ...
CDD:270244	228	PRK	Bacteria:11	cd13526, PBP2_lipoprotein_MetQ_like, The periplasmic-binding component of ABC-type methionine uptake transporter system and its related lipoproteins; the type 2 periplasmic-binding protein fold.  This family represents the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ) and its related homologs. Members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, ...
CDD:270246	264	PRK	Bacteria:37	cd13528, PBP2_osmoprotectants, Substrate-binding domain of osmoregulatory ABC-type transporters; the type 2 periplasmic-binding protein fold.  This family represents the periplasmic substrate-binding component of ABC transport systems that are involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. To counteract the efflux of water, bacteria and archaea accumulate the compatible ...
CDD:270247	298	EUK	Invertebrates:18,Mammals:3,Plants:1,Primates:1,Vertebrates:4,nodiv:1	cd13529, PBP2_transferrin, Transferrin family of the type 2 periplasmic-binding protein superfamily.  Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe ...
CDD:270248	217	EUKprk	Bacteria:99,Plants:1	cd13530, PBP2_peptides_like, Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold.  This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating.  The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, but have a different topology. They are typically comprised of two globular subdomains connected by a flexible ...
CDD:270250	184	EUKprk	Bacteria:27,Environmental:2,Plants:42	cd13532, PBP2_PDT_like, Catalytic domain of prephenate dehydratase and similar proteins; the type 2 periplasmic binding protein fold.  Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The ...
CDD:270251	222	PRK	Bacteria:12	cd13533, PBP2_Yhfz, Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 periplasmic-binding protein fold.  This subfamily contains periplasmic binding protein type II (BPBII).  This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating.  The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a ...
CDD:270252	261	EUKprk	Bacteria:4,Plants:1	cd13534, PBP2_MqnD_like, Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 periplasmic-binding protein fold.  This family represents MqnD, an enzyme within the alternative menaquinone biosynthetic pathway, and related conserved hypothetical proteins. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. The members ...
CDD:270254	227	PRK	Bacteria:6	cd13536, PBP2_EcModA, Substrate binding domain of ModA from Escherichia coli and its closest homologs;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ...
CDD:270255	225	PRK	Bacteria:13	cd13537, PBP2_YvgL_like, Substrate binding domain of putative molybdate-binding protein YvgL and similar proteins;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins of putative ABC-type transporter. ModA proteins serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate ...
CDD:270256	230	PRK	Bacteria:15	cd13538, PBP2_ModA_like_1, Substrate binding domain of putative molybdate-binding protein;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins of putative ABC-type transporter. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial ...
CDD:270257	226	PRK	Bacteria:44	cd13539, PBP2_AvModA, Substrate binding domain of ModA/WtpA from Azotobacter vinelandii and its closest homologs;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After ...
CDD:270258	263	PRK	Bacteria:23	cd13540, PBP2_ModA_WtpA, Substrate binding domain of ModA/WtpA from Pyrococcus furiosus and its closest homologs;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After ...
CDD:270259	238	PRK	Bacteria:7	cd13541, PBP2_ModA_like_2, Substrate binding domain of molybdate-binding proteins;the type 2 periplasmic binding protein fold.  This subfamily contains domains found in ModA proteins of putative ABC-type transporter. ModA proteins serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) ...
CDD:270260	314	PRK	Bacteria:11	cd13542, PBP2_FutA1_ilke, Substrate binding domain of ferric iron-binding protein, a member of the type 2 periplasmic binding fold superfamily.  FutA1 is the periplasmic component of an ABC-type iron transporter and serves as the primary receptor in Synerchosystis species. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria and is critical for survival of these pathogens within the host. After ...
CDD:270261	306	PRK	Bacteria:15	cd13543, PBP2_Fbp, Substrate binding domain of ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily.  The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic protein (Fbp) has high affinities for ferric iron and serves as the primary ...
CDD:270262	292	PRK	Bacteria:44	cd13544, PBP2_Fbp_like_1, Substrate binding domain of a putative ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily.  The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the ...
CDD:270263	269	PRK	Bacteria:12,Environmental:1	cd13545, PBP2_TbpA, Substrate binding domain of thiamin transporter, a member of the type 2 periplasmic binding fold superfamily.  Thiamin-binding protein TbpA is the periplasmic component of ABC-type transporter in E. coli, while the transmembrane permease and ATPase are ThiP and ThiQ, respectively. Thiamin (vitamin B1) is an essential confactor in all living systems that  most prokaryotes, plants, and fungi can synthesized thiamin. However,  in ...
CDD:270264	258	PRK	Bacteria:19,nodiv:1	cd13546, PBP2_BitB, Substrate binding domain of a putative iron transporter BitB, a member of the type 2 periplasmic binding fold superfamily.  The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the ...
CDD:270265	259	PRK	Bacteria:26	cd13547, PBP2_Fbp_like_2, Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily.  The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and ...
CDD:270269	267	PRK	Bacteria:7	cd13551, PBP2_Fbp_like_5, Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily.  The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and ...
CDD:270271	212	PRK	Bacteria:59	cd13553, PBP2_NrtA_CpmA_like, Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily.  This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are ...
CDD:270273	268	PRK	Bacteria:10	cd13555, PBP2_sulfate_ester_like, Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold.   This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine ...
CDD:270275	275	PRK	Bacteria:14	cd13557, PBP2_SsuA, Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily.  This subfamily includes the sulfonate binding domains SsuA found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization ...
CDD:270276	267	PRK	Bacteria:21	cd13558, PBP2_SsuA_like_2, Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding protein fold.  This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are ...
CDD:270278	218	PRK	Bacteria:13	cd13560, PBP2_taurine, Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold.  This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) ...
CDD:270279	212	PRK	Bacteria:7	cd13561, PBP2_SsuA_like_4, Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold.  This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are ...
CDD:270281	208	PRK	Bacteria:21	cd13563, PBP2_SsuA_like_6, Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 periplasmic binding protein fold.  This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest ...
CDD:270283	254	EUKprk	Bacteria:44,Plants:2	cd13565, PBP2_PstS, Substrate binding domain of ABC-type phosphate transporter, a member of the type 2 periplasmic-binding fold superfamily.  This subfamily contians phosphate binding domain found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically ...
CDD:270284	245	PRK	Bacteria:90,Environmental:2	cd13566, PBP2_phosphate, Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily.  This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral ...
CDD:270285	284	PRK	Bacteria:19,Environmental:1	cd13567, PBP2_TtGluBP, Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold.  This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted ...
CDD:270286	289	PRK	Bacteria:13	cd13568, PBP2_TAXI_TRAP_like_3, Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold.  This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although ...
CDD:270287	283	PRK	Bacteria:11	cd13569, PBP2_TAXI_TRAP_like_1, Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold.  This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although ...
CDD:270289	253	PRK	Bacteria:17	cd13571, PBP2_PnhD_1, Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold.  This subfamily includes putative periplasmic binding components of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and ...
CDD:270290	249	PRK	Bacteria:11	cd13572, PBP2_PnhD_2, Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold.  This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and ...
CDD:270292	250	PRK	Bacteria:11,Environmental:1	cd13574, PBP2_PnhD_4, Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold.  This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in ...
CDD:270295	292	PRK	Bacteria:7	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold.  The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a ...
CDD:270296	291	PRK	Bacteria:19	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold.  Bug27 binds non-carboxylated solute nicotinamide, in contrast to BugD (aspartic acid transporter) and BugE (glutamate transporter) which both bind aliphatic carboxylated ligands. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial ...
CDD:270297	292	EUKprk	Bacteria:11,Plants:1	cd13579, PBP2_Bug_NagM, Uncharacterized NagM-like protein of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold.  The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in ...
CDD:270298	471	PRK	Bacteria:13	cd13580, PBP2_AlgQ_like_1, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold.  This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ...
CDD:270299	490	PRK	Bacteria:12	cd13581, PBP2_AlgQ_like_2, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold.  This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ...
CDD:270300	504	EUKprk	Bacteria:9,Plants:1	cd13582, PBP2_AlgQ_like_3, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold.  This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ...
CDD:270301	478	PRK	Bacteria:8	cd13583, PBP2_AlgQ_like_4, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold.  This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding ...
CDD:270303	383	PRK	Bacteria:144	cd13585, PBP2_TMBP_like, The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold.  This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains ...
CDD:270304	367	PRK	Bacteria:21	cd13586, PBP2_Maltose_binding_like, The periplasmic-binding component of ABC transport systems specific for maltose and related polysaccharides; possess type 2 periplasmic binding fold.  This subfamily represents the periplasmic binding component of ABC transport systems involved in uptake of polysaccharides including maltose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two ...
CDD:270306	279	PRK	Bacteria:19	cd13588, PBP2_polyamine_1, The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold.  This group represents the periplasmic binding domain that functions as the primary high-affinity receptor of an uncharactertized ABC-type polyamine transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be ...
CDD:270307	268	PRK	Bacteria:89,nodiv:1	cd13589, PBP2_polyamine_RpCGA009, The periplasmic-binding component of an uncharacterized ABC transport system from Rhodopseudomonas palustris CGA009 and related proteins; contains the type 2 periplasmic-binding fold.  This group represents the periplasmic binding domain that serves as the primary high-affinity receptor of an uncharacterized ABC-type polyamine transporter from Rhodopseudomonas palustris Cga009 and related proteins from other bacteria. ...
CDD:270308	315	EUKprk	Bacteria:68,Plants:1	cd13590, PBP2_PotD_PotF_like, The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in ...
CDD:270310	208	EUKprk	Bacteria:9,Invertebrates:1,Plants:7	cd13592, PBP2_HisGL2, The catalytic domain of hexameric long form HisGL2; contains the type 2 periplasmic binding protein fold.  Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl  1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two ...
CDD:270311	220	EUKprk	Bacteria:11,Environmental:1,Plants:5	cd13593, PBP2_HisGL3, The catalytic domain of hexameric long form HisGL3; contains the type 2 periplasmic binding protein fold.  Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl  1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two ...
CDD:270312	207	PRK	Bacteria:7	cd13594, PBP2_HisGL4, The catalytic domain of hexameric long form HisGL4; contains the type 2 periplasmic binding fold.  Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl  1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, ...
CDD:270313	205	PRK	Bacteria:38	cd13595, PBP2_HisGs, The catalytic domain of hetero-octomeric short form HisGs; contains the type 2 periplasmic binding protein fold.  Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl  1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a ...
CDD:270314	230	PRK	Bacteria:5	cd13596, PBP2_lipoprotein_GmpC, The periplasmic substrate-binding domain of the membrane-associated lipoprotein-9 GmpC; contains the type 2 periplasmic-binding protein fold.  This group includes the membrane-associated lipoprotein-9 from Staphylococcus aureus that binds the dipeptide glycylmethionine (GlyMet). The lipoprotein-9 has both structural and sequential homology to the MetQ family of substrate-binding protein. The GlyMet binding protein belongs to the type ...
CDD:270315	236	PRK	Bacteria:14	cd13597, PBP2_lipoprotein_Tp32, The substrate-binding domain of the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum binds L-methionine; the type 2 periplasmic-binding protein fold.  This group includes the lipoprotein Tp32, a periplasmic component of a methionine uptake transporter system, and its closely related homologs. The Tp32 has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus it belongs to the type 2 ...
CDD:270316	227	EUKprk	Bacteria:6,Plants:2	cd13598, PBP2_lipoprotein_IlpA_like, Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus and similar lipoproteins; the type 2 periplasmic binding protein fold.  This group includes the IlpA protein which has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular ...
CDD:270318	228	PRK	Bacteria:11	cd13600, PBP2_lipoprotein_like_1, Putative periplasmic-binding component of ABC-type methionine uptake transporter system-like; the type 2 periplasmic binding protein fold.  This subgroup shares significant sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the ...
CDD:270319	302	PRK	Bacteria:19	cd13601, PBP2_TRAP_DctP1_3_4_like, Periplasmic substrate-binding component of uncharacterized TRAP-type C4-dicarboxylate transporter subfamilies; the type 2 periplasmic-binding protein fold.  This model includes uncharacterized DctP subfamilies of the TRAP Transporters. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P ...
CDD:270320	300	PRK	Bacteria:32	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold.  DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding ...
CDD:270321	297	EUKprk	Bacteria:144,Environmental:1,Invertebrates:1,nodiv:1	cd13603, PBP2_TRAP_Siap_TeaA_like, Substrate-binding domain of a sialic acid binding Tripartite ATP-independent  Periplasmic transport system (SiaP) and related proteins; the type 2 periplasmic-binding protein fold.  This subfamily includes the periplasmic-binding component of TRAP transport systems such as SiaP (a sialic acid binding virulence factor), TeaA (an ectoine binding protein), and an uncharacterized TM0322 from ...
CDD:270322	306	PRK	Bacteria:31	cd13604, PBP2_TRAP_ketoacid_lactate_like, Substrate-binding domain of an alpha-keto acid binding Tripartite ATP-independent Periplasmic transporter and related proteins; the type 2 periplasmic-binding protein fold.  This family constitutes TRAP transporters that bind to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They ...
CDD:270323	303	PRK	Bacteria:10	cd13605, PBP2_TRAP_DctP_like_2, Substrate-binding component of uncharacterized Tripartite ATP-independent  Periplasmic transporter; the type 2 periplasmic-binding protein fold.  This family represents the TRAP Transporters that are specific to various ligands, including sialic acid (N-acetyl neuraminic acid), glutamate, ectoine, xylulose, C4-dicarboxylates such as succinate, malate and fumarate, and keto acids such as pyruvate and alpha-ketobutyrate. TRAP ...
CDD:270324	260	PRK	Bacteria:58	cd13606, PBP2_ProX_like, Bacterial substrate-binding protein ProX of ABC-type osmoregulated transporter and its related proteins; the type 2 periplasmic-binding protein fold.  This group includes periplasmic substrate-binding component of ABC transport systems from gram-negative and -positive bacteria that are involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. To counteract the ...
CDD:270325	261	PRK	Bacteria:33	cd13607, PBP2_AfProX_like, Substrate-binding protein ProX of ABC-type osmoregulatory transporter from Archaeoglobus fulgidus and its related proteins; the type 2 periplasmic-binding protein fold.  This subfamily includes the periplasmic substrate-binding protein ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus and its related proteins. AfProX is involved in uptake of compatible solutes such as the trimethylammonium compound glycine betaine and the ...
CDD:270326	265	PRK	Bacteria:29	cd13608, PBP2_OpuCC_like, Substrate-binding protein OpuCC of ABC-type osmoregulatory transporter and related proteins; the type 2 periplasmic-binding protein fold.  This subfamily includes the periplasmic substrate-binding protein OpuCC of the ABC transporter OpuC (where Opu is osmoprotectant uptake), which can recognize a broad spectrum of compatible solutes, and its paralog OpuBC that can solely bind choline. To counteract the efflux of water, many microorganisms ...
CDD:270327	263	PRK	Bacteria:26	cd13609, PBP2_Opu_like_1, Substrate-binding domain of putative ABC-type osmoprotectant uptake system; the type 2 periplasmic-binding protein fold.  This group includes the periplasmic substrate-binding component of a putative ABC transport system that is predicted to be involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline.  The relative substrate preference of this group is not ...
CDD:270328	264	PRK	Bacteria:31	cd13610, PBP2_ChoS, Substrate-binding domain ChoS of an osmoregulated ABC-type transporter and related proteins; type 2 periplasmic-binding protein fold.  Osmoprotectant binding lipoprotein ChoS of Lactococcus lactis is predicted to be involved in uptake of compatible solutes such as choline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained ...
CDD:270329	267	PRK	Bacteria:33	cd13611, PBP2_YehZ, Substrate-binding domain YehZ of an osmoregulated ABC-type transporter; the type 2 periplasmic-binding protein fold.  Osmoprotectant binding lipoprotein YehZ of Clostridium sticklandii is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained ...
CDD:270330	267	PRK	Bacteria:20	cd13612, PBP2_ProWX, Substrate-binding protein ProWX of ABC-type osmoregulated transporter and its related proteins; the type 2 periplasmic-binding protein fold.  Osmoprotectant binding lipoprotein ProWX of Helicobacter pylori is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible ...
CDD:270331	264	PRK	Bacteria:8	cd13613, PBP2_Opu_like_2, Substrate-binding domain of putative ABC-type osmoprotectant uptake system; the type 2 periplasmic-binding protein fold.  This group includes the periplasmic substrate-binding component of a putative ABC transport system that is predicted to be involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. The relative substrate preference of this group is not ...
CDD:270334	274	PRK	Bacteria:12	cd13616, PBP2_OsmF, Substrate-binding domain OsmF of an osmoregulated ABC-type transporter; the type 2 periplasmic-binding protein fold.  Osmoprotectant binding lipoprotein OsmF of an ABC transporter (YehZYXW) from Escherichia coli is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible ...
CDD:270337	220	PRK	Bacteria:15	cd13619, PBP2_GlnP, Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily.  Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary ...
CDD:270338	227	PRK	Bacteria:9	cd13620, PBP2_GltS, Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily.  This family comprises of the periplasmic-binding protein component (GltS) of an ABC transporter specific for glutamate or arginine from Lactococcus lactis, as well as its closely related proteins. The GltS domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many  members are ...
CDD:270340	222	PRK	Bacteria:7	cd13622, PBP2_Arg_3, Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold.  This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein ...
CDD:270341	220	EUKprk	Bacteria:11,Plants:1	cd13623, PBP2_AA_hypothetical, Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic binding protein fold.  This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains ...
CDD:270342	219	PRK	Bacteria:78	cd13624, PBP2_Arg_Lys_His, Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold.  This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ belongs to the type 2 periplasmic-binding fold protein (PBP2) ...
CDD:270343	230	PRK	Bacteria:7	cd13625, PBP2_AA_binding_like_1, Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold.  This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a ...
CDD:270344	219	PRK	Bacteria:13	cd13626, PBP2_Cystine_like, Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold.  Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters.  Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three ...
CDD:270347	221	PRK	Bacteria:32	cd13629, PBP2_Dsm1740, Amino acid-binding domain of the type 2 periplasmic binding fold superfamily.  This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating.  The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically ...
CDD:270348	180	EUKprk	Bacteria:104,Environmental:2,Invertebrates:1,Plants:3	cd13630, PBP2_PDT_1, Catalytic domain of prephenate dehydratase and similar proteins, subgroup 1; the type 2 periplasmic binding protein fold.  Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other ...
CDD:270349	182	EUKprk	Bacteria:192,Environmental:6,Plants:11	cd13631, PBP2_Ct-PDT_like, Catalytic domain of prephenate dehydratase from Chlorobium tepidum and similar proteins, subgroup 2; the type 2 periplasmic binding protein fold.  Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by ...
CDD:270350	183	PRK	Bacteria:50	cd13632, PBP2_Aa-PDT_like, Catalytic domain of prephenate dehydratase from Arthrobacter aurescens and similar proteins, subgroup 3; the type 2 periplasmic binding protein fold.  Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino ...
CDD:270351	184	PRK	Bacteria:51	cd13633, PBP2_Sa-PDT_like, Catalytic domain of prephenate dehydratase from Staphylococcus aureus and similar proteins, subgroup 4; the type 2 periplasmic binding protein fold.  Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino ...
CDD:270352	256	PRK	Bacteria:95,Environmental:3	cd13634, PBP2_Sco4506, The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein fold.  This group includes the SCO4506 protein from Streptomyces coelicolor and related hypothetical proteins. SCO4506 is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to ...
CDD:270353	260	PRK	Bacteria:48	cd13635, PBP2_Ttha1568_Mqnd, A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold.  This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein ...
CDD:270354	259	EUKprk	Bacteria:17,Environmental:2,Plants:1	cd13636, PBP2_Af1704, The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold.  This group includes the Af1704 protein from from Archaeoglobus fulgidus DSM 4304, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to ...
CDD:270355	273	EUKprk	Bacteria:17,Environmental:1,Invertebrates:3,Plants:18	cd13637, PBP2_Ca3427_like, The conserved hypothetical protein Ca3427 exhibits the type 2 periplasmic-binding protein fold.  This group includes the Ca3427 protein from candida albicans, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8, and other related hypothetical proteins. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic ...
CDD:270356	299	PRK	Bacteria:18	cd13638, PBP2_EcProx_like, Substrate binding domain of Escherichia coli betaine transport system-like; the type 2 periplasmic binding protein fold.  This group includes the periplasmic substrate-binding protein ProX. ProX from the Escherichia coli ATP-binding cassette transport system ProU binds the compatible solutes glycine betaine and proline betaine with high affinity and specificity. Many microorganisms accumulate these compatible solutes in response to high ...
CDD:270357	254	PRK	Bacteria:83	cd13639, PBP2_OpuAC_like, Substrate binding domain of Lactococcus lactis ABC-type transporter OpuA and related proteins; the type 2 periplasmic binding protein fold.  This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to betaine compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in ...
CDD:270358	266	PRK	Bacteria:30	cd13640, PBP2_ChoX, Substrate binding domain of ABC-type choline transport system; the type 2 periplasmic binding protein fold.  This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to choline and acetylcholine for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants ...
CDD:270359	261	EUKprk	Bacteria:36,Plants:1	cd13641, PBP2_HisX_like, Substrate-binding domain of ABC-type histidine transporter involves in betaine and proline uptake; the type 2 periplasmic-binding protein fold.  This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette ...
CDD:270360	292	PRK	Bacteria:14	cd13642, PBP2_BCP_1, Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold.  This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette ...
CDD:270361	283	PRK	Bacteria:26,Environmental:3	cd13643, PBP2_BCP_2, Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold.  This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding ...
CDD:270362	273	PRK	Bacteria:3,Environmental:1	cd13644, PBP2_HemC_archaea, Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein fold.  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes ...
CDD:270363	282	EUKprk	Bacteria:2,Invertebrates:5,Plants:5,Primates:1,Rodents:1,Vertebrates:3	cd13645, PBP2_HuPBGD_like, Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold.  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane ...
CDD:270364	274	EUKprk	Bacteria:13,Plants:1	cd13646, PBP2_EcHMBS_like, cd00494.  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  This subfamily includes the three domains of Escherichia coli HMBS and its closely related proteins. The enzyme is ...
CDD:270365	282	EUKprk	Bacteria:7,Environmental:2,Invertebrates:1	cd13647, PBP2_PBGD_2, An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold.  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  This subfamily ...
CDD:270370	217	PRK	Bacteria:8	cd13652, PBP2_ThiY_THI5_like_1, Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold.  This subfamily is phylogenetically similar to ThiY, which is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. ...
CDD:270371	240	PRK	Bacteria:3	cd13653, PBP2_phosphate_like_1, Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily.  This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains ...
CDD:270372	259	miss	miss	cd13654, PBP2_phosphate_like_2, Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily.  This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and ...
CDD:270373	363	PRK	Bacteria:12	cd13655, PBP2_oligosaccharide_1, The periplasmic binding component of ABC tansport system specific for an unknown oligosaccharide; possess the type 2 periplasmic binidng fold.  This group represents an uncharacterized periplasmic-binding protein of an ATP-binding cassette transporter predicted to be involved in uptake of an unknown oligosaccharide molecule. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two ...
CDD:270375	368	PRK	Bacteria:10	cd13657, PBP2_Maltodextrin, The periplasmic binding component of ABC transport system specific for maltodextrin.  This group includes the periplasmic maltodextrin-binding protein of a binding protein-dependent ATP-binding cassette transporter. Maltodextrin is a polysaccharide that is used as a food addtive and can be enzymatically produced from any starch . Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two ...
CDD:270377	331	PRK	Bacteria:9	cd13659, PBP2_PotF, The periplasmic substrate-binding component of an ABC putrescine transport system and related proteins; contains the type 2 periplasmic-binding fold.  This group represents the periplasmic substrate-binding domain that serves as the primary polyamine receptor of ABC-type putrescine-preferential transporter from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known ...
CDD:270379	319	EUKprk	Bacteria:3,Plants:5	cd13661, PBP2_PotD_PotF_like_1, The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold.  This group represents the periplasmic binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from plants and plant-symbiotic cyanobacteria. Polyamine transport plays an essential ...
CDD:270381	323	PRK	Bacteria:17	cd13663, PBP2_PotD_PotF_like_2, The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold.  This group represents the periplasmic substrate-binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from gram-negative bacteria. Polyamine transport plays an essential role in the ...
CDD:270382	315	PRK	Bacteria:6	cd13664, PBP2_PotD_PotF_like_3, TThe periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold.  This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular ...
CDD:270383	302	PRK	Bacteria:52	cd13665, PBP2_TRAP_Dctp3_4, Periplasmic substrate-binding component of TRAP-type C4-dicarboxylate transport system DctP3 and DctP4; the type 2 periplasmic-binding protein fold.  This group includes uncharacterized DctP3 and DctP 4 subfamilies of TRAP Transporters specific to C4-dicarboxylates such as succinate, malate and fumarate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This CD also included some ...
CDD:270384	303	PRK	Bacteria:36,Environmental:1	cd13666, PBP2_TRAP_DctP_like_1, Substrate-binding component of an uncharacterized TRAP-type C4-dicarboxylate transport system; the type 2 periplasmic-binding protein fold.  This group includes a DctP subfamily of TRAP Transporters specific to C4-dicarboxylates such as succinate, malate and fumarate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This CD also included some eukaryotic homologs ...
CDD:270385	295	PRK	Bacteria:9	cd13667, PBP2_TRAP_DctP1, Periplasmic substrate-binding component of an uncharacterized TRAP-type C4-dicarboxylate transport system DctP1; contains the type 2 periplasmic-binding protein fold.  This group includes an uncharacterized DctP1 subfamily of the TRAP Transporters. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P ...
CDD:270386	305	PRK	Bacteria:13	cd13668, PBP2_TRAP_UehA_TeaA, Periplasmic substrate-binding component of osmoregulatory TRAP transporters TeaA and UehA; the type 2 periplasmic-binding protein fold.  This subfamily includes the periplasmic-binding component of the ectoine-specific TRAP transporters TeaA from Halomonas elongata and UehA from Ruegeria pomeroyi. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic ...
CDD:270387	296	PRK	Bacteria:30	cd13669, PBP2_TRAP_TM0322_like, Periplasmic component of TRAP-type C4-dicarboxylate transport system TM0322 from Thermotoga maritima and similar proteins; the type 2 periplasmic binding protein fold.  This subgroup includes the hyperthermophilic bacterium Thermotoga maritima TRAP-type C4-dicarboxylate transport system TM0322 and its closely related proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They ...
CDD:270388	298	PRK	Bacteria:23,Environmental:1	cd13670, PBP2_TRAP_Tp0957_like, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes the putative periplasmic substrate-binding protein Tp0957 from Treponema pallidum, which is similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a ...
CDD:270389	296	PRK	Bacteria:41	cd13671, PBP2_TRAP_SBP_like_3, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously ...
CDD:270390	295	PRK	Bacteria:20	cd13672, PBP2_TRAP_Siap, Substrate-binding domain of a sialic acid binding Tripartite ATP-independent  Periplasmic transport system (SiaP); the type 2 periplasmic-binding protein fold.  This subfamily represents the periplasmic-binding component of TRAP transport system SiaP, a sialic acid binding virulence factor. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic ...
CDD:270391	301	PRK	Bacteria:17	cd13673, PBP2_TRAP_SBP_like_2, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously ...
CDD:270392	299	PRK	Bacteria:14	cd13674, PBP2_TRAP_SBP_like_1, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously ...
CDD:270393	296	EUKprk	Bacteria:21,Plants:1	cd13675, PBP2_TRAP_SBP_like_5, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ...
CDD:270394	297	PRK	Bacteria:18	cd13676, PBP2_TRAP_DctP2_like, Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP2 and related proteins;  the type 2 periplasmic-binding protein fold.  This subgroup includes TRAP transporter DctP2 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two ...
CDD:270395	304	PRK	Bacteria:15	cd13677, PBP2_TRAP_SBP_like_6, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously ...
CDD:270396	300	PRK	Bacteria:14,nodiv:1	cd13678, PBP2_TRAP_DctP10, Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP10;  the type 2 periplasmic-binding protein fold.  This subgroup includes TRAP transporter DctP10 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized ...
CDD:270397	298	PRK	Bacteria:25	cd13679, PBP2_TRAP_YiaO_like, Substrate-binding domain of 2,3-diketo-L-gulonate-binding Tripartite ATP-independent  Periplasmic transport system and related proteins; the type 2 periplasmic-binding protein fold.  This subfamily includes the solute receptor protein YiaO of TRAP transport system. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) ...
CDD:270398	300	PRK	Bacteria:14	cd13680, PBP2_TRAP_SBP_like_4, Uncharacterized substrate-binding protein of the Tripartite ATP-independent  Periplasmic transporter family; the type 2 periplasmic-binding protein fold.  This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously ...
CDD:270400	323	PRK	Bacteria:10	cd13682, PBP2_TRAP_alpha-ketoacid, Substrate-binding component of an alpha-keto acid binding Tripartite ATP-independent Periplasmic transporter and related proteins; contains the type 2 periplasmic-binding protein fold.  This subgroup includes TRAP transporters that bind to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. ...
CDD:270401	304	PRK	Bacteria:12	cd13683, PBP2_TRAP_DctP6_7, Substrate-binding domain of Tripartite ATP-independent Periplasmic transporter DctP6 and DctP7; type 2 periplasmic-binding protein fold.  This subgroup includes TRAP-type mannitol/chloroaromatic compound transport system (Dctp6) and similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally ...
CDD:270402	314	PRK	Bacteria:8	cd13684, PBP2_TRAP_Dctp5_like, Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP5 and related proteins;  the type 2 periplasmic-binding protein fold.  This subgroup includes TRAP transporter DctP5 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two ...
CDD:270403	252	EUK	Invertebrates:21,Rodents:1,Vertebrates:10	cd13685, PBP2_iGluR_non_NMDA_like, The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors,  a member of the type 2 periplasmic-binding fold protein superfamily.  This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate ...
CDD:270404	232	EUK	Plants:12	cd13686, GluR_Plant, Plant glutamate receptor domain; the type 2 periplasmic binding protein fold.  This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like ...
CDD:270405	239	EUK	Invertebrates:10,Mammals:1,Primates:2,Rodents:2,Vertebrates:9,nodiv:2	cd13687, PBP2_iGluR_NMDA, The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.  The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type ...
CDD:270406	238	PRK	Bacteria:22	cd13688, PBP2_GltI_DEBP, Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold.  This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many  members are involved in chemotaxis and uptake ...
CDD:270407	229	EUKprk	Bacteria:19,Invertebrates:1,Plants:1	cd13689, PBP2_BsGlnH, Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 periplasmic-bindig protein fold.  This group includes periplasmic glutamine-binding domain GlnP from Bacillus subtilis and its related proteins. The GlnP domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small ...
CDD:270408	231	PRK	Bacteria:19	cd13690, PBP2_GluB, Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold.  This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary ...
CDD:270410	236	PRK	Bacteria:23,Environmental:1	cd13692, PBP2_BztA, Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type 2 periplasmic binding protein fold.  BztA is the periplamic-binding protein component of ABC transporter specific for carboxylic amino acids, glutamine and asparagine. The BZtA domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other ...
CDD:270411	228	PRK	Bacteria:10,nodiv:1	cd13693, PBP2_polar_AA, Substrate binding domain of polar amino-acid uptake  ABC transporter; the type 2 periplasmic binding protein fold.  This group includes the periplamic-binding protein component of putative polar amino acid ABC transporter. The polar amino-acid binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from ...
CDD:270412	229	PRK	Bacteria:9	cd13694, PBP2_Cysteine, Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold.  This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many  members are involved in chemotaxis and uptake of nutrients and other small molecules ...
CDD:270414	227	PRK	Bacteria:8	cd13696, PBP2_Atu4678_like, The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold.  This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of ...
CDD:270420	223	EUKprk	Bacteria:11,Invertebrates:1	cd13702, PBP2_mlr5654_like, Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold.  This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which  serve as initial receptors in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids.  This group belongs to the type 2 periplasmic-binding ...
CDD:270421	229	PRK	Bacteria:23	cd13703, PBP2_HisJ_LAO, Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; the type 2 periplasmic-binding protein fold.  This subgroup includes the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids. They are  belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis ...
CDD:270422	220	PRK	Bacteria:48,Environmental:1	cd13704, PBP2_HisK, The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein.  This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic ...
CDD:270423	221	PRK	Bacteria:40	cd13705, PBP2_BvgS_D1, The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein.  This group contains the first domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a histidine-kinase (HK), a ...
CDD:270424	219	EUKprk	Bacteria:42,Plants:1	cd13706, PBP2_HisK_like_1, Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein.  This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The ...
CDD:270425	221	PRK	Bacteria:20	cd13707, PBP2_BvgS_D2, The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein.  This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a ...
CDD:270426	220	PRK	Bacteria:8	cd13708, PBP2_BvgS_like_1, Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain.  BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response ...
CDD:270427	227	PRK	Bacteria:9	cd13709, PBP2_YxeM, Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold.  This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are ...
CDD:270428	233	PRK	Bacteria:12	cd13710, PBP2_TcyK, Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding protein fold.  This group contains periplasmic cystine-binding domain (TcyK) of an ATP-binding cassette transporter from Bacillus subtilus and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and ...
CDD:270429	222	PRK	Bacteria:14	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold.  This subgroup includes cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette transporters from Neisseria gonorrhoeae and Bacillus subtilis and their related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC ...
CDD:270431	218	PRK	Bacteria:17	cd13713, PBP2_Cystine_like_1, Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold.  This group contains uncharacterized periplasmic cystine-binding domain of ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are ...
CDD:270432	251	EUK	Invertebrates:22,Primates:3,Rodents:2,Vertebrates:3	cd13714, PBP2_iGluR_Kainate, Kainate receptor of the type 2 periplasmic-binding fold superfamily.  This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted ...
CDD:270435	360	EUK	Invertebrates:3	cd13717, PBP2_iGluR_putative, The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.  This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically ...
CDD:270436	283	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:1	cd13718, PBP2_iGluR_NMDA_Nr2, The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.  This group contains the ligand-binding domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, ...
CDD:270437	277	EUK	Invertebrates:2,Mammals:1,Primates:1,Rodents:1,Vertebrates:1	cd13719, PBP2_iGluR_NMDA_Nr1, The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.  This group contains the ligand binding domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical ...
CDD:240492	169	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:5	cd13734, SPRY_PRY_C-I, PRY/SPRY domain in tripartite motif-containing proteins 1, 9, 18, 36, 46, 67,76 (TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76).  This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class I TRIM proteins, including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67 and TRIM76.  TRIM1 (also known as MID2) and its close ...
CDD:259839	115	EUK	Plants:15	cd13746, Sir4p-SID_like, The SID domain of Saccharomyces cerevisiae silent information regulator 4, a Sir2p interaction domain; and related domains.  Saccharomyces cerevisiae Sir2p, Sir3p, and Sir4p form a heterotrimeric complex which binds chromatin and represses transcription at the homothallic mating type (HM) loci and at subtelomeric regions. This domain model spans residues 742-893 of Sir4p. Sir4p forms a stable heterodimer with Sir2p, mediated by Sir4p residues ...
CDD:259834	167	PRK	Bacteria:11,Environmental:1	cd13747, UreI_AmiS_like_1, UreI/Amis family, subgroup 1. Putative proton-gated urea channel and putative amide transporters.  This subfamily includes putative UreI proton-gated urea channels and putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, leading ...
CDD:259796	47	EUK	Invertebrates:26,Plants:14,Vertebrates:2	cd13749, Zn-ribbon_TFIIS, domain III/zinc ribbon domain of Transcription Factor IIS.  TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are ...
CDD:259841	61	EUK	Invertebrates:3,Plants:10,Primates:1,Vertebrates:3	cd13768, DSS1_Sem1, proteasome complex subunit DSS1/Sem1.  The evolutionarily conserved deleted in split hand/split foot protein 1 (DSS1)/Sem1 is a subunit of the regulatory particle (RP) of the proteasome. It is implicated in ubiquitin-mediated proteolysis, is required for the maintenance of genomic stability, and functions in DNA damage response. DSS1/Sem1 also displays RP-independent functions; it serves as a functional ...
CDD:259842	158	EUK	Invertebrates:13	cd13769, ApoLp-III_like, Apolipophorin-III and similar insect proteins.  Exchangeable apolipoproteins play vital roles in the transport of lipids and lipoprotein metabolism. Apolipophorin III (apoLp-III) assists in the loading of diacylglycerol, generated from triacylglycerol stores in the fat body through the action of adipokinetic hormone, into lipophorin, the hemolymph lipoprotein. ApoLp-III increases the lipid carrying capacity of lipophorin by covering ...
CDD:259817	177	PRK	Bacteria:23	cd13775, SPFH_eoslipins_u3, Uncharacterized prokaryotic subfamily of the stomatin-like proteins (slipins), a subgroup of the SPFH family (stomatin, prohibitin, flotillin, and HflK/C).  This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria and archaebacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may ...
CDD:260099	126	EUKprk	Bacteria:2,Invertebrates:39,Mammals:1,Plants:72,Vertebrates:4,nodiv:1	cd13777, Aar2_N, N-terminal domain of Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor.  This family consists of the N-terminal domain of eukaryotic Aar2 and Aar2-like proteins. Aar2 is a U5 small nuclear ribonucleoprotein (snRNP) particle assembly factor and part of Prp8, which forms a large complex containing U5 snRNA, Snu114, and seven Sm proteins (B, D1, D2, D3, E, F and G). Upon ...
CDD:260100	155	EUK	Invertebrates:8,Plants:17	cd13778, Aar2_C, C-terminal domain of Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor.  This family consists of the C-terminal domain of eukaryotic Aar2 and Aar2-like proteins. Aar2 is a U5 small nuclear ribonucleoprotein (snRNP) particle assembly factor and part of Prp8, which forms a large complex containing U5 snRNA, Snu114, and seven Sm proteins (B, D1, D2, D3, E, F and G). Upon import of the complex into the nucleus, Aar2 ...
CDD:260102	67	PRK	Bacteria:16	cd13784, SP_1775_like, Uncharacterized protein conserved in Streptococci.  Streptococcus pneumoniae SP_1775 and related proteins from other Streptococci; may form homooctamers that may bind hydrophobic ligands.
CDD:259853	86	EUKprk	Bacteria:257,Environmental:4,Invertebrates:3,Plants:10,nodiv:1	cd13831, HU, histone-like DNA-binding protein HU.  This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can ...
CDD:259854	85	PRK	Bacteria:82,Environmental:4	cd13832, IHF, Integration host factor (IHF) and similar proteins.  This subfamily includes integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in ...
CDD:259855	97	PRK	Bacteria:2	cd13833, HU_IHF_like, Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains.  This subfamily consists of uncharacterized proteins similar to integration host factor (IHF) and HU domains, including hypothetical protein Bvu_2165 from Bacteroides vulgatus. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly ...
CDD:259856	94	EUKprk	Bacteria:21,Environmental:2,Plants:7	cd13834, HU_like, DNA-binding proteins similar to HU domains.  This subfamily consists of DNA-binding proteins similar to HU domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like ...
CDD:259857	88	PRK	Bacteria:62,Environmental:2,nodiv:1	cd13835, IHF_A, Alpha subunit of integration host factor (IHFA).  This subfamily consists of the alpha subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at ...
CDD:259858	89	EUKprk	Bacteria:71,Environmental:2,Plants:1	cd13836, IHF_B, Beta subunit of integration host factor (IHFB).  This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at ...
CDD:260104	89	PRK	Bacteria:16	cd13840, SMBP_like, Small metal-binding protein conserved in proteobacteria.  This periplasmic protein appears capable of binding multiple equivalents of a variety of divalent and trivalent metals, including Cu(2+) and Fe(3+) but also Mn(2+), Ni(2+), Mg(2+), and Zn(2+). It has been suggested that SMBP is a metal scavenging protein that plays a role in cellular copper management in Nitrosomonas europaea.
CDD:259911	95	PRK	Bacteria:15	cd13842, CuRO_HCO_II_like, Cupredoxin domain of Heme-copper oxidase subunit II.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian ...
CDD:259913	162	EUKprk	Bacteria:30,Invertebrates:3,Plants:7	cd13844, CuRO_1_BOD_CotA_like, The first Cupredoxin domain of Bilirubin oxidase (BOD), the bacterial endospore coat component CotA, and similar proteins.  Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and it is required for spore resistance against hydrogen ...
CDD:259917	116	PRK	Bacteria:13	cd13848, CuRO_1_CopA, The first cupredoxin domain of CopA copper resistance protein family.  CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in the inner cell membrane and ...
CDD:259918	117	EUK	Plants:9	cd13849, CuRO_1_LCC_plant, The first cupredoxin domain of plant laccases.  Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase ...
CDD:259919	117	EUK	Plants:13	cd13850, CuRO_1_Abr2_like, The first cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus.  Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, ...
CDD:259920	121	EUK	Plants:20	cd13851, CuRO_1_Fet3p, The first Cupredoxin domain of multicopper oxidase Fet3P.  Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) and  a four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the exocellular space  and the carboxyl terminus in the cytoplasm. The periplamic produced Fe(III) is transferred to the permease Ftr1p for import into the ...
CDD:259921	114	PRK	Bacteria:15,Synthetic:1	cd13852, CuRO_1_McoP_like, The first cupredoxin domain of multicopper oxidase McoP and similar proteins.  This family includes archaeal and bacterial multicopper oxidases (MCOs), represented by the extremely thermostable McoP from the hyperthermophilic archaeon Pyrobaculum aerophilum. McoP is an efficient metallo-oxidase that catalyzes the oxidation of cuprous and ferrous ions. It is noteworthy that McoP has three-fold higher catalytic efficiency when ...
CDD:259922	139	EUKprk	Bacteria:40,Invertebrates:7,Plants:9	cd13853, CuRO_1_Tth-MCO_like, The first cupredoxin domain of the bacterial laccases similar to Tth-MCO from Thermus Thermophilus.  The subfamily of bacterial laccases includes Tth-MCO and similar proteins. Tth-MCO is a hyperthermophilic multicopper oxidase (MCO) from thermus thermophilus HB27. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to ...
CDD:259923	122	EUK	Plants:20	cd13854, CuRO_1_MaLCC_like, The first cupredoxin domain of the fungal laccases similar to Ma-LCC  from Melanocarpus albomyces.  The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers.  Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and ...
CDD:259925	125	EUK	Plants:12	cd13856, CuRO_1_Tv-LCC_like, The first cupredoxin domain of fungal laccases similar to Tv-LCC from Trametes versicolor.  This subfamily of fungal laccases includes Tv-LCC from Trametes versicolor and Rs-LCC2 from plant pathogenic fungus Rhizoctonia solani. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in ...
CDD:259926	119	EUK	Plants:16	cd13857, CuRO_1_Diphenol_Ox, The first cupredoxin domain of fungal laccase, diphenol oxidase.  Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue multicopper ...
CDD:259927	105	EUK	Invertebrates:18	cd13858, CuRO_1_tcLCC2_insect_like, The first cupredoxin domain of insect laccases similar to laccase 2 in Tribolium castaneum.  This multicopper oxidase (MCO) family includes the majority of insect laccases. One member of the family is laccase 2 from Tribolium castaneum. Laccase 2 is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates ...
CDD:259929	119	EUKprk	Bacteria:17,Environmental:1,Plants:1	cd13860, CuRO_1_2dMco_1, The first cupredoxin domain of bacteria two domain multicopper oxidase.  This subfamily includes bacterial two domain multicopper oxidases (2dMCOs) with similarity to McoN from Nitrosomonas europaea. 2dMCO is a trimeric type C blue copper oxidase. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The 2dMCO is proposed to be a key ...
CDD:259930	119	PRK	Bacteria:27,Environmental:1	cd13861, CuRO_1_CumA_like, The first cupredoxin domain of CumA like multicopper oxidase.  This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida, which is involved in the oxidation of Mn(II). However, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other substrates. MCO ...
CDD:259933	115	PRK	Bacteria:15	cd13865, CuRO_1_LCC_like_3, The second cupredoxin domain of uncharacterized multicopper oxidase.  Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two ...
CDD:259934	152	EUKprk	Bacteria:8,Plants:7	cd13866, CuRO_2_BOD, The second cupredoxin domain of Bilirubin oxidase (BOD).  Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. It is used in diagnosing jaundice through the determination of bilirubin in serum. BOD is a member of the multicopper oxidase (MCO) family that also includes laccase, ascorbate oxidase and ceruloplasmin. MCOs are capable of oxidizing a vast ...
CDD:259935	146	PRK	Bacteria:19,Environmental:1	cd13867, CuRO_2_CueO_FtsP, The second Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins.  CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP ...
CDD:259936	155	EUKprk	Bacteria:8,Plants:3	cd13868, CuRO_2_CotA_like, The second Cupredoxin domain of bacterial laccases including CotA, a bacterial endospore coat component.  CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and it is required for spore resistance against hydrogen peroxide and UV light. Laccase is composed of three cupredoxin-like domains and includes one mononuclear and one trinuclear copper center. It is a member of the multicopper ...
CDD:259938	117	PRK	Bacteria:3	cd13870, CuRO_2_CopA_like_1, The second cupredoxin domain of CopA copper resistance protein like family.  The members of this family are copper resistance protein (CopA) homologs. CopA is multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. CopA is involved in copper resistance in bacteria. CopA mutant causes a loss of function, including copper tolerance and oxidase activity, and copA transcription is inducible in ...
CDD:259941	161	EUK	Plants:12	cd13873, CuRO_2_AAO_like_2, The second cupredoxin domain of plant  Ascorbate oxidase homologs.  This family includes plant laccases similar to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to multicopper oxidase (MCO) family which couples oxidation of substrates with ...
CDD:259942	112	EUKprk	Bacteria:4,Environmental:1,Plants:1	cd13874, CuRO_2_CopA, The second cupredoxin domain of  CopA copper resistance protein family.  CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in ...
CDD:259943	148	EUK	Plants:11	cd13875, CuRO_2_LCC_plant, The second cupredoxin domain of the plant laccases.  Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase ...
CDD:259944	138	EUK	Plants:18	cd13876, CuRO_2_Abr2_like, The second cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus.  Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, ...
CDD:259945	148	EUK	Plants:34	cd13877, CuRO_2_Fet3p_like, The second Cupredoxin domain of multicopper oxidase Fet3P.  Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) with the four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the extracellular space and the carboxyl terminus in the cytoplasm. The periplasmic produced Fe(III) is transferred to the permease Ftr1p for import ...
CDD:259946	162	PRK	Bacteria:5,Environmental:1	cd13879, CuRO_2_McoP_like, The second cupredoxin domain of multicopper oxidase McoP and similar proteins.  This family includes archaeal and bacterial multicopper oxidases (MCOs), represented by the extremely thermostable McoP from the hyperthermophilic archaeon Pyrobaculum aerophilum. McoP is an efficient metallo-oxidase that catalyzes the oxidation of cuprous and ferrous ions. It is noteworthy that McoP has three-fold higher catalytic efficiency ...
CDD:259947	167	EUK	Plants:19	cd13880, CuRO_2_MaLCC_like, The second cupredoxin domain of the fungal laccases similar to Ma-LCC  from Melanocarpus albomyces.  The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a  multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and ...
CDD:259948	142	PRK	Bacteria:11,Environmental:1	cd13881, CuRO_2_McoC_like, The second cupredoxin domain of a multicopper oxidase McoC and similar proteins.  This family includes bacterial multicopper oxidases (MCOs) represented by McoC from the pathogenic bacterium Campylobacter jejuni. McoC is a periplasmic MCO, which has been characterized to be associated with copper homeostasis. McoC may also function to protect against oxidative stress as it may convert metallic ions into their less toxic ...
CDD:259950	164	EUK	Plants:5	cd13883, CuRO_2_Diphenol_Ox, The second cupredoxin domain of fungal laccase, diphenol oxidase.  Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue ...
CDD:259951	150	EUK	Invertebrates:15,nodiv:1	cd13884, CuRO_2_tcLCC_insect_like, The second cupredoxin domain of the insect laccases similar to laccase 2 in Tribolium castaneum.  This multicopper oxidase (MCO) subfamily includes the majority of insect laccases. One member is laccase 2 from Tribolium castaneum, which is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled ...
CDD:259952	132	PRK	Bacteria:9,Environmental:1	cd13885, CuRO_2_CumA_like, The second cupredoxin domain of CumA like multicopper oxidase.  This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida. CumA is involved in the oxidation of Mn(II) in Pseudomonas putida; however, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other ...
CDD:259953	163	EUK	Plants:11	cd13886, CuRO_2_MCO_like_1, The second cupredoxin domain of uncharacterized multicopper oxidase.  Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two ...
CDD:259956	124	EUKprk	Bacteria:9,Plants:2	cd13889, CuRO_3_BOD, The third cupredoxin domain of Bilirubin oxidase (BOD).  Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. It is used in diagnosing jaundice through the determination of bilirubin in serum. BOD is a member of the multicopper oxidase (MCO) family that also includes laccase, ascorbate oxidase and ceruloplasmin. MCOs are capable of oxidizing a vast ...
CDD:259957	124	PRK	Bacteria:17	cd13890, CuRO_3_CueO_FtsP, The third Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins.  CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP (also named SufI) ...
CDD:259958	143	EUKprk	Bacteria:4,Invertebrates:1,Plants:2	cd13891, CuRO_3_CotA_like, The third Cupredoxin domain of bacterial laccases including CotA, a bacterial endospore coat component.  CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and is required for spore resistance against hydrogen peroxide and UV light. CotA belongs to the laccase-like multicopper oxidase (MCO) family, which are able to couple oxidation of substrates with reduction of dioxygen ...
CDD:259962	188	EUK	Plants:5	cd13895, CuRO_3_AAO_like_2, The third cupredoxin domain of Ascorbate oxidase homologs.  This family includes fungal proteins with similarity to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to multicopper oxidase (MCO) family which couple oxidation of substrates with ...
CDD:259963	115	EUKprk	Bacteria:14,Plants:1	cd13896, CuRO_3_CopA, The third cupredoxin domain of CopA copper resistance protein family.  CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in the inner cell ...
CDD:259964	139	EUK	Plants:5	cd13897, CuRO_3_LCC_plant, The third cupredoxin domain of the plant laccases.  Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple ...
CDD:259965	164	EUK	Plants:12	cd13898, CuRO_3_Abr2_like, The third cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus.  Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, ...
CDD:259966	160	EUK	Plants:7	cd13899, CuRO_3_Fet3p, The third Cupredoxin domain of multicopper oxidase Fet3p.  Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) with the four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the extracellular space and the carboxyl terminus in the cytoplasm. The periplasmic produced Fe(III) is transferred to the permease Ftr1p for import into the ...
CDD:259967	123	EUKprk	Bacteria:20,Invertebrates:1	cd13900, CuRO_3_Tth-MCO_like, The third cupredoxin domain of the bacterial laccases similar to Tth-MCO from Thermus Thermophilus.  The subfamily of bacterial laccases includes Tth-MCO and similar proteins. Tth-MCO is a hyperthermophilic multicopper oxidase (MCO) from thermus thermophilus HB27. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the ...
CDD:259968	157	EUK	Plants:42	cd13901, CuRO_3_MaLCC_like, The third cupredoxin domain of the fungal laccases similar to Ma-LCC  from Melanocarpus albomyces.  The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers.  Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and ...
CDD:259969	125	PRK	Bacteria:1	cd13902, CuRO_3_McoC_like, The third cupredoxin domain of a multicopper oxidase McoC and similar proteins.  This family includes bacteria multicopper oxidases (MCOs) represented by McoC from pathogenic bacterium Campylobacter jejuni. McoC is a periplasmic multicopper oxidase, which has been characterized to be associated with copper homeostasis. McoC may also function to protect against oxidative stress as it may convert metallic ions into their less toxic form. ...
CDD:259970	147	EUK	Plants:17	cd13903, CuRO_3_Tv-LCC_like, The third cupredoxin domain of the fungal laccases similar to Tv-LCC from Trametes Versicolor.  This subfamily of fungal laccases includes Tv-LCC from Trametes versicolor and Rs-LCC2 from plant pathogenic fungus Rhizoctonia solani. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated ...
CDD:259971	158	EUK	Plants:5	cd13904, CuRO_3_Diphenol_Ox, The third cupredoxin domain of fungal laccase, diphenol oxidase.  Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue multicopper ...
CDD:259972	174	EUK	Invertebrates:11	cd13905, CuRO_3_tcLLC2_insect_like, The third cupredoxin domain of the insect laccases similar to laccase 2 in Tribolium castaneum.  This multicopper oxidase (MCO) family includes the majority of insect laccases. One member of the family is laccase 2 from Tribolium castaneum. Laccase 2 is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates ...
CDD:259973	138	PRK	Bacteria:6	cd13906, CuRO_3_CumA_like, The third cupredoxin domain of CumA like multicopper oxidase.  This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida, which is involved in the oxidation of Mn(II). However, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other substrates. MCO catalyzes the oxidation ...
CDD:259977	166	EUK	Plants:16	cd13910, CuRO_3_MCO_like_4, The third cupredoxin domain of uncharacterized multicopper oxidase.  Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two ...
CDD:259979	130	EUKprk	Bacteria:6,Invertebrates:17,Plants:11,Vertebrates:3	cd13912, CcO_II_C, C-terminal domain of Cytochrome c Oxidase subunit II.  Cytochrome c Oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies ...
CDD:259980	99	PRK	Bacteria:33	cd13913, ba3_CcO_II_C, C-terminal cupredoxin domain of Ba3-like heme-copper oxidase subunit II.  The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea, which catalyze the reduction of O2 and simultaneously pump protons across the membrane. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. The ba3 family contains oxidases ...
CDD:259982	98	PRK	Bacteria:27	cd13915, CuRO_HCO_II_like_2, Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in ...
CDD:259983	93	PRK	Bacteria:11	cd13916, CuRO_HCO_II_like_1, Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in ...
CDD:259986	107	PRK	Bacteria:28,Environmental:3	cd13919, CuRO_HCO_II_like_5, Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain.  Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies ...
CDD:259987	101	EUK	Plants:8	cd13920, Stellacyanin, Stellacyanin is a subclass of phytocyanins, a plant type I copper protein.  Stellacyanin is a subclass of the phytocyanins, a ubiquitous family of plant cupredoxins. Stellacyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. The copper is tetrahedrally coordinated by a cysteine, 2 histidines, and a glutamine residue. The glutamine residue substitutes for a ...
CDD:259988	81	PRK	Bacteria:16	cd13921, Amicyanin, Amicyanin is a type I blue copper protein that plays an essential role in electron transfer.  In Paracoccus denitrificans bacteria, amicyanin acts as an intermediary of a three-member redox complex along with methylamine dehydrogenase (MADH) and cytochrome c-551i. The electron is transferred from the active site of MADH via the amicyanin copper ion to the cytochrome heme iron. The electron transfer from MADH to cytochrome c-551i does not involve ...
CDD:259989	125	PRK	Bacteria:58,Environmental:1	cd13922, Azurin, Azurin is a redox partner for enzymes such as nitrite reductase or arsenite oxidase.  Azurin is a bacterial blue copper-binding protein. It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The copper of Azurin is tetrahedrally coordinated by a cysteine, 2 histidines, and a methionine residue. The electron transfer reactions are carried out with the Cu center transitioning between the oxidized ...
CDD:260106	392	EUK	Plants:52	cd13929, PT-DMATS_CymD, aromatic prenyltransferases (PTases) of the DMATS/CymD familiy.  Members of the DMATS/CymD family of ABBA prenyltransferases prenylate indole, tyrosine, and xanthone derivatives. This family of fungal proteins includes cyclic dipeptide N-prenyltransferase (CdpNPT), Brevianamide F prenyltransferase (ftmPT1), fumigaclavine C synthase (FgaPT1), dimethylallyltryptophan synthase (DMATS) and related proteins. CdpNPT accepts a variety of ...
CDD:260107	348	EUKprk	Bacteria:6,Plants:4	cd13930, PT-Tnase, Aromatic Prenyltransferases (PTases) associated with tryptophanase.  This group of bacterial and fungal proteins shows homology to the DMATS/CymD family of ABBA prenyltransferases, which prenylates indole, tyrosine, and xanthone derivatives. Some of the members, mostly fungal proteins, are associated with tryptophanase-like domains (Tnase) which catalyzes the degradation of L-tryptophan to yield indole, pyruvate and ammonia, or the ...
CDD:260108	274	EUKprk	Bacteria:13,Plants:3	cd13931, PT-CloQ_NphB, Aromatic Prenyltransferases (PTases) of the CloQ/NphB family.  Members of the CloQ/NphB family of ABBA prenyltransferases catalyze the prenylation of phenols, naphthalenes, and phenazines. This family of fungal and bacterial proteins includes dihydrophenazine-1-carboxylate dimethylallyltransferase PpzP, the aromatic prenyltransferase from the clorobiocin biosynthetic pathway CloQ, and related proteins. CloQ catalyzes the ...
CDD:259826	99	EUK	Invertebrates:9,Mammals:3,Plants:5,Rodents:1,Vertebrates:3	cd13932, HN_RTEL1, harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL).  Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination ...
CDD:260014	153	EUK	Plants:36	cd13934, RNase_H_Dikarya_like, Fungal (dikarya) Ribonuclease H, uncharacterized.  This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is ...
CDD:260110	149	EUK	Invertebrates:7,Plants:1,Primates:1,Rodents:1,nodiv:1	cd13936, PANDER_like, Domains similar to the Pancreatic-derived factor.  FAM3B or PANDER (PANcreatic DERived factor) has been identifed as a regulator of glucose homeostasis and beta cell function. The protein is expressed in the endocrine pancreas and co-secreted with insulin in response to glucose, particularly under conditions of insulin resistance. The protein had initially been predicted to be a member of the ...
CDD:260111	148	EUK	Invertebrates:12,Vertebrates:3	cd13937, PANDER_GnT-1_2_like, PANDER-like domain of N-acetylglucosaminyltransferases.  O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 participates in O-mannosyl glycosylation and may be responsible for creating GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moieties on alpha dystroglycan and other O-mannosylated proteins. The domain characterized by this model lies N-terminal to the catalytic domain. Its function has not been determined.
CDD:260112	168	EUK	Invertebrates:1,Primates:1,Vertebrates:5	cd13938, PANDER_like_TMEM2, PANDER-like domain of the transmembrane protein TMEM2.  TMEM2 has been characterized as a transmembrane protein that maps to the DFNB7-DFNB11 deafness locus on human chromosome 9. It contains a domain similar to the Pancreatic-derived factor PANDER, C-terminal to a glycine rich G8-domain. The function of the PANDER-like domain in TMEM2 has not been characterized.
CDD:260114	171	EUK	Invertebrates:1,Primates:1,Vertebrates:10	cd13940, ILEI_FAM3C, Interleukin-like EMT inducer.  The secreted factor FAM3C or ILEI (InterLeukin-like Emt Inducer) has been identifed as a protein involved in the epithelial-mesenchymal transition (EMT) and in processes associated with metastasis formation and the progression of cancer. The protein had initially been predicted to be a member of the four-helical cytokine family, hence the FAM3C designation. ILEI has been found to be ...
CDD:260116	275	EUKprk	Bacteria:246,Environmental:6,Invertebrates:7,Plants:10,nodiv:2	cd13944, lytB_ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase.  The 4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) reductase (called lytB or ispH) is the terminal enzyme of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, one of the two metabolic routes for isoprenoid biosynthesis. The MEP pathway is essential in many eubacteria, plants, and the malaria parasite. LytB ...
CDD:260117	73	EUK	Invertebrates:1,Plants:25	cd13945, Chs5_N, N-terminal dimerization domain of Chs5 and similar proteins.  Chs5/6 is a multi-protein complex conserved in fungi that interacts with chitin synthase III (Chs3p) and is involved in its transport to the cell surface from the trans-Golgi network, functioning as an exomer cargo adapter. Chs5p appears to form a complex with Chs6p and its paralogs Bch1p, Bud7p, and Bch2p. In this complex, Chs5p may act as a central scaffold. The N-terminal ...
CDD:260118	54	PRK	Bacteria:25,Environmental:1	cd13946, LysW, Lysine biosynthesis protein LysW.  LysW functions as a carrier protein in the biosynthesis pathway of lysine. The C-terminal glutamate sidechain of LysW attaches to the amino group of alpha-aminoadipate (AAA); this peptide bond formation is catalyzed by the ligase LysX. AAA remains associated with LysW throughout its biosynthetic conversion to lysine. LysW also acts to protect the amino group of glutamate in arginine biosynthesis.
CDD:260119	271	EUKprk	Bacteria:55,Plants:3	cd13956, PT_UbiA, UbiA family of prenyltransferases (PTases).  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl ...
CDD:260120	271	EUKprk	Bacteria:184,Environmental:6,Invertebrates:21,Plants:26,Rodents:1,Vertebrates:3	cd13957, PT_UbiA_Cox10, Protoheme IX farnesyltransferase.  Protoheme IX farnesyltransferase (also called heme O synthase, heme A:farnesyltransferase, cytochrome c oxidase subunit X [Cox10]) converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of the heme B porphyrin ring with a hydroxyethyl farnesyl side group. It is localized at the mitochondrial inner ...
CDD:260121	277	EUKprk	Bacteria:13,Plants:8	cd13958, PT_UbiA_chlorophyll, Bacteriochlorophyll/chlorophyll synthetase.  Chlorophyll synthase catalyzes the last step of chlorophyll (Chl) biosynthesis, the addition of the tetraprenyl (phytyl or geranylgeranyl) side chain. In plant chloroplast, the chlorophyll synthase is located in thylakoid membrane and has been shown to also have a regulatory or channeling function. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties ...
CDD:260122	272	EUKprk	Bacteria:199,Invertebrates:25,Plants:56,Primates:1,Vertebrates:1	cd13959, PT_UbiA_COQ2, 4-Hydroxybenzoate polyprenyltransferase.  4-Hydroxybenzoate polyprenyltransferase, also known as Coq2, catalyzes the prenylation of p-hydroxybenzoate with an all-trans polyprenyl group, an important step in ubiquinone (CoQ) biosynthesis. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many ...
CDD:260123	289	EUKprk	Bacteria:5,Plants:22	cd13960, PT_UbiA_HPT1, Tocopherol phytyltransferase.  Tocopherol polyprenyltransferase (TPT1), also known as homogentisate phytyltransferase 1 (HPT1), tocopherol phytyltransferase, or VTE2, catalyzes the first step in the biosynthesis of the tocopherol forms of vitamin E, which involves the prenylation of homogentisate using phytyl diphosphate (PDP) as the prenyl donor. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties ...
CDD:260124	270	PRK	Bacteria:97	cd13961, PT_UbiA_DGGGPS, Geranylgeranylglycerol-phosphate geranylgeranyltransferase.  Digeranylgeranylglyceryl phosphate synthase (DGGGPS) transfers a geranylgeranyl group from geranylgeranyl diphosphate to (S)-3-O-geranylgeranylglyceryl phosphate to form (S)-2,3-di-O-geranylgeranylglyceryl phosphate, as part of the isoprenoid ether lipid biosynthesis. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates ...
CDD:260125	283	EUKprk	Bacteria:366,Invertebrates:12,Plants:14,Rodents:1,Vertebrates:2,nodiv:1	cd13962, PT_UbiA_UBIAD1, 1,4-Dihydroxy-2-naphthoate octaprenyltransferase.  Human UBIAD1 is an enzyme involved in the synthesis of MK-4. Menaquinones (MKs, also called bacterial forms) are one of the two forms of natural vitamin K, the other being the plant form, phylloquinone (PK). All forms of vitamin K have a 2-methyl-1,4-naphthoquinone (menadione; K3) ring structure in common. At the 3-position of ...
CDD:260126	278	PRK	Bacteria:186,Environmental:2	cd13963, PT_UbiA_2, UbiA family of prenyltransferases (PTases), Unknown subgroup.  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the ...
CDD:260127	282	PRK	Bacteria:62	cd13964, PT_UbiA_1, UbiA family of prenyltransferases (PTases), Unknown subgroup.  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of ...
CDD:260128	273	EUKprk	Bacteria:9,Plants:34	cd13965, PT_UbiA_3, UbiA family of prenyltransferases (PTases), Unknown subgroup.  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective ...
CDD:260129	272	EUKprk	Bacteria:26,Environmental:1,Plants:3	cd13966, PT_UbiA_4, UbiA family of prenyltransferases (PTases), Unknown subgroup.  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the ...
CDD:260130	277	PRK	Bacteria:26	cd13967, PT_UbiA_5, UbiA family of prenyltransferases (PTases), Unknown subgroup.  Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of ...
CDD:270870	136	miss	miss	cd13968, PKc_like, Catalytic domain of the Protein Kinase superfamily.  The PK superfamily contains the large family of typical PKs that includes serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins, as well as pseudokinases that lack crucial residues for catalytic activity and/or ATP binding. It also includes phosphoinositide 3-kinases (PI3Ks), ...
CDD:270871	253	EUK	Invertebrates:23,Plants:25,Primates:1,Vertebrates:3	cd13969, ADCK1-like, aarF domain containing kinase 1 and similar proteins.  This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 1 (ADCK1). Eukaryotes contain at least three ABC1-like proteins: in humans, these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases ...
CDD:270872	251	EUKprk	Bacteria:37,Invertebrates:19,Plants:12,Vertebrates:2	cd13970, ABC1_ADCK3, Activator of bc1 complex (ABC1) kinases, also called aarF domain containing kinase 3.  This subfamily is composed of the atypical yeast protein kinase Abc1p, its human homolog ADCK3 (also called CABC1), and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. It ...
CDD:270873	298	EUK	Invertebrates:9,Plants:19,Vertebrates:1	cd13971, ADCK2-like, aarF domain containing kinase 2 and similar proteins.  This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 2 (ADCK2). Eukaryotes contain at least three ABC1-like proteins; in humans, these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases required ...
CDD:270874	247	PRK	Bacteria:19	cd13972, UbiB, Ubiquinone biosynthetic protein UbiB.  UbiB is the prokaryotic homolog of yeast Abc1p and human ADCK3 (aarF domain containing kinase 3). It is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. It is required in the first monooxygenase step in Q biosynthesis. Mutant strains with disrupted ubiB genes lack Q and accumulate octaprenylphenol, a Q biosynthetic ...
CDD:270875	236	PRK	Bacteria:29	cd13973, PK_MviN-like, Pseudokinase domain of the peptidoglycan biosynthetic protein MviN.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. This family is composed of the mycobacterial protein MviN and similar proteins. MviN is an integral membrane protein that is essential for growth and is required for cell wall integrity and peptidogylcan (PG) biosynthesis. It comprises of 14 predicted transmembrane ...
CDD:270881	265	EUK	Invertebrates:5,Vertebrates:4	cd13979, STKc_Mos, Catalytic domain of the Serine/Threonine kinase, Oocyte maturation factor Mos.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mos (or c-Mos) is a germ-cell specific kinase that plays roles in both the release of primary arrest and the induction of secondary arrest in oocytes. It is expressed towards the end of meiosis I and is quickly degraded upon ...
CDD:270882	278	EUK	Invertebrates:10,Plants:7,Primates:1,Vertebrates:2	cd13980, STKc_Vps15, Catalytic domain of the Serine/Threonine kinase, Vacuolar protein sorting-associated protein 15.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Vps15 is a large protein consisting of an N-terminal kinase domain, a C-terminal WD-repeat containing domain, and an intermediate bridge domain that contain HEAT repeats. The kinase domain is ...
CDD:270883	298	EUK	Invertebrates:5,Plants:3,Vertebrates:1	cd13981, STKc_Bub1_BubR1, Catalytic domain of the Serine/Threonine kinases, Spindle assembly checkpoint proteins Bub1 and BubR1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Bub1 (Budding uninhibited by benzimidazoles 1), BubR1, and similar proteins. They contain an N-terminal Bub1/Mad3 homology domain essential for Cdc20 binding and a ...
CDD:270884	269	EUK	Invertebrates:3,Plants:5,Vertebrates:2	cd13982, STKc_IRE1, Catalytic domain of the Serine/Threonine kinase, Inositol-requiring protein 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), is an ER-localized type I transmembrane protein with kinase and endoribonuclease domains in the cytoplasmic side. It acts as an ER stress ...
CDD:270885	258	EUK	Invertebrates:9,Plants:9,Primates:1,Vertebrates:1,nodiv:1	cd13983, STKc_WNK, Catalytic domain of the Serine/Threonine kinase, With No Lysine (WNK) kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNKs comprise a subfamily of STKs with an unusual placement of a catalytic lysine relative to all other protein kinases. They are critical in regulating ion balance and are thus, important components in the ...
CDD:270887	272	EUK	Invertebrates:4,Plants:1,Primates:1	cd13985, STKc_GAK_like, Catalytic domain of cyclin G-Associated Kinase-like proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes cyclin G-Associated Kinase (GAK), Drosophila melanogaster Numb-Associated Kinase (NAK)-like proteins, and similar protein kinases. GAK plays regulatory roles in clathrin-mediated membrane trafficking, the maintenance ...
CDD:270888	282	EUK	Invertebrates:3,Plants:5,Vertebrates:3	cd13986, STKc_16, Catalytic domain of Serine/Threonine Kinase 16.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK16 is associated with many names including Myristylated and Palmitylated Serine/threonine Kinase 1 (MPSK1), Kinase related to cerevisiae and thaliana (Krct), and Protein Kinase expressed in day 12 fetal liver (PKL12). It is widely expressed in mammals ...
CDD:270889	259	EUK	Invertebrates:3,Vertebrates:4	cd13987, STKc_SBK1, Catalytic domain of the Serine/Threonine kinase, SH3 Binding Kinase 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SBK1, also called BSK146, is predominantly expressed in the brain. Its expression is increased in the developing brain during the late embryonic stage, coinciding with dramatic neuronal proliferation, migration, and maturation. SBK1 may play ...
CDD:270892	279	EUK	Invertebrates:11,Plants:4,Primates:1	cd13990, STKc_TLK, Catalytic domain of the Serine/Threonine kinase, Tousled-Like Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TLKs play important functions during the cell cycle and are implicated in chromatin remodeling, DNA replication and repair, and mitosis. They phosphorylate and regulate Anti-silencing function 1 protein (Asf1), a histone H3/H4 chaperone ...
CDD:270894	268	EUK	Invertebrates:1,Rodents:1,Vertebrates:1	cd13992, PK_GC, Pseudokinase domain of membrane Guanylate Cyclase receptors.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of ...
CDD:270895	267	EUK	Plants:4	cd13993, STKc_Pat1_like, Catalytic domain of Fungal Pat1-like Serine/Threonine kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Schizosaccharomyces pombe Pat1 (also called Ran1), Saccharomyces cerevisiae VHS1 and KSP1, and similar fungal STKs. Pat1 blocks Mei2, an RNA-binding protein which is indispensable in the initiation of meiosis. Pat1 is inactivated and ...
CDD:270896	265	EUK	Plants:10	cd13994, STKc_HAL4_like, Catalytic domain of Fungal Halotolerance protein 4-like Serine/Threonine kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of HAL4, Saccharomyces cerevisiae Ptk2/Stk2, and similar fungal proteins. Proteins in this subfamily are involved in regulating ion transporters. In budding and fission yeast, HAL4 promotes potassium ion uptake, which ...
CDD:270898	273	EUK	Invertebrates:7,Plants:1,Primates:1,Rodents:1	cd13996, STKc_EIF2AK, Catalytic domain of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. eIF-2 phosphorylation is induced in response to cellular stresses including virus ...
CDD:270901	245	EUK	Invertebrates:8,Plants:11,Primates:1	cd13999, STKc_MAP3K-like, Catalytic domain of Mitogen-Activated Protein Kinase (MAPK) Kinase Kinase-like Serine/Threonine kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed mainly of MAP3Ks and similar proteins, including TGF-beta Activated Kinase-1 (TAK1, also called MAP3K7), MAP3K12, MAP3K13, Mixed lineage kinase (MLK), MLK-Like ...
CDD:270904	253	EUK	Invertebrates:17,Plants:8,Vertebrates:2	cd14002, STKc_STK36, Catalytic domain of Serine/Threonine Kinase 36.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK36, also called Fused (or Fu) kinase, is involved in the Hedgehog signaling pathway. It is activated by the Smoothened (SMO) signal transducer, resulting in the stabilization of GLI transcription factors and the phosphorylation of SUFU to facilitate ...
CDD:270905	252	EUK	Invertebrates:10,Plants:10,Primates:1,Rodents:2	cd14003, STKc_AMPK-like, Catalytic domain of AMP-activated protein kinase-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The AMPK-like subfamily is composed of AMPK, MARK, BRSK, NUAK, MELK, SNRK, TSSK, and SIK, among others. LKB1 serves as a master upstream kinase that activates AMPK and most AMPK-like kinases. AMPK, also called ...
CDD:270907	255	EUK	Invertebrates:7,Primates:1,Vertebrates:3	cd14005, STKc_PIM, Catalytic domain of the Serine/Threonine kinase, Proviral Integration Moloney virus (PIM) kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PIM gene locus was discovered as a result of the cloning of retroviral intergration sites in murine Moloney leukemia virus, leading to the identification of PIM kinases. They are constitutively active ...
CDD:270908	247	EUK	Invertebrates:3,Primates:1,Rodents:1	cd14006, STKc_MLCK-like, Catalytic kinase domain of Myosin Light Chain Kinase-like Serine/Threonine Kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This family is composed of MLCKs and related MLCK-like kinase domains from giant STKs such as titin, obscurin, SPEG, Unc-89, Trio, kalirin, and Twitchin. Also included in this family are Death-Associated Protein ...
CDD:270909	253	EUK	Invertebrates:21,Plants:14,Primates:1,Vertebrates:1	cd14007, STKc_Aurora, Catalytic domain of the Serine/Threonine kinase, Aurora kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Aurora kinases are key regulators of mitosis and are essential for the accurate and equal division of genomic material from parent to daughter cells. Yeast contains only one Aurora kinase while most higher eukaryotes have ...
CDD:270910	267	EUK	Invertebrates:12,Plants:21,Primates:1	cd14008, STKc_LKB1_CaMKK, Catalytic domain of the Serine/Threonine kinases, Liver Kinase B1, Calmodulin Dependent Protein Kinase Kinase, and similar proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Both LKB1 and CaMKKs can phosphorylate and activate AMP-activated protein kinase (AMPK). LKB1, also called STK11, serves as a master upstream kinase that activates ...
CDD:270911	251	EUK	Invertebrates:4,Plants:14,Primates:1,Vertebrates:1	cd14009, STKc_ATG1_ULK_like, Catalytic domain of the Serine/Threonine kinases, Autophagy-related protein 1 and Unc-51-like kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes yeast ATG1 and metazoan homologs including vertebrate ULK1-3. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the ...
CDD:270912	269	EUK	Invertebrates:9,Plants:7,Vertebrates:2	cd14010, STKc_ULK4, Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 4.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ULK4 is a functionally uncharacterized kinase that shows similarity to ATG1/ULKs. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that ...
CDD:270913	287	EUK	Invertebrates:14,Plants:3,Primates:1,Vertebrates:3	cd14011, PK_SCY1_like, Pseudokinase domain of Scy1-like proteins.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. This subfamily is composed of the catalytically inactive kinases with similarity to yeast Scy1. It includes four mammalian proteins called SCY1-like protein 1 (SCYL1), SCYL2, SCYL3, as well as Testis-EXpressed protein 14 (TEX14). SCYL1 binds to and ...
CDD:270914	254	EUK	Invertebrates:2,Plants:12,Vertebrates:4	cd14012, PK_eIF2AK_GCN2_rpt1, Pseudokinase domain, repeat 1, of eukaryotic translation Initiation Factor 2-Alpha Kinase 4 or General Control Non-derepressible-2.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the overall downregulation of protein synthesis. eIF-2 phosphorylation is induced in response to ...
CDD:270916	260	EUKprk	Bacteria:85,Invertebrates:1	cd14014, STKc_PknB_like, Catalytic domain of bacterial Serine/Threonine kinases, PknB and similar proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes many bacterial eukaryotic-type STKs including Staphylococcus aureus PknB (also called PrkC or Stk1), Bacillus subtilis PrkC, and Mycobacterium tuberculosis Pkn proteins (PknB, PknD, PknE, PknF, PknL, ...
CDD:270917	300	EUKprk	Invertebrates:9,Primates:1,Viruses:2	cd14015, STKc_VRK, Catalytic domain of the Serine/Threonine protein kinase, Vaccinia Related Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. VRKs were initially discovered due to its similarity to vaccinia virus B1R STK, which is important for viral replication. They play important roles in cell signaling, nuclear envelope dynamics, apoptosis, and stress ...
CDD:270918	266	EUK	Invertebrates:17,Mammals:1,Plants:28,Primates:1,Rodents:1	cd14016, STKc_CK1, Catalytic domain of the Serine/Threonine protein kinase, Casein Kinase 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of ...
CDD:270919	263	EUK	Invertebrates:9,Primates:1,Vertebrates:1	cd14017, STKc_TTBK, Catalytic domain of the Serine/Threonine protein kinase, Tau-Tubulin Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TTBK is a neuron-specific kinase that phosphorylates the microtubule-associated protein tau and promotes its aggregation. Higher vertebrates contain two TTBK proteins, TTBK1 and TTBK2, both of which have been implicated in ...
CDD:270921	252	EUK	Invertebrates:5,Plants:8,Vertebrates:2	cd14019, STKc_Cdc7, Catalytic domain of the Serine/Threonine Kinase, Cell Division Cycle 7 kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Cdc7 kinase (or Hsk1 in fission yeast) is a critical regulator in the initiation of DNA replication. It forms a complex with a Dbf4-related regulatory subunit, a cyclin-like molecule that activates the kinase in late G1 ...
CDD:270923	229	EUK	Invertebrates:13,Plants:1	cd14021, ChoK-like_euk, Euykaryotic Choline Kinase and similar proteins.  This group is composed of eukaryotic choline kinase, ethanolamine kinase, and similar proteins. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC), and sphingomyelin (SM). Although choline is the ...
CDD:270939	277	EUK	Invertebrates:6,Plants:4,Vertebrates:3	cd14037, STKc_NAK_like, Catalytic domain of Numb-Associated Kinase (NAK)-like Serine/Threonine kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Drosophila melanogaster NAK, human BMP-2-inducible protein kinase (BMP2K or BIKe) and similar vertebrate proteins, as well as the Saccharomyces cerevisiae proteins Prk1, Actin-regulating ...
CDD:270944	279	EUK	Invertebrates:5,Vertebrates:2	cd14042, PK_GC-A_B, Pseudokinase domain of the membrane Guanylate Cyclase receptors, GC-A and GC-B.  The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. GC-A binds and is activated by the atrial and B-type natriuretic peptides, ANP and BNP, which are important in blood pressure regulation and cardiac pathophysiology. GC-B binds the C-type natriuretic peptide, CNP, which ...
CDD:270948	278	EUK	Invertebrates:2,Plants:3	cd14046, STKc_EIF2AK4_GCN2_rpt2, Catalytic domain, repeat 2, of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 4 or General Control Non-derepressible-2.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GCN2 (or EIF2AK4) is activated by amino acid or serum starvation and UV irradiation. It induces GCN4, a transcriptional activator of amino acid ...
CDD:270952	249	EUK	Invertebrates:7,Primates:1,Vertebrates:2	cd14050, PKc_Myt1, Catalytic domain of the Dual-specificity protein kinase, Myt1.  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. Myt1 is a cytoplasmic cell cycle checkpoint kinase that can keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of N-terminal thr (T14) and tyr (Y15) residues, leading to ...
CDD:270955	290	EUK	Invertebrates:10,Primates:1,nodiv:1	cd14053, STKc_ACVR2, Catalytic domain of the Serine/Threonine Kinase, Activin Type II Receptor.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ACVR2 belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins (BMPs), activins, growth and differentiation factors (GDFs), and anti-Mullerian ...
CDD:270956	300	EUK	Invertebrates:6,Primates:1,Vertebrates:5	cd14054, STKc_BMPR2_AMHR2, Catalytic domain of the Serine/Threonine Kinases, Bone Morphogenetic Protein and Anti-Muellerian Hormone Type II Receptors.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BMPR2 and AMHR2 belong to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, BMPs, activins, growth and differentiation ...
CDD:270958	287	EUK	Invertebrates:7,Primates:1	cd14056, STKc_TGFbR_I, Catalytic domain of the Serine/Threonine Kinases, Transforming Growth Factor beta family Type I Receptors.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of type I receptors for the TGFbeta family of secreted signaling molecules including TGFbeta, bone morphogenetic proteins, activins, growth and differentiation factors, and ...
CDD:270968	272	EUK	Invertebrates:2,Plants:2,Primates:1,Vertebrates:1	cd14066, STKc_IRAK, Catalytic domain of the Serine/Threonine kinases, Interleukin-1 Receptor Associated Kinases and related STKs.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. Some IRAKs ...
CDD:270971	261	EUK	Invertebrates:2,Plants:1,Primates:1,Vertebrates:3	cd14069, STKc_Chk1, Catalytic domain of the Serine/Threonine kinase, Checkpoint kinase 1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chk1 is implicated in many major checkpoints of the cell cycle, providing a link between upstream sensors and the cell cycle engine. It plays an important role in DNA damage response and maintaining genomic stability. Chk1 ...
CDD:270981	256	EUK	Invertebrates:9,Plants:7,Primates:1,Vertebrates:3	cd14079, STKc_AMPK_alpha, Catalytic domain of the Alpha subunit of the Serine/Threonine Kinase, AMP-activated protein kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. AMPK, also called SNF1 (sucrose non-fermenting1) in yeasts and SnRK1 (SNF1-related kinase1) in plants, is a heterotrimeric enzyme composed of a catalytic alpha subunit and two regulatory ...
CDD:270982	262	EUK	Invertebrates:18,Primates:1	cd14080, STKc_TSSK-like, Catalytic domain of testis-specific serine/threonine kinases and similar proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their ...
CDD:270983	255	EUK	Invertebrates:13,Plants:9,Primates:1,Vertebrates:4	cd14081, STKc_BRSK1_2, Catalytic domain of Brain-specific serine/threonine-protein kinases 1 and 2.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BRSK1, also called SAD-B or SAD1 (Synapses of Amphids Defective homolog 1), and BRSK2, also called SAD-A, are highly expressed in mammalian forebrain. They play important roles in establishing neuronal polarity. ...
CDD:270991	263	EUK	Invertebrates:15,Primates:1,Vertebrates:1	cd14089, STKc_MAPKAPK, Catalytic domain of the Serine/Threonine kinases, Mitogen-activated protein kinase-activated protein kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the MAPK-activated protein kinases MK2, MK3, MK5 (also called PRAK for p38-regulated/activated protein kinase), and related proteins. These proteins contain ...
CDD:270993	291	EUK	Invertebrates:17,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd14091, STKc_RSK_C, C-terminal catalytic domain of the Serine/Threonine Kinases, Ribosomal S6 kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated ...
CDD:270994	311	EUK	Invertebrates:12,Rodents:1,nodiv:1	cd14092, STKc_MSK_C, C-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress ...
CDD:270997	258	EUK	Invertebrates:7,Mammals:1,Primates:1,Vertebrates:1	cd14095, STKc_DCKL, Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase (also called Doublecortin-like and CAM kinase-like).  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DCKL (or DCAMKL) proteins belong to the doublecortin (DCX) family of proteins which are involved in neuronal migration, neurogenesis, and eye receptor development, ...
CDD:271001	258	EUK	Invertebrates:10,Plants:7,Primates:1,Vertebrates:1	cd14099, STKc_PLK, Catalytic domain of the Serine/Threonine Kinases, Polo-like kinases.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal ...
CDD:271005	250	EUK	Invertebrates:13,Primates:1,Vertebrates:2	cd14103, STKc_MLCK, Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK phosphorylates myosin regulatory light chain and controls the contraction of all muscle types. In vertebrates, different MLCKs function in smooth (MLCK1), skeletal (MLCK2), and cardiac (MLCK3) muscles. A fourth protein, ...
CDD:271021	255	EUK	Invertebrates:16,Plants:1,Vertebrates:3	cd14119, STKc_LKB1, Catalytic domain of the Serine/Threonine kinase, Liver Kinase B1.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LKB1, also called STK11, was first identified as a tumor suppressor responsible for Peutz-Jeghers syndrome, a disorder that leads to an increased risk of spontaneous epithelial cancer. It serves as a master upstream kinase that ...
CDD:271023	252	EUK	Invertebrates:13,Vertebrates:3	cd14121, STKc_ULK3, Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 3.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic ...
CDD:271033	271	EUK	Invertebrates:7,Plants:10,Primates:1,Vertebrates:3	cd14131, PKc_Mps1, Catalytic domain of the Dual-specificity Mitotic checkpoint protein kinase, Monopolar spindle 1 (also called TTK).  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TTK/Mps1 is a spindle checkpoint kinase that was first discovered due to its necessity in centrosome duplication in budding yeast. It was ...
CDD:271034	306	EUK	Invertebrates:19,Plants:8,Primates:1,Vertebrates:3	cd14132, STKc_CK2_alpha, Catalytic subunit (alpha) of the Serine/Threonine Kinase, Casein Kinase 2.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK2 is a tetrameric protein with two catalytic (alpha) and two regulatory (beta) subunits. It is constitutively active and ubiquitously expressed, and is found in the cytoplasm, nucleus, as well as in the plasma ...
CDD:271035	262	EUK	Invertebrates:3,Plants:4,Primates:1	cd14133, PKc_DYRK_like, Catalytic domain of Dual-specificity tYrosine-phosphorylated and -Regulated Kinase-like protein kinases.  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of the dual-specificity DYRKs and YAK1, as well as the S/T kinases (STKs), HIPKs. DYRKs and YAK1 autophosphorylate themselves on ...
CDD:271036	332	EUK	Invertebrates:18,Plants:13,Primates:1	cd14134, PKc_CLK, Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases.  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. CLKs are involved in the phosphorylation and regulation of serine/arginine-rich (SR) proteins, which play a crucial role in pre-mRNA splicing by directing splice site selection. SR ...
CDD:271037	318	EUK	Invertebrates:13,Plants:9,Primates:1,Vertebrates:2	cd14135, STKc_PRP4, Catalytic domain of the Serine/Threonine Kinase, Pre-mRNA-Processing factor 4.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PRP4 phosphorylates a number of factors involved in the formation of active spliceosomes, which catalyze pre-mRNA splicing. It phosphorylates PRP6 and PRP31, components of the U4/U6-U5 tri-small nuclear ...
CDD:271038	320	EUK	Invertebrates:16,Plants:7,Primates:1,Vertebrates:2	cd14136, STKc_SRPK, Catalytic domain of the Serine/Threonine Kinase, Serine-aRginine Protein Kinase.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SRPKs phosphorylate and regulate splicing factors from the SR protein family by specifically phosphorylating multiple serine residues residing in SR/RS dipeptide motifs (also known as RS domains). ...
CDD:271039	293	EUK	Invertebrates:33,Plants:15,Primates:1,Vertebrates:3,nodiv:1	cd14137, STKc_GSK3, The catalytic domain of the Serine/Threonine Kinase, Glycogen Synthase Kinase 3.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GSK3 is a mutifunctional kinase involved in many cellular processes including cell division, proliferation, differentiation, adhesion, and apoptosis. In plants, GSK3 plays a role in the response to ...
CDD:271064	259	EUK	Invertebrates:9	cd14162, STKc_TSSK4-like, Catalytic domain of testis-specific serine/threonine kinase 4 and similar proteins.  STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and ...
CDD:271112	311	EUK	Invertebrates:9,Plants:14,Primates:1	cd14210, PKc_DYRK, Catalytic domain of the protein kinase, Dual-specificity tYrosine-phosphorylated and -Regulated Kinase.  Protein Kinases (PKs), Dual-specificity tYrosine-phosphorylated and -Regulated Kinase (DYRK) subfamily, catalytic (c) domain. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. The DYRK subfamily is part of a ...
CDD:271114	330	EUK	Invertebrates:2,Plants:8	cd14212, PKc_YAK1, Catalytic domain of the Dual-specificity protein kinase, YAK1.  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of proteins with similarity to Saccharomyces cerevisiae YAK1 (or Yak1p), a dual-specificity kinase that autophosphorylates at tyrosine residues and phosphorylates substrates on S/T ...
CDD:271128	339	EUK	Invertebrates:14,Primates:1,Vertebrates:3	cd14226, PKc_DYRK1, Catalytic domain of the protein kinase, Dual-specificity tYrosine-phosphorylated and -Regulated Kinase 1.  Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. Mammals contain two types of DYRK1 proteins, DYRK1A and DYRK1B. DYRK1A was previously called minibrain kinase homolog (MNBH) or dual-specificity ...
CDD:260089	78	EUK	Plants:10	cd14231, GAT_GGA_like_plant, GAT domain found in uncharacterized Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like proteins mainly found in plants.  The family includes a group of uncharacterized plant proteins containing an N-terminal VHS (Vps27p/Hrs/STAM)-domain and a GAT (GGA and TOM1) domain. Both domains are also present in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs), which belong to a family of ubiquitously expressed, ...
CDD:260090	78	EUK	Plants:31	cd14232, GAT_LSB5, GAT domain found in yeast LAS seventeen-binding protein 5 (Lsb5p) and similar proteins.  Lsb5p, also termed LAS17-binding protein 5, is a Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like protein located to the plasma membrane in an actin-independent manner. It plays important roles in membrane-trafficking events through association with the actin regulators, the yeast Wiskott-Aldrich syndrome protein (WASP) homologue Las17p and ...
CDD:260091	87	EUK	Invertebrates:20,Primates:1,Vertebrates:2	cd14233, GAT_TOM1_like, GAT domain found in target of myb protein 1 (Tom1) protein family.  Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS (Vps27p/Hrs/STAM)-domain followed by a GAT (GGA and TOM1) domain, both of which are also conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). In contrast to GGAs, the Tom1 family proteins bind to ubiquitin, ubiquitinated ...
CDD:260092	84	EUK	Invertebrates:21,Primates:1	cd14234, GAT_GGA_meta, GAT domain found in metazoan ADP-ribosylation factor (Arf)-binding proteins (GGAs).  GGAs, also termed Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Moreover, GGAs play important roles in ...
CDD:260093	92	EUK	Plants:26	cd14235, GAT_GGA_fungi, GAT domain found in fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs).  GGAs, also termed Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Two GGAs (Gga1p and Gga2p) have been identified in the budding yeast ...
CDD:260131	144	EUKprk	Bacteria:16,Invertebrates:1,Plants:6	cd14241, PAD, Phenolic Acid Decarboxylase.  This family of bacterial and fungal phenolic acid decarboxylases catalyzes the non-oxidative decarboxylation of phenolic acids to produce 4-vinyl derivates. Phenolic acid, like ferulic, p-coumaric, and caffeic acids, are important lignin-related aromatic acids and are natural constituents of plant cell walls. They act as crosslinkers between lignin polymers and hemicellulose/cellulose in ...
CDD:260109	294	PRK	Bacteria:15,Environmental:1	cd14243, PT-AcyF_like, Putative ABBA-type prenyltransferases acting on cyanobactins.  Members of this family are found in gene clusters responsible for the production and posttranslational modification of cyanobactins, small ribosomal cyclic peptides produced by cyanobacteria. The AcyF_like proteins are structurally similar to the ABBA-type aromatic prenyltransferases, and may be responsible for the reverse- and forward-O-prenylation of tyrosine, ...
CDD:271203	298	PRK	Bacteria:43	cd14244, GH_101_like, Endo-a-N-acetylgalactosaminidase and related glcyosyl hydrolases.  This family contains the enzymatically active domain of cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins (EC:3.2.1.97). It has been classified as glycosyl hydrolase family 101 in the Cazy resource. Virulence of pathogenic organisms such as the ...
CDD:271205	60	EUK	Invertebrates:9,Primates:1,Vertebrates:5	cd14246, ADAM17_MPD, Membrane-proximal domain of a disintegrin and metalloprotease 17 (ADAM17).  ADAM17 is a multi-domain protein that acts as a sheddase; is involved in the cleavage and release of the soluble ectodomain of tumor necrosis factor alpha from the cell surface and in the trans-Golgi network, as well as in the release of various other targets such as cytokines and cell adhesion molecules. This links ADAM17 to a variety of ...
CDD:271208	46	EUK	Rodents:3	cd14249, ESP1_like, Exocrine gland-secreting peptide 1 (ESP1) and similar pheromones.  ESP1 is a peptide pheromone found in male mouse tear fluid, which is recognized by a specific G-protein-coupled receptor in the vomeronasal sensory neurons and affects female mouse sexual receptive behaviour. This small family appears restricted to rodents; the functions of members other than mouse ESP1 have not yet been determined.
CDD:271209	55	EUK	Rodents:2	cd14250, ESP36_like, Exocrine gland-secreting peptide 36 (ESP36) and similar pheromones.  ESP36 is a peptide pheromone expressed only in the female mouse extraorbital lacrimal gland. This family also includes the juvenile pheromone ESP22 which is secreted from the lacrimal gland and released into the tears of 2-3 week old mice. ESP22 activates the vomeronasal response pathway, and inhibits male sexual behavior. This small family appears restricted to rodents; the ...
CDD:271210	369	PRK	Bacteria:44	cd14251, PL-6, Polysaccharide Lyase Family 6.  Polysaccharide Lyase Family 6 is a family of beta-helical polysaccharide lyases. Members include alginate lyase (EC 4.2.2.3) and chondroitinase B (EC 4.2.2.19). Chondroitinase B is an enzyme that only cleaves the beta-(1,4)-linkage of dermatan sulfate (DS), leading to 4,5-unsaturated dermatan sulfate disaccharides as the product. DS is a highly sulfated, unbranched polysaccharide belonging to a family of ...
CDD:271211	57	EUKprk	Bacteria:6,Plants:1	cd14252, Dockerin_like, Dockerin repeat domains and domains resembling dockerin repeats.  Dockerins are modules in the cellulosome complex that often anchor catalytic subunits by binding to cohesin domains of scaffolding proteins. Three types of dockerins and their corresponding cohesin have been described in the literature. This alignment models two consecutive dockerin repeats, the functional unit.
CDD:271212	56	PRK	Bacteria:4	cd14253, Dockerin, Dockerin repeat domain.  Dockerins are modules in the cellulosome complex that often anchor catalytic subunits by binding to cohesin domains of scaffolding proteins. Three types of dockerins and their corresponding cohesin have been described in the literature. This alignment models two consecutive dockerin repeats, the functional unit.
CDD:271213	54	PRK	Bacteria:27	cd14254, Dockerin_II, Type II dockerin repeat domain.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and ...
CDD:271214	65	PRK	Bacteria:1	cd14255, Dockerin_III, Type III dockerin repeat domain.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents the atypical type III dockerins and related domains.
CDD:271215	57	EUKprk	Bacteria:38,Invertebrates:1	cd14256, Dockerin_I, Type I dockerin repeat domain.  Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions ...
CDD:271222	106	EUK	Invertebrates:11,Primates:1	cd14259, PUFD_like, PCGF Ub-like fold discriminator and related domains.  The PUFD domain binds the RAWUL (RING finger and WD40-associated ubiquitin-like) domain of the polycomb-group RING finger homologs PCGF1 and PCGF3. PUFD was characterized as a domain of the BCL6 corepressor BCOR. It does not appear to bind to PCGF2 and PCGF4. PCGF1 is a component of the Polycomb group (PcG) multi-protein BCOR complex, which is involved in repressing the ...
CDD:271354	173	PRK	Bacteria:83,Environmental:1	cd14262, VirB5_like, VirB5 protein family.  This family contains VirB5 domains, including TraC, a VirB5 homolog encoded by the pKM101 plasmid, and similar proteins. VirB5 is one of 11 conserved proteins (VirB1-VirB11) in Agrobacterium tumefaciens, the causative agent of crown gall disease, that span the inner and the outer membrane, and is involved in type IV DNA secretion systems (T4SS) which mediate the translocation of virulence factors (proteins ...
CDD:260132	106	EUKprk	Bacteria:81,Environmental:1,Plants:1	cd14263, DAGK_IM_like, Integral membrane diacylglycerol kinase and similar enzymes.  This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of substrates such as diacylglycerol to phosphatidic acid or of undecaprenol to undecaprenyl phosphate. They are not related other cytosolic or membrane-associated kinases, including the eukaryotic ...
CDD:260133	109	EUKprk	Bacteria:162,Environmental:2,Invertebrates:1,Plants:2	cd14264, DAGK_IM, Integral membrane diacylglycerol kinase.  This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Escherichia coli DAGK participates in the membrane-derived oligosaccharide cycle (MDO cycle) by recycling lipids to restore phosphatidylglycerols that were used up in the ...
CDD:260134	106	PRK	Bacteria:234,Environmental:1	cd14265, UDPK_IM_like, Integral membrane undecaprenol kinase and similar enzymes.  This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of undecaprenol to undecaprenyl phosphate. C55-isoprenyl (undecaprenyl) pyroposphate acts as a scaffold for the assembly of peptidoglycan components; undecaprenol kinase (UDPK) is involved in recycling undecaprenyl units ...
CDD:260135	106	PRK	Bacteria:23	cd14266, UDPK_IM_PAP2_like, Integral membrane undecaprenol kinase domain co-occurring with type 2 phosphatidic acid phosphatase-like domains.  This bacterial family of homo-trimeric integral membrane enzyme domains catalyzes the ATP-dependent phosphorylation of of undecaprenol to undecaprenyl phosphate. They sit N-terminally to phosphatase domains that are members of the type 2 phosphatidic acid phosphatase superfamily, and the function of members of this domain ...
CDD:270456	30	EUKprk	Bacteria:1,Invertebrates:64,Plants:85,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd14270, UBA, UBA domain found in proteins involved in ubiquitin-mediated proteolysis.  The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. ...
CDD:270458	38	EUK	Invertebrates:2,Primates:1	cd14272, UBA_AMPK-RKs, UBA domain of AMPK related kinases.  The AMPK-RK family comprises AMP-activated protein kinases (AMPKs), MAP/microtubule affinity-regulating kinases (MARKs), Brain-specific kinases (BRSKs), Salt inducible kinases (SIKs), maternal embryonic leucine zipper kinase (MELK), and SNF-related serine/threonine-protein kinase (SNRK). It is the only kinase family in the human genome containing an ubiquitin-associated (UBA) or UBA-like ...
CDD:270459	31	EUK	Invertebrates:41,Plants:84,Primates:1	cd14273, UBA_TAP-C_like, UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins.  This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 ...
CDD:270461	37	EUKprk	Bacteria:39,Invertebrates:32,Plants:29,Primates:1,Vertebrates:3,nodiv:1	cd14275, UBA_EF-Ts, UBA domain found in elongation factor Ts (EF-Ts) from bacteria, chloroplasts and mitochondria of eukaryotes.  EF-Ts functions as a nucleotide exchange factor in the functional cycle of EF-Tu, another translation elongation factor that facilitates the binding of aminoacylated transfer RNAs (aminoacyl-tRNA) to the ribosomal A site as a ternary complex with guanosine triphosphate during ...
CDD:270463	38	EUK	Invertebrates:20,Primates:1,Vertebrates:3,nodiv:1	cd14277, UBA_UBP2_like, UBA domain found in ubiquitin-associated protein 2 (UBAP-2) like proteins.  The family contains some uncharacterized ubiquitin-associated proteins, including UBAP-2 and its homolog, UBAP2-like [UBP2L, also called protein NICE-4 (for newly identified cDNA from the epidermal differentiation complex EDC)], both of which contain an N-terminal ubiquitin-associated (UBA) domain along with a highly conserved, ...
CDD:270464	37	EUKprk	Bacteria:1,Invertebrates:16,Plants:13,Primates:1	cd14278, UBA_NAC_like, UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins.  The family contains nascent polypeptide-associated complex subunit alpha (NACA), putative NACA-like protein (NACP1), nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD), and similar proteins found in archaea and bacteria. NACA, also called NAC-alpha or ...
CDD:270465	38	EUK	Invertebrates:31,Plants:92,Primates:1,Rodents:1,Vertebrates:1,nodiv:1	cd14279, CUE, CUE domain found in ubiquitin-binding CUE proteins.  This family includes many coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domain containing proteins that are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry ...
CDD:270466	39	EUK	Invertebrates:15,Plants:11,nodiv:1	cd14280, UBA1_Rad23_like, UBA1 domain of Rad23 proteins found in eukaryotes.  The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the ...
CDD:270467	38	EUK	Invertebrates:12,Plants:9	cd14281, UBA2_Rad23_like, UBA2 domain of Rad23 proteins found in eukaryotes.  The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ...
CDD:270477	36	EUK	Invertebrates:14,Plants:7,Vertebrates:5	cd14291, UBA1_NUB1_like, UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins.  NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as ...
CDD:270480	44	EUK	Invertebrates:16,Plants:1,Vertebrates:1	cd14294, UBA1_UBP5_like, UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins.  UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains ...
CDD:270481	45	EUK	Invertebrates:6,Plants:4	cd14295, UBA1_atUBP14, UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins.  atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant ...
CDD:270482	39	EUK	Invertebrates:13,Plants:12	cd14296, UBA1_scUBP14_like, UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins.  scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been ...
CDD:270483	39	EUK	Invertebrates:11,Plants:14	cd14297, UBA2_spUBP14_like, UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins.  spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ...
CDD:270484	38	EUK	Invertebrates:8,Plants:3	cd14298, UBA2_scUBP14_like, UBA2 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins.  scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been ...
CDD:270487	41	EUK	Invertebrates:16,Plants:1,Vertebrates:3	cd14302, UBA_UBXN1, UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins.  UBXN1, also called SAPK substrate protein 1 (SAKS1) or UBA/UBX 33.3 kDa protein, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (UBX) domain. It binds polyubiquitin and valosin-containing protein (VCP), and has been identified as a substrate ...
CDD:270489	39	EUK	Invertebrates:13,Plants:2,Vertebrates:3	cd14304, UBA2_KPC2, UBA2 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins.  KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation ...
CDD:270490	38	EUK	Invertebrates:8,Vertebrates:3,nodiv:1	cd14305, UBA_UBAC2, UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins.  UBAC2, also called phosphoglycerate dehydrogenase-like protein 1, is a ubiquitin-associated domain (UBA)-domain containing protein encoded by gene UBAC2 (or PHGDHL1), a risk gene for Behcet's disease (BD). It may play an important role in the development of BD through its transcriptional modulation. Members in this family ...
CDD:270491	36	EUK	Invertebrates:19,Plants:3,Vertebrates:3,nodiv:1	cd14306, UBA_VP13D, UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins.  VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin ...
CDD:270492	38	EUK	Invertebrates:1,Plants:11	cd14307, UBA_RUP1p, UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins.  RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.
CDD:270494	36	EUK	Invertebrates:5,Plants:22	cd14309, UBA_scDdi1_like, UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins.  Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (UBL) shuttle protein that is required for the proteasome to enable ubiquitin-dependent ...
CDD:270495	30	EUK	Invertebrates:5,Plants:9	cd14310, UBA_cnDdi1_like, UBA domain found in Cryptococcus neoformans DNA-damage response protein Ddi1 and similar proteins.  The family includes some uncharacterized Ddi and similar proteins which show a high level of sequence similarity with yeast Ddi1. Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in yeast. It functions as a ubiquitin association domain (UBA)- ...
CDD:270496	48	EUK	Invertebrates:1,Plants:15,nodiv:1	cd14311, UBA_II_E2_UBC1, UBA domain of yeast ubiquitin-conjugating enzyme E2 1 (UBC1) and similar proteins.  UBC1, also called ubiquitin-conjugating enzyme E2-24 kDa, or ubiquitin-protein ligase, is the yeast homolog of mammalian ubiquitin-conjugating enzyme E2 K (UBE2K or E2-25K). UBC1 and UBE2K are unique class II E2 conjugating enzymes, both of which contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal ...
CDD:270498	36	EUK	Invertebrates:9	cd14313, UBA_II_E2_UBE2K_like, UBA domain found in vertebrate ubiquitin-conjugating enzyme E2 K (UBE2K), Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins.  UBE2K, also called Huntingtin-interacting protein 2 (HIP-2), ubiquitin carrier protein, ubiquitin-conjugating enzyme E2-25 kDa (E2-25K), or ubiquitin-protein ligase, is a multi-ubiquitinating enzyme with the ability to synthesize Lys48-linked polyubiquitin chains ...
CDD:270499	37	EUK	Invertebrates:9,Plants:2	cd14314, UBA_II_E2_pyUCE_like, UBA domain found in a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE) and similar proteins.  P. Yoelii ubiquitin-conjugating enzyme and other uncharacterized family members show high sequence similarity to the human Huntingtin interacting protein-2 (HIP2) which belongs to a class II E2 ubiquitin-conjugating enzyme family. These proteins may play roles in the ubiquitin-mediated protein degradation ...
CDD:270501	37	EUK	Invertebrates:13,Plants:3,Primates:1,Vertebrates:4	cd14316, UBA2_UBAP1_like, UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins.  UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar ...
CDD:270502	38	EUK	Invertebrates:4,Plants:1,Vertebrates:4	cd14317, UBA_DHX57, UBA domain found in putative ATP-dependent RNA helicase DHX57 and similar proteins.  DHX57, also called DEAH box protein 57, is a multi-domain protein with an N-terminal ubiquitin-association (UBA) domain, a Zinc finger domain, a RWD domain, a DEAD-like helicase domain and two C-terminal helicase associated domains. Although the precise biological function of DHX57 remains unclear, it may function as a putative ...
CDD:270504	39	EUK	Invertebrates:17,Plants:9,Vertebrates:2,nodiv:1	cd14319, UBA_NBR1, UBA domain of next to BRCA1 gene 1 protein (NBR1) and similar proteins.  NBR1, also called cell migration-inducing gene 19 protein, membrane component chromosome 17 surface marker 2, neighbor of BRCA1 gene 1 protein, or protein 1A1-3B, is a scaffold protein that may be involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Moreover, NBR1 functions as an ...
CDD:270505	40	EUK	Invertebrates:14,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd14320, UBA_SQSTM, UBA domain of sequestosome-1 (SQSTM) and similar proteins.  SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role ...
CDD:270506	44	EUK	Invertebrates:15,Vertebrates:2	cd14321, UBA_IAPs, UBA domain found in inhibitor of apoptosis proteins (IAPs).  IAPs are frequently overexpressed in cancer and associated with tumor cell survival, chemoresistance, disease progression and poor prognosis. They function primarily as negative regulators of cell death. They regulate caspases and apoptosis through the inhibition of specific members of the caspase family of cysteine proteases. In addition, IAPs has been implicated in a ...
CDD:270512	38	EUK	Invertebrates:3,Plants:10	cd14327, UBA_atUPL1_2_like, UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins.  The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ...
CDD:270513	40	EUK	Invertebrates:8,Primates:1,Vertebrates:4	cd14328, UBA_TNK1, UBA domain found in non-receptor tyrosine-protein kinase TNK1 and similar proteins.  TNK1, also called CD38 negative kinase 1, is a non-receptor protein tyrosine kinase (NRPTK) that has been implicated in the regulation of apoptosis, cell growth, nuclear factor-kappaB, and Ras. It associates with phospholipase C (PLC)-gamma1 and may play a role in phospholipid signal transduction. TNK1 contains an NH2-terminal kinase, ...
CDD:270514	36	EUK	Plants:12	cd14329, UBA_SWA2p_like, UBA domain found in yeast auxilin-like clathrin uncoating factor SWA2 (Swa2p) and similar proteins.  The lineage specific group includes Swa2p and other uncharacterized hypothetical proteins from Saccharomyces. Swa2p, also called bud site selection protein 24, DnaJ-related protein SWA2, or synthetic lethal with ARF1 protein 2, is the yeast auxilin ortholog that is a multifunctional protein with three N-terminal clathrin-binding (CB) motifs, a ...
CDD:270517	45	EUKprk	Bacteria:200,Environmental:5,Invertebrates:1	cd14332, UBA_RuvA_C, C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA.  RuvA, along with RuvB and RuvC proteins, is involved in branch migration of heteroduplex DNA in homologous recombination that is a crucial process for maintaining genomic integrity and generating biological diversity in all living organisms. RuvA has a tetrameric architecture in which each subunit comprised of three distinct ...
CDD:270519	48	EUK	Plants:17	cd14334, UBA_SNF1_fungi, UBA domain of yeast carbon catabolite-derepressing protein kinases (Snf1) and similar proteins found in fungi.  Snf1, also called yeast adenosine monophosphate (AMP)-activated protein kinase (AMPK), is a global regulator of carbon metabolism in the yeast Saccharomyces cerevisiae. Its phosphorylation is essential for the regulation by carbon catabolite repression in eukaryotic cells. Snf1 is involved in the cellular responses to nutrient ...
CDD:270520	41	EUK	Invertebrates:5,Plants:5	cd14335, UBA_SnRK1_plant, UBA domain found in the plant sucrose nonfermenting-1-related kinase (SnRK1) proteins.  The plant SnRK1 proteins (also known as AKIN10/11) family contains plant orthologs of the yeast sucrose non-fermenting (Snf1) kinase and mammalian AMP-activated protein kinase (AMPK), including two catalytic alpha-subunits of plant Snf1-related kinases (SnRKs): SNF1-related protein kinase catalytic subunit alpha KIN10 (also called AKIN10 or ...
CDD:270521	65	EUK	Invertebrates:14,Primates:1,nodiv:1	cd14336, UBA_AID_AMPKalpha, UBA-like autoinhibitory domain (AID) found in vertebrate 5'-AMP-activated protein kinase catalytic alpha (AMPKalpha) subunits.  The family corresponds to the catalytic subunits of adenosine monophosphate (AMP)-activated protein kinase (AMPK) which includes two isoforms encoded by two distinct genes, AMPKalpha-1 (PRKAA1) and AMPKalpha-2 (PRKAA2). Skeletal muscle predominantly expresses the AMPKalpha-2, whereas the ...
CDD:270522	40	EUK	Invertebrates:20,Mammals:2,Primates:1,Rodents:3,Vertebrates:1	cd14337, UBA_MARK_Par1, UBA domain found in microtubule-associated protein (MAP)/microtubule affinity-regulating kinase (MARK)/ partitioning-defective 1 (Par-1) and similar proteins.  The MARK/Par-1 subfamily contains serine/threonine-protein kinases including mammal MARKs, and polarity kinases Par-1 found in Caenorhabditis elegans and Drosophila melanogaster. Those proteins are frequently found associated with ...
CDD:270523	45	EUK	Invertebrates:19,Plants:1,Primates:1,nodiv:1	cd14338, UBA_SIK, UBA domain found in salt-inducible kinase SIK1, SIK2, SIK3 and similar proteins.  Salt-inducible kinase SIK1, SIK2, SIK3 are serine/threonine kinases that belong to the AMP-activated protein kinases (AMPK) family involved in the regulation of metabolism during energy stress. SIK1, also called serine/threonine-protein kinase SNF1-like kinase 1 (SNF1LK), is required for myogenic differentiation. It is degraded by the ...
CDD:270524	48	EUK	Invertebrates:16,Plants:2,Vertebrates:3,nodiv:1	cd14339, UBA_SNRK, UBA domain of SNF-related serine/threonine-protein kinase (SNRK) and similar proteins mainly found in metazoa.  SNRK, also called Sucrose nonfermenting 1 (Snf1)-related kinase, is a serine/threonine kinase highly expressed in the testis. It is a distant member of the largely adenosine monophosphate (AMP)-activated protein kinase (AMPK) family. SNRK can be phosphorylated and activated by LKB1 and may mediate ...
CDD:270525	54	EUK	Invertebrates:8,Vertebrates:2,nodiv:1	cd14340, UBA_BRSK, UBA domain found in serine/threonine-protein kinase BRSK1, BRSK2 and similar proteins.  The family includes brain-specific kinases BRSK1 and BRSK2. They are AMP-activated protein kinase (AMPK)-related kinases that are highly expressed in mammalian forebrain and crucial for establishing neuronal polarity.BRSK1, also called brain-selective kinase 1, brain-specific serine/threonine-protein kinase 1, BR ...
CDD:270526	52	EUK	Invertebrates:12,nodiv:1	cd14341, UBA_MELK, UBA domain found in maternal embryonic leucine zipper kinase (MELK) and similar proteins.  MELK, also called protein kinase Eg3 (pEg3 kinase), protein kinase PK38 (PK38), or tyrosine-protein kinase MELK, is a cell cycle dependent protein kinase involved in diverse cell processes including stem cell renewal, cell cycle progression, cell proliferation, apoptosis and mRNA processing. It is expressed in normal tissues and especially in ...
CDD:270527	51	EUK	Invertebrates:31,Mammals:4,Plants:50,Primates:3,Rodents:2,Vertebrates:4,nodiv:1	cd14342, UBA_TAP-C, UBA-like domain found in nuclear RNA export factor NXF1, NXF2 and similar proteins.  The NXF family of mRNA nuclear export factors including vertebrate NXF1 (also called tip-associated protein or mRNA export factor TAP), NXF2 (also called cancer/testis antigen CT39 or TAP-like protein TAPL-2), Caenorhabditis elegans NXF1 (ceNXF1), Saccharomyces cerevisiae mRNA nuclear export ...
CDD:270530	37	EUK	Invertebrates:11,Plants:2,Vertebrates:2,nodiv:1	cd14345, UBA_UBXD7, UBA-like domain found in UBX domain-containing protein 7 (UBXD7) and similar proteins.  UBXD7, also known as UBXN7, functions as a ubiquitin-binding adaptor that mediates the interaction between the AAA+ ATPase p97 (also known as VCP or Cdc48) and the transcription factor HIF1alpha. It binds only to the active, NEDD8- or Rub1-modified form of cullins. UBXD7 contains the ubiquitin-associated (UBA), ...
CDD:270531	39	EUK	Invertebrates:1,Plants:12	cd14346, UBA_Ubx5_like, UBA-like domain found in Saccharomyces cerevisiae UBX domain-containing protein 5 (Ubx5) and similar proteins.  Ubx5 is a ubiquitin regulatory X (UBX) domain-containing protein encoded by the open reading frame (ORF) YDR330W in yeast. As the yeast ortholog of mammalian UBXD7, Ubx5 functions as the cofactor of AAA+ ATPase p97, also known as VCP or Cdc48. It binds only to the active, NEDD8- or Rub1-modified form of cullins. Ubx5 ...
CDD:270533	40	EUK	Invertebrates:21,Plants:14,Vertebrates:3,nodiv:1	cd14348, UBA_p47, UBA-like domain found in NSFL1 cofactor p47 and similar proteins.  p47, also called UBX domain-containing protein 2C, is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. p47, together with p97, forms the p97-p47 complex that plays an important role in regulation of membrane ...
CDD:270534	41	EUK	Invertebrates:26,Plants:3,Vertebrates:3,nodiv:1	cd14349, UBA_CF106, UBA-like domain found in uncharacterized protein C6orf106 and similar proteins.  The family corresponds to a group of uncharacterized protein C6orf106 and its homologs mainly found in Metazoa. All family members contain a ubiquitin-associated (UBA)-like domain.
CDD:270535	42	EUK	Invertebrates:15,Plants:9,Primates:1,nodiv:1	cd14350, UBA_DCNL, UBA-like domain found in DCN1-like protein DCNL1, DCNL2 and similar proteins.  DCNL1 (defective in cullin neddylation protein 1-like protein 1), also called DCUN1 domain-containing protein 1, is encoded by squamous cell carcinoma-related oncogene SCCRO (DCUN1D1). It interacts with known cullin isoforms as well as ROC1, Ubc12 and CAND1, the components of the neddylation pathway. It plays an essential role in the ...
CDD:270536	37	EUK	Invertebrates:5,Plants:17	cd14351, UBA_Ubx1_like, UBA-like domain found in yeast UBX domain-containing protein 1 (Ubx1) and similar proteins.  Ubx1, also called suppressor of high-copy PP1 protein (Shp1), is the substrate-recruiting cofactor of AAA-adenosine triphosphatase Cdc48 in Saccharomyces cerevisiae. In concert with ubiquitin-like Atg8, Cdc48 and Ubx1 are involved in the regulation of autophagosome biogenesis. Ubx1 also functions as a regulator of phosphoprotein ...
CDD:270537	36	EUK	Invertebrates:5,Plants:7	cd14352, UBA_DCN1, UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins.  DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity. It contains an N-terminal ubiquitin-associated (UBA)-like domain and a unique C-terminal PONY domain that is ...
CDD:270538	32	EUK	Invertebrates:2,Plants:5,Primates:1,nodiv:1	cd14353, UBA_FAF, UBA-like domain found in FAS-associated factor FAF1, FAF2 and similar proteins.  FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and ...
CDD:270541	37	EUK	Invertebrates:17,Plants:19,Primates:1	cd14358, UBA_NAC_euk, UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and its homologs mainly found in eukaryotes.  The subfamily contains nascent polypeptide-associated complex subunit alpha (NACA), putative NACA-like protein (NACP1), nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD), and similar proteins. NACA, also called NAC-alpha or Alpha-NAC, together with ...
CDD:270542	40	PRK	Bacteria:22	cd14359, UBA_AeNAC, UBA-like domain found in archaeal nascent polypeptide-associated complex homolog from Methanothermobacter marburgensis (AeNAC) and similar proteins.  AeNAC is a functional archaeal homolog of eukaryotic nascent polypeptide-associated complex (NAC). Both AeNAC and eukaryotic NAC function as the cytosolic chaperone that can bind to ribosomal RNA, interact with the nascent polypeptide chains as they emerge from the ribosome, and assist in ...
CDD:270543	38	PRK	Bacteria:10	cd14360, UBA_NAC_like_bac, UBA-like domain found in uncharacterized bacteria proteins similar to eukaryotic nascent polypeptide-associated complex proteins (NAC).  This subfamily contains a group of uncharacterized proteins found in bacteria. They all contain an N-terminal ubiquitin-associated (UBA) that shows high sequence similarity with that of eukaryotic nascent polypeptide-associated complex proteins (NAC) which is one of the cytosolic chaperones that contact ...
CDD:270544	41	EUK	Invertebrates:25,Plants:35,Vertebrates:3,nodiv:1	cd14361, UBA_HYPK, UBA-like domain found in Huntingtin-interacting protein K (HYPK) and similar proteins.  HYPK, also called Huntingtin yeast partner K or Huntingtin yeast two-hybrid protein K, is an intrinsically unstructured Huntingtin (HTT)-interacting protein with chaperone-like activity. It is involved in regulating cell growth, cell cycle, unfolded protein response, and cell death. All members in this subfamily contain an ...
CDD:270545	42	EUK	Invertebrates:9,Primates:1,Vertebrates:5	cd14362, CUE_TAB2_TAB3, CUE domain found in the N-terminal of TGF-beta-activated kinase 1 and MAP3K7-binding proteins TAB2, TAB3 and similar proteins.  TAB2, also called mitogen-activated protein kinase kinase kinase 7-interacting protein 2, TAK1-binding protein 2, or TGF-beta-activated kinase 1-binding protein 2, is an adaptor protein that regulates activation of TAK1, a MAP kinase kinase kinase (MAPKKK), through linking TAK1 to TRAF6 ...
CDD:270546	41	EUK	Invertebrates:16,Vertebrates:3	cd14363, CUE_TOLIP, CUE domain found in the C-terminal of toll-interacting protein (Tollip) and similar proteins.  Tollip is a new component of the IL-1RI pathway which contains an N-terminal C2 domain and a C-terminal CUE domain. Tollip binds to the cytoplasmic TIR domain of IL-1Rs after IL-1 stimulation. It is sufficient for recruitment of IRAK to IL-1Rs and negatively regulates IL-1-induced signaling by inhibiting IRAK phosphorylation. In ...
CDD:270547	40	EUK	Invertebrates:30,Plants:30,Vertebrates:3	cd14364, CUE_ASCC2, CUE domain found in activating signal cointegrator 1 complex subunit 2 (ASCC2) and similar proteins.  ASCC2, also called ASC-1 complex subunit p100 or Trip4 complex subunit p100, together with ASCC1 (also called p50) and ASCC3 (also called p300), form the activating signal cointegrator complex (ASCC). ASCC plays an essential role in activating protein 1 (AP-1), serum response factor (SRF), and nuclear factor kappaB ...
CDD:270548	42	EUK	Invertebrates:5,Plants:1,Vertebrates:2	cd14365, CUE_N4BP2, CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins.  N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an ...
CDD:270549	42	EUK	Invertebrates:15,Plants:2,Vertebrates:3	cd14366, CUE_CUED1, CUE domain found in CUE domain-containing protein 1 (CUED1) and similar proteins.  The subfamily includes a group of uncharacterized CUE domain-containing protein termed CUED1. Their biological function remains unknown.
CDD:270550	42	EUK	Invertebrates:11,Mammals:1,Plants:1,Vertebrates:3	cd14367, CUE_CUED2, CUE domain found in CUE domain-containing protein 2 (CUED2) and similar proteins.  CUEDC2 is a novel negative regulator of progesterone receptor (PR) and functions to promote the progesterone-induced PR degradation by the ubiquitin-proteasome pathway. It also acts as the regulator of JAK1/STAT3 signaling through inhibiting cytokine-induced phosphorylation of JAK1 and STAT3 and the subsequent STAT3 ...
CDD:270551	41	EUK	Invertebrates:1,Plants:31	cd14368, CUE_DEF1_like, CUE domain found in fungal RNA polymerase II degradation factor 1 (DEF1) and similar proteins.  DEF1, also called RRM3-interacting protein 1, is a RNA Polymerase II (RNAPII) degradation factor that may be required to couple arrested RNAPII to the proteasome to facilitate its degradation. It contains a CUE domain that is responsible for the binding of ubiquitin. The family also includes many uncharacterized hypothetical proteins. ...
CDD:270552	42	EUK	Invertebrates:1,Plants:18	cd14369, CUE_VPS9_like, CUE domain found in vacuolar protein sorting-associated protein 9 (VPS9) and similar proteins.  VPS9, also called vacuolar protein-targeting protein 9, is a cytosolic yeast protein required for localization of vacuolar proteins, such as the soluble vacuolar hydrolases CPY and PrA. It may bind and act as an effector of a rab GTPase and plays a role in vacuolar protein sorting (VPS) pathway. VPS9 contains a region called GBH ...
CDD:270553	40	EUK	Invertebrates:17,Primates:1,nodiv:1	cd14370, CUE_DMA, CUE-like DMA domain found in the DM domain gene family encodes putative transcription factors DMRTA1, DMRTA2 and DMRTA3.  The DM domain proteins are related to the sexual regulators doublesex from Drosophila melanogaster and MAB-3 from Caenorhabditis elegans. Thus, they have been named as doublesex- and mab-3-related transcription factors and may be involved in sexual development or in somite development. All DM domain ...
CDD:270554	43	EUK	Invertebrates:1,Plants:11	cd14371, CUE_CID7_like, CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins.  CID7 is encoded by ubiquitously expressed gene CID7. It contains an N-terminal PABC-interacting domain (PAM2 or PABP-interacting motif 2) which is also found in the human Paip1 and Paip2. At this point, it functions as an interaction partner of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. It also harbors an ...
CDD:270555	45	EUK	Plants:11	cd14372, CUE_Cue5p_like, CUE domain found in yeast ubiquitin-binding protein CUE5 (Cue5p), donuts protein 1 (DON1p) and similar proteins.  Cue5p, also called coupling of ubiquitin conjugation to ER degradation protein 5, is encoded by the open reading frame (ORF) Yor042. It contains a CUE domain which exhibits weak ubiquitin binding properties. Donuts protein 1 (DON1p) is encoded by the ORF YDR273w. It localizes specifically to the prospore membrane and is expressed ...
CDD:270556	41	EUK	Invertebrates:3,Plants:22	cd14373, CUE_Cue3p_like, CUE domain found in yeast ubiquitin-binding protein CUE3 (Cue3p) and similar proteins.  Cue3p, also called coupling of ubiquitin conjugation to ER degradation protein 3, is encoded by the open reading frame (ORF) YGL110C. It is involved in the intramolecular monoubiquitination that serves as a regulatory signal in a variety of cellular processes in yeast. Cue3p contains a CUE domain.
CDD:270559	37	EUK	Invertebrates:10,Plants:5,Primates:1,nodiv:1	cd14376, CUE_AUP1_AMFR_like, CUE domain found in ancient ubiquitous protein 1 (AUP1), autocrine motility factor receptor (AMFR) and similar proteins.  AUP1 is a component of the HRD1-SEL1L endoplasmic reticulum (ER) quality control complex and is essential for US11-mediated dislocation of class I MHC heavy chains. AMFR is an internalizing cell surface glycoprotein that is localized in both plasma membrane caveolae and the ER, and ...
CDD:270569	43	EUK	Invertebrates:8,Plants:1,Primates:1,Vertebrates:2	cd14386, UBA2_UBP5, UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5).  UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin ...
CDD:270574	36	EUK	Invertebrates:13	cd14391, UBA_II_E2_UBCD4, UBA domain found in Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins.  UbcD4, also called ubiquitin carrier protein or ubiquitin-protein ligase, is a class II E2 ubiquitin-conjugating enzyme encoded by Drosophila E2 gene which is only expressed in pole cells in embryos. It is a putative E2 enzyme homologous to the Huntingtin interacting protein-2 (HIP2) of human. UbcD4 specifically interacts ...
CDD:270582	40	EUK	Invertebrates:21,Plants:12,Primates:1,Rodents:1,Vertebrates:5	cd14399, UBA_PLICs, UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins.  The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 ...
CDD:270583	39	EUK	Invertebrates:4,Plants:9	cd14400, UBA_Gts1p_like, UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins.  Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in ...
CDD:270584	44	EUK	Invertebrates:5,Vertebrates:2	cd14401, UBA_HERC1, UBA domain found in probable E3 ubiquitin-protein ligase HERC1 and similar proteins.  HERC1, also called HECT domain and RCC1-like domain-containing protein 1, or p532, or p619, is an ubiquitously expressed multi-domain protein involved in ubiquitin-dependent intracellular membrane trafficking through its interaction with vesicle coat proteins such as clathrin and ARF. Moreover, it has been identified as a tuberous sclerosis ...
CDD:270585	45	EUK	Invertebrates:9,Vertebrates:3	cd14402, UBA_HERC2, UBA domain found in probable E3 ubiquitin-protein ligase HERC2 and similar proteins.  HERC2, also called HECT domain and RCC1-like domain-containing protein 2, is a SUMO-regulated E3 ubiquitin ligase that plays an important role in the SUMO-dependent pathway which orchestrates the DNA double-strand break (DSB) response. Moreover, HERC2 functions as a RNF8 auxiliary factor that regulates ubiquitin-dependent retention of repair ...
CDD:270596	33	EUK	Invertebrates:13,Vertebrates:3	cd14413, UBA_FAF1, UBA-like domain found in FAS-associated factor 1 (FAF1) and similar proteins.  FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is a multi-functional Fas associating protein that contains an N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains, p150 subunit of a chromatin assembly factor like domain (CAF) and a novel nuclear localization signal (NLS). FAF1 ...
CDD:270600	40	EUK	Invertebrates:5,Vertebrates:4	cd14417, CUE_DMA_DMRTA1, CUE-like DMA domain found in doublesex- and mab-3-related transcription factor A1 (DMRTA1) and similar proteins.  DMRTA1 is encoded by gene DMRT1, a vertebrate equivalent of the Drosophila melanogaster master sex regulator gene, doublesex. In D. melanogaster, doublesex controls the terminal switch of the pathway leading to sex fate choice. DMRT1 may function as regulator of sex differentiation in vertebrate. Especially, it ...
CDD:270603	45	EUK	Invertebrates:15,Vertebrates:3,nodiv:1	cd14420, CUE_AUP1, CUE domain found in ancient ubiquitous protein 1 (AUP1) and similar proteins.  AUP1 is a component of the HRD1-SEL1L endoplasmic reticulum (ER) quality control complex and is essential for US11-mediated dislocation of class I MHC heavy chains. It also binds to the membrane-proximal KVGFFKR motif of the cytoplasmic tail of the integrin alphaCTs that plays a crucial role in the inside-out signaling of alpha(IIb)beta(3). ...
CDD:270604	41	EUK	Invertebrates:15,Plants:2,Primates:1,Vertebrates:3	cd14421, CUE_AMFR, CUE domain found in autocrine motility factor receptor (AMFR) and similar proteins.  AMFR is an internalizing cell surface glycoprotein that is localized in both plasma membrane caveolae and the endoplasmic reticulum (ER), and involves in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. It is also called ER-protein gp78 that has been ...
CDD:270607	37	EUK	Invertebrates:1,Plants:21	cd14424, CUE_Cue1p_like, CUE domain found in yeast ubiquitin-binding protein CUE1 (Cue1p), CUE4 (Cue4p) and similar proteins.  Cue1p, also called coupling of ubiquitin conjugation to ER degradation protein 1 or kinetochore-defect suppressor 4, is encoded by the open reading frame (ORF) YMR264W in yeast. It is an N-terminally membrane-anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ...
CDD:259859	87	PRK	Bacteria:19,Phages:1	cd14435, SPO1_TF1_like, Bacteriophage SPO1-encoded TF1 binds and bends DNA.  This group contains proteins related to bacillus phage SPO1-encoded transcription factor 1 (TF1),  a type II DNA-binding protein related to the DNA sequence specific (IHF) and non-specific (HU) domains. Type II DNA-binding proteins bind and bend DNA as dimers. Like IHF, TF1 binds DNA specifically and bends DNA sharply.  Bacteriophage SPO1-encoded TF1 recognizes SPO1 phage DNA ...
CDD:271228	41	EUK	Invertebrates:28,Mammals:2,Plants:9,Primates:1,Rodents:1,Vertebrates:4,nodiv:1	cd14438, Hip_N, N-terminal dimerization domain of the Hsp70-interacting protein (Hip) and similar proteins.  The Hsc70/Hsp70-interacting protein (Hip, also p48 or suppressor of tumorigenicity ST13) functions as a regulator of the cyclic action of Hsp70. Hip forms homodimers, and this model characterizes the N-terminal dimerization domain, which may not be directly involved in its regulatory function. ...
CDD:270205	316	PRK	Bacteria:10,Environmental:1	cd14439, AlgX_N_like, N-terminal catalytic domain of putative alginate O-acetyltranferase and similar proteins.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles ...
CDD:270206	315	PRK	Bacteria:20,Environmental:1	cd14440, AlgX_N_like_3, Uncharacterized proteins similar to putative alginate O-acetyltransferase.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH ...
CDD:270207	310	PRK	Bacteria:21	cd14441, AlgX_N, N-terminal catalytic domain of the putative alginate O-acetyltranferase AlgX.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. This N-terminal catalytic domain resembles SGNH hydrolases, though with a ...
CDD:270208	321	PRK	Bacteria:19	cd14442, AlgJ_like, putative alginate O-acetyltranferases AlgJ, AlgV, and similar proteins.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a ...
CDD:270210	298	PRK	Bacteria:19	cd14444, AlgX_N_like_1, Uncharacterized proteins similar to putative alginate O-acetyltranferase.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such those as by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with ...
CDD:271220	89	EUK	Invertebrates:13,Mammals:2,Primates:2,Rodents:2,Vertebrates:8	cd14445, RILP-like, Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2).  This domain is found in Rab interacting lysosomal protein-like 1 and 2, and appears to be conserved in Bilateria. The Rilp-like proteins regulate the concentration of ciliary membrane proteins in the primary cilium. Rilpl2 interacts with myosin-Va and has been linked to the regulation of cellular morphology in neurons; it forms a ...
CDD:271219	266	PRK	Bacteria:16,Environmental:2	cd14446, bt3222_like, Uncharacterized proteins similar to Bacteriodes thetaiotaomicron bt3222.  This family appears to be specific to Bacteroidetes; the two-domain protein forms a homodimer.
CDD:269894	143	EUK	Invertebrates:22,Plants:43,Primates:1	cd14447, SPX, Domain found in Syg1, Pho81, XPR1, and related proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). This domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta ...
CDD:259990	144	EUKprk	Bacteria:3,Plants:1	cd14448, CuRO_2_BOD_CotA_like, Cupredoxin domain 2 of Bilirubin oxidase (BOD), the bacterial endospore coat component CotA, and similar proteins.  Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and is required for spore resistance against hydrogen peroxide and UV light. Also ...
CDD:271218	437	EUK	Invertebrates:25,Mammals:1,Plants:1,Primates:1,Vertebrates:4	cd14456, Menin, Scaffolding protein menin encoded by the MEN1 gene.  MEN1 is the gene responsible for multiple endocrine neoplasia type 1, and it has been characterized as a tumor suppressor gene that encodes a protein called menin. Menin is mostly found in the nucleus and can regulate gene expression in a positive and in a negative way, and it has been shown to interact with transcription activators, transcription ...
CDD:271217	105	EUK	Invertebrates:26,Mammals:1,Plants:28,Primates:1,Vertebrates:3	cd14458, DP_DD, Dimerization domain of DP.  DP functions as a binding partner for E2F transcription factors. DP and E2F form heterodimers and play important roles in regulating genes involved in DNA synthesis, cell cycle progression, proliferation and apoptosis. The transcriptional activity of E2F is inhibited by the retinoblastoma protein (Rb) which binds to the E2F-DP heterodimer, blocks the transactivation ...
CDD:271216	99	EUK	Invertebrates:19,Plants:5,Primates:1,Rodents:1,Vertebrates:5,nodiv:1	cd14473, FERM_B-lobe, FERM domain B-lobe.  The FERM domain has a cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The ...
CDD:269895	144	EUK	Plants:57	cd14474, SPX_YDR089W, SPX domain of the yeast protein YDR089W and related proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The uncharacterized yeast protein YDR089W has not been shown to be involved in phosphate homeostasis, in contrast to most of the other SPX-domain containing proteins.
CDD:269896	139	EUK	Invertebrates:1,Plants:64	cd14475, SPX_SYG1_like, SPX domain of the yeast plasma protein Syg1 and related proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1, the N-terminus binds directly to the G-protein beta subunit and inhibits transduction of the mating pheromone signal, and it co-occurs with a C-terminal domain from the EXS family.
CDD:269897	139	EUK	Plants:10	cd14476, SPX_PHO1_like, SPX domain of the plant protein PHOSPHATE1 (PHO1).  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The PHO1 gene family conserved in plants is involved in a variety of processes, most notably the transport of inorganic phosphate from the root to the shoot of the plant and mediating the response to low levels of inorganic phosphate. More recently it has ...
CDD:269898	161	EUK	Invertebrates:20,Mammals:1,Vertebrates:5,nodiv:1	cd14477, SPX_XPR1_like, SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-terminus of the human XPR1 protein (xenotropic and polytropic retrovirus receptor 1) binds directly to the beta subunit of the G-protein heterotrimer leading to ...
CDD:269899	148	EUK	Plants:113	cd14478, SPX_PHO87_PHO90_like, SPX domain of the phosphate transporters Pho87, Pho90, Pho91, and related proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The SPX domain of the Saccharomyces cerevisiae membrane-localized low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the ...
CDD:269900	140	EUK	Plants:20	cd14479, SPX-MFS_plant, SPX domain of proteins found in plants and stramenopiles; most have a C-terminal MFS domain.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The SPX domain is found at the amino terminus of a variety of proteins. This family, mostly found in plants, contains a C-terminal MFS domain (major facilitator superfamily), suggesting a function as a secondary transporter. The function of this N-terminal region is unclear, ...
CDD:269901	135	EUK	Plants:103	cd14480, SPX_VTC2_like, SPX domain of the vacuolar transport chaperone Vtc2 and similar proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. Vtc2 is part of the Saccharomyces cerevisiae membrane-integral VTC complex, together with Vtc1, Vtc3, and Vtc4. It contains an N-terminal SPX domain next to a central polyphosphate polymerase domain and a C-terminal domain of ...
CDD:269902	149	EUK	Plants:18	cd14481, SPX_AtSPX1_like, SPX domain of the plant protein SPX1 and similar proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. This family of plant proteins contains a single SPX domain. Arabidopsis thaliana SPX1 and SPX3 have been reported to play roles in the adaptation to low-phosphate conditions, SPX3 may be involved in the regulation of SPX1 activity. Oryza sativa ...
CDD:269903	156	EUK	Plants:12	cd14482, SPX_BAH1-like, SPX domain of the E3 ubiquitin-protein ligase BAH1/NLA and similar proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. BAH1 (benzoic acid hypersensitive 1) appears to function as an E3 ubiquitin ligase; the protein contains an SPX and a RING finger domain. It has been suggested that BAH1/NLA is involved in the regulation of plant immune ...
CDD:269904	162	EUK	Invertebrates:1,Plants:40	cd14483, SPX_PHO81_NUC-2_like, SPX domain of Pho81, NUC-2, and similar proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this ...
CDD:269905	134	EUK	Plants:59	cd14484, SPX_GDE1_like, SPX domain of Gde1 and similar proteins.  This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The yeast protein Gde1/Ypl110c ...
CDD:270618	159	EUKprk	Bacteria:139,Environmental:7,Plants:1,nodiv:2	cd14485, mltA_like_LT_A, Domain A of MltA and related lytic transglycosylase; domain A is interrupted by domain B.  Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is ...
CDD:270619	104	EUKprk	Bacteria:15,Invertebrates:1	cd14486, 3D_domain, 3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic transglycosylases and numerous other contexts.  This family contains the 3D domain, named for its 3 conserved aspartates. It is found in conjunction with numerous other domains such as MltA (membrane-bound lytic murein transglycosylase A).  These aspartates are critical active site residues of mltA-like lytic transglycosylases. Escherichia coli ...
CDD:271153	128	PRK	Bacteria:7	cd14487, AlgX_C, C-terminal carbohydrate-binding domain of the alginate O-acetyltranferase AlgX.  The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. This N-terminal catalytic domain resembles SGNH hydrolases, though with a ...
CDD:271154	132	EUKprk	Bacteria:12,Environmental:1,Invertebrates:1	cd14488, CBM6-CBM35-CBM36_like_2, uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily.  Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate ...
CDD:271155	150	PRK	Bacteria:8	cd14489, CBM_SBP_bac_1_like, Putative Carbohydrate Binding Module (CBM) of extracellular solute-binding protein family 1.  Domains in this family co-occur with extracellular solute-binding domains which are periplasmic components of ABC-type sugar transport systems involved in carbohydrate transport and metabolism. Carbohydrate binding modules of family 6 (CBM6), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36) are ...
CDD:271156	156	PRK	Bacteria:10	cd14490, CBM6-CBM35-CBM36_like_1, uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily.  Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, ...
CDD:271237	24	EUK	Plants:33	cd14653, ZIP_Gal4p-like, Leucine zipper Dimerization domain of Gal4p-like transcription factors.  The Gal4p family of transcriptional activators contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Included in ...
CDD:271238	47	EUKprk	Plants:38,Synthetic:1	cd14654, ZIP_Gal4, Leucine zipper Dimerization domain of transcription factor Gal4 and similar fungal proteins.  Gal4p is one of several GAL proteins required for the growth of yeast on galactose; GAL proteins are responsible for the transport of galactose into the cell and for its metabolism through the glycolytic pathway. Gal4p functions in the induction of GAL genes in the presence of galactose through an upstream activating sequence (UAS) present in ...
CDD:271239	32	EUK	Plants:5	cd14655, ZIP_Hap1, Leucine zipper Dimerization domain of transcription factor Hap1 and similar fungal proteins.  Hap1p mediates oxygen sensing and heme signaling in yeast. In response to heme, it promotes transcription of genes required for respiration and controlling oxidative damage. It is a member of the Gal4/Gal4p family of transcriptional activators which contain an N-terminal DNA binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and ...
CDD:271139	239	EUKprk	Bacteria:122,Invertebrates:1	cd14656, Imelysin-like_EfeO, EfeO is a component of the EfeUOB operon.  This family includes the EfeO domain, an essential component of the EfeUOB operon which is highly conserved in bacteria. However, its biochemical function is unknown. EfeO contains an N-terminal cupredoxin (CUP)-like domain and C-terminal imelysin-like domain that may bind iron. Algp7, a member of EfeO family protein from Sphingomonas sp. A1, is found to bind alginate at ...
CDD:271140	345	PRK	Bacteria:44	cd14657, Imelysin_IrpA-like, Imelysin-like iron-regulated protein A-like.  This family includes putative iron-regulated protein A (IrpA) mainly from Bacteriodes, proteobacteria and cyanobacteria, as well as uncharacterized proteins with domains similar to insulin-cleaving membrane protease (imelysin, ICMP) protein. IrpA has been shown to be essential for growth under iron-deficient conditions in the cyanobacteria Synechococcus sp. The conserved GxHxxE motif is ...
CDD:271141	282	PRK	Bacteria:44,Environmental:9	cd14658, Imelysin-like_IrpA, Imelysin-like domain in iron-regulated protein A.  This family includes putative iron-regulated protein A (IrpA) mainly from Bacteriodes, proteobacteria and cyanobacteria, with domain similar to insulin-cleaving membrane protease (imelysin, ICMP) protein. It has been shown to be essential for growth under iron-deficient conditions in the cyanobacteria Synechococcus sp. The conserved GxHxxE motif is similar to other known ...
CDD:271142	331	PRK	Bacteria:189,Environmental:3,nodiv:1	cd14659, Imelysin-like_IPPA, Imelysin-like protein.  This family includes insulin-cleaving membrane protease (imelysin, ICMP)-like protein (IPPA from Psychrobacter arcticus), the Pseudomonas aeruginosa PA4372 and Vibrio cholera VC1266 Fur-regulated imelysin-like protein. They share the overall fold and a similar functional site as the insulin-cleaving membrane protease (ICMP). However, IPPA adopts a structure distinctive from the known HxxE ...
CDD:271137	104	EUK	Invertebrates:29,Mammals:2,Plants:27,Primates:1,Rodents:2,Vertebrates:11,nodiv:1	cd14660, E2F_DD, Dimerization domain of E2F transcription factors.  E2F transcription factors are involved in the regulation of DNA synthesis, cell cycle progression, proliferation and apoptosis. It associates with the retinoblastoma (Rb) protein, negatively regulating the G1-S transition until cyclin-dependent kinases phosphorylate Rb, which causes E2F release. E2F forms heterodimers with DP, a ...
CDD:271136	347	PRK	Bacteria:8,Environmental:3	cd14661, Imelysin_like_PIBO, Permuted imelysin-like protein from Bacteroides ovatus (PIBO) and similar proteins.  This family includes imelysin-like proteins such as imelysin-like protein from gut bacteria Bacteroides ovatus (PIBO) that have a circularly permuted topology compared with the canonical imelysin fold, such that the N-terminal and C-terminal regions are swapped in the primary sequence. PIBO is highly similar to imelysin-like protein from ...
CDD:270620	90	EUKprk	Bacteria:129,Environmental:33,Plants:4	cd14667, 3D_containing_proteins, Non-mltA associated 3D domain containing proteins, named for 3 conserved aspartate residues.  This family contains the 3D domain, named for its 3 conserved aspartates, including similar uncharacterized proteins. These proteins contain the critical active site aspartate of mltA-like lytic transglycosylases where the 3D domain forms a larger domain with the N-terminal region. This domain is also found in ...
CDD:270616	159	EUKprk	Bacteria:61,Environmental:4,Plants:1	cd14668, mlta_B, Domain B insert of mltA_like lytic transglycosylases.  Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is ...
CDD:270614	128	PRK	Bacteria:21	cd14670, BslA_like, Bacterial immunoglobulin-like hydrophobin BslA and similar proteins.  BslA (YuaB) is a protein from Bacillus subtilis acting as a hydrophobin, which forms surface layers around biofilms and participates in biofilm assembly. BslA contains an unusually hydrophobic "cap structure", which is essential for its activity and for the ability of bacteria to form hydrophobic, non-wetting biofilms. A number of domains in various proteins from Bacilli and ...
CDD:269821	77	PRK	Bacteria:32	cd14671, PAAR_like, proline-alanine-alanine-arginine (PAAR) repeat superfamily.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat superfamily, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey ...
CDD:270612	37	EUK	Invertebrates:9	cd14672, UBA_ceTYDP2_like, UBA-like domain found in Caenorhabditis elegans tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins.  The family includes C. elegans TDP2 and its homologs found in bilateria. TDP2 (also known as TTRAP or EAPII) belongs to the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. It required for the efficient repair of ...
CDD:270194	115	EUK	Invertebrates:19,Primates:1,Rodents:1,Vertebrates:7,nodiv:1	cd14675, PH-SEC3_like, PH-like domain of Sec3-like protein.  Fungal Sec3, as well as its homolog in higher eukaryotes Exocyst complex component 1 (EXOC1) are part of the exocyst is a conserved octameric complex involved in the docking of post-Golgi transport vesicles to sites of membrane remodeling during cellular processes such as polarization, migration, and division. PH domains have diverse functions, but in ...
CDD:270202	117	miss	miss	cd14683, PH-EXOC1, PH-like domain of Exocyst complex component 1.  Exocyst complex component 1 (EXOC1, also known as SEC3) is the higher eukaryotes homolog of yeast Sec3. The Exocyst is a conserved octameric complex involved in the docking of post-Golgi transport vesicles to sites of membrane remodeling during cellular processes such as polarization, migration, and division. PH domains have diverse functions, but in general are involved in targeting proteins to the ...
CDD:269834	52	EUKprk	Bacteria:2,Invertebrates:42,Mammals:1,Plants:110,Primates:1,Rodents:3,Vertebrates:2,Viruses:1,nodiv:1	cd14686, bZIP, Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain.  Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning ...
CDD:269835	61	EUK	Invertebrates:11,Plants:77,Vertebrates:1,nodiv:1	cd14687, bZIP_ATF2, Basic leucine zipper (bZIP) domain of Activating Transcription Factor-2 (ATF-2) and similar proteins: a DNA-binding and dimerization domain.  ATF-2 is a sequence-specific DNA-binding protein that belongs to the Basic leucine zipper (bZIP) family of transcription factors. In response to stress, it activates a variety of genes including cyclin A, cyclin D, and c-Jun. ATF-2 also plays a role in the DNA damage ...
CDD:269836	63	EUK	Plants:162	cd14688, bZIP_YAP, Basic leucine zipper (bZIP) domain of Yeast Activator Protein (YAP) and similar proteins: a DNA-binding and dimerization domain.  This subfamily is composed predominantly of AP-1-like transcription factors including Saccharomyces cerevisiae YAPs, Schizosaccharomyces pombe PAP1, and similar proteins. Members of this subfamily belong to the Basic leucine zipper (bZIP) family of transcription factors. The YAP subfamily is composed of eight members ...
CDD:269837	61	EUK	Invertebrates:22,Primates:1,Vertebrates:5	cd14689, bZIP_CREB3, Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 3 (CREB3) and similar proteins: a DNA-binding and dimerization domain.  This subfamily is composed of CREB3 (also called LZIP or Luman), and the CREB3-like proteins CREB3L1 (or OASIS), CREB3L2, CREB3L3 (or CREBH), and CREB3L4 (or AIbZIP). They are type II membrane-associated members of the Basic leucine zipper (bZIP) family of ...
CDD:269838	55	EUK	Invertebrates:15,Plants:7,Rodents:1,Vertebrates:4	cd14690, bZIP_CREB1, Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 1 (CREB1) and similar proteins: a DNA-binding and dimerization domain.  CREB1 is a Basic leucine zipper (bZIP) transcription factor that plays a role in propagating signals initiated by receptor activation through the induction of cAMP-responsive genes. Because it responds to many signal transduction pathways, CREB1 is ...
CDD:269839	58	EUK	Invertebrates:29,Plants:5,Vertebrates:2	cd14691, bZIP_XBP1, Basic leucine zipper (bZIP) domain of X-box binding protein 1 (XBP1) and similar proteins: a DNA-binding and dimerization domain.  XBP1, a member of the Basic leucine zipper (bZIP) family, is the key transcription factor that orchestrates the unfolded protein response (UPR). It is the most conserved component of the UPR and is critical for cell fate determination in response to ER stress. The inositol-requiring enzyme ...
CDD:269840	63	EUK	Invertebrates:20,Mammals:1,Plants:1,Vertebrates:3	cd14692, bZIP_ATF4, Basic leucine zipper (bZIP) domain of Activating Transcription Factor-4 (ATF-4) and similar proteins: a DNA-binding and dimerization domain.  ATF-4 was also isolated and characterized as the cAMP-response element binding protein 2 (CREB2). It is a Basic leucine zipper (bZIP) transcription factor that has been reported to act as both an activator or repressor. It is a critical component in both the unfolded ...
CDD:269841	60	EUK	Invertebrates:20,Primates:1,Vertebrates:2,nodiv:1	cd14693, bZIP_CEBP, Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein (CEBP) and similar proteins: a DNA-binding and dimerization domain.  CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate the cell cycle, differentiation, growth, survival, energy metabolism, innate and adaptive immunity, and inflammation, among others. They are also associated with cancer and viral disease. ...
CDD:269842	60	EUK	Invertebrates:9,Primates:1,Vertebrates:3	cd14694, bZIP_NFIL3, Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain.  NFIL3, also called E4 promoter-binding protein 4 (E4BP4), is a Basic leucine zipper (bZIP) transcription factor that was independently identified as a transactivator of the IL3 promoter in T-cells and as a transcriptional repressor that binds to a DNA sequence site in the adenovirus E4 ...
CDD:269843	60	EUK	Invertebrates:19,Vertebrates:2	cd14695, bZIP_HLF, Basic leucine zipper (bZIP) domain of Hepatic leukemia factor (HLF) and similar proteins: a DNA-binding and dimerization domain.  HLF, also called vitellogenin gene-binding protein (VBP) in birds, is a circadian clock-controlled Basic leucine zipper (bZIP) transcription factor which is a direct transcriptional target of CLOCK/BMAL1. It is implicated, together with bZIPs DBP and TEF, in the regulation of genes involved in the ...
CDD:269844	61	EUK	Invertebrates:19,Primates:1,Vertebrates:4,nodiv:1	cd14696, bZIP_Jun, Basic leucine zipper (bZIP) domain of Jun proteins and similar proteins: a DNA-binding and dimerization domain.  Jun is a member of the activator protein-1 (AP-1) complex, which is mainly composed of Basic leucine zipper (bZIP) dimers of the Jun and Fos families, and to a lesser extent, the activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial ...
CDD:269845	70	EUK	Invertebrates:7,Rodents:1	cd14697, bZIP_Maf, Basic leucine zipper (bZIP) domain of musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain.  Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two ...
CDD:269846	68	EUK	Invertebrates:12,Mammals:1	cd14698, bZIP_CNC, Basic leucine zipper (bZIP) domain of Cap'n'Collar (CNC) transcription factors: a DNA-binding and dimerization domain.  CNC proteins form a subfamily of Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. This subfamily includes Drosophila Cnc and four vertebrate counterparts, NFE2 (nuclear factor, ...
CDD:269847	59	EUK	Invertebrates:11,Primates:1	cd14699, bZIP_Fos_like, Basic leucine zipper (bZIP) domain of the oncogene Fos (Fos)-like transcription factors: a DNA-binding and dimerization domain.  This subfamily is composed of Fos proteins (c-Fos, FosB, Fos-related antigen 1 (Fra-1), and Fra-2), Activating Transcription Factor-3 (ATF-3), and similar proteins. Fos proteins are members of the activator protein-1 (AP-1) complex, which is mainly composed of bZIP dimers of the Jun and Fos families, ...
CDD:269848	52	EUK	Invertebrates:15,Vertebrates:3	cd14700, bZIP_ATF6, Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain.  ATF-6 is a type I membrane-bound Basic leucine zipper (bZIP) transcription factor that binds to the consensus ER stress response element (ERSE) and enhances the transcription of genes encoding glucose-regulated proteins Grp78, Grp94, and calreticulum. ATF-6 is one of three sensors of the ...
CDD:269850	52	EUK	Plants:36	cd14702, bZIP_plant_GBF1, Basic leucine zipper (bZIP) domain of Plant G-box binding factor 1 (GBF1)-like transcription factors: a DNA-binding and dimerization domain.  This subfamily is composed of plant bZIP transciption factors including Arabidopsis thaliana G-box binding factor 1 (GBF1), Zea mays Opaque-2 and Ocs element-binding factor 1 (OCSBF-1), Triticum aestivum Histone-specific transcription factor HBP1 (or HBP-1a), Petroselinum crispum Light-inducible protein ...
CDD:269851	52	EUK	Plants:23	cd14703, bZIP_plant_RF2, Basic leucine zipper (bZIP) domain of Plant RF2-like transcription factors: a DNA-binding and dimerization domain.  This subfamily is composed of plant bZIP transciption factors with similarity to Oryza sativa RF2a and RF2b, which are important for plant development. They interact with, as homodimers or heterodimers with each other, and activate transcription from the RTBV (rice tungro bacilliform virus) promoter, which is regulated by ...
CDD:269852	52	EUK	Invertebrates:5,Plants:13	cd14704, bZIP_HY5-like, Basic leucine zipper (bZIP) domain of Plant Elongated/Long Hypocotyl5 (HY5)-like transcription factors and similar proteins: a DNA-binding and dimerization domain.  This subfamily is predominantly composed of plant Basic leucine zipper (bZIP) transcription factors with similarity to Solanum lycopersicum and Arabidopsis thaliana HY5. Also included are the Dictyostelium discoideum bZIP transcription factors E and F. HY5 plays an ...
CDD:269853	55	EUK	Invertebrates:3,Plants:37	cd14705, bZIP_Zip1, Basic leucine zipper (bZIP) domain of Fungal Zip1-like transcription factors: a DNA-binding and dimerization domain.  This subfamily is composed of fungal bZIP transcription factors including Schizosaccharomyces pombe Zip1, Saccharomyces cerevisiae Methionine-requiring protein 28 (Met28p), and Neurospora crassa cys-3, among others. Zip1 is required for the production of key proteins involved in sulfur metabolism and also plays a ...
CDD:269854	54	EUK	Invertebrates:13,Vertebrates:1	cd14706, bZIP_CREBZF, Basic leucine zipper (bZIP) domain of CREBZF/Zhangfei transcription factor and similar proteins: a DNA-binding and dimerization domain.  CREBZF (also called Zhangfei, ZF, LAZip, or SMILE) is a neuronal bZIP transcription factor that is involved in the infection cycle of herpes simplex virus (HSV) and related cellular processes. It suppresses the ability of the HSV transactivator VP16 to initiate the viral replicative cycle. ...
CDD:269855	55	EUK	Plants:25	cd14707, bZIP_plant_BZIP46, Basic leucine zipper (bZIP) domain of uncharaterized Plant BZIP transcription factors: a DNA-binding and dimerization domain.  This subfamily is composed of uncharacterized plant bZIP transciption factors with similarity to Glycine max BZIP46, which may be a drought-responsive gene. Plant bZIPs are involved in developmental and physiological processes in response to stimuli/stresses such as light, hormones, and temperature changes. bZIP ...
CDD:269857	56	EUK	Invertebrates:8,Plants:2,Vertebrates:3	cd14709, bZIP_CREBL2, Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein-like 2 (CREBL2): a DNA-binding and dimerization domain.  CREBL2 is a bZIP transcription factor that interacts with CREB and plays a critical role in adipogenesis and lipogenesis. Its overexpression upregulates the expression of PPARgamma and CEBPalpha to promote adipogenesis as well as accelerate lipogenesis by increasing GLUT1 and ...
CDD:269858	53	EUK	Plants:22	cd14710, bZIP_HAC1-like, Basic leucine zipper (bZIP) domain of Fungal HAC1-like transcription factors: a DNA-binding and dimerization domain.  HAC1 (also called Hac1p or HacA) is a bZIP transcription factor that plays a critical role in the unfolded protein response (UPR). The UPR is initiated by the ER-resident protein kinase and endonuclease IRE1, which promotes non-conventional splicing of the HAC1 mRNA, facilitating its translation. HAC1 binds to and activates ...
CDD:269865	70	EUK	Invertebrates:8,Mammals:1,Primates:1,Rodents:2,Vertebrates:5	cd14717, bZIP_Maf_small, Basic leucine zipper (bZIP) domain of small musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain.  Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, ...
CDD:269866	70	EUK	Invertebrates:9,Primates:1,Rodents:1,Vertebrates:5	cd14718, bZIP_Maf_large, Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain.  Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among ...
CDD:269868	68	EUK	Primates:1,Vertebrates:7	cd14720, bZIP_NFE2-like, Basic leucine zipper (bZIP) domain of Nuclear Factor, Erythroid-derived 2 (NFE2) and similar proteins: a DNA-binding and dimerization domain.  This subfamily is composed of NFE2 and NFE2-like proteins including NFE2-like 1 or NFE2-related factor 1 (NFE2L1 or Nrf1), NFE2L2 (or Nrf2), and NFE2L3 (or Nrf3). These are Cap'n'Collar (CNC) Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid ...
CDD:269869	62	EUK	Invertebrates:11,Vertebrates:3	cd14721, bZIP_Fos, Basic leucine zipper (bZIP) domain of the oncogene Fos (Fos): a DNA-binding and dimerization domain.  Fos proteins are members of the activator protein-1 (AP-1) complex, which is mainly composed of Basic leucine zipper (bZIP) dimers of the Jun and Fos families, and to a lesser extent, the activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial possibilities for various ...
CDD:271240	25	EUK	Plants:18	cd14723, ZIP_Ppr1, Leucine zipper Dimerization coil of Ppr1-like transcription factors.  Ppr1/Ppr1p activates transcription of the URA1, URA3, and URA4 genes, which encode enzymes involved in the regulation of pyrimidine levels. Also included in this subfamily is Colletotrichum acutatum Nir1 which plays a role during nitrogen-starvation conditions. Proteins in this subfamily are members of the Gal4p family of transcriptional activators which contain an N-terminal ...
CDD:271241	24	EUK	Plants:9	cd14724, ZIP_Gal4-like_1, Leucine zipper Dimerization domain of Gal4-like transcription factors.  The Gal4p family of transcriptional activators contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Gal4p family ...
CDD:269830	509	EUKprk	Bacteria:16,Plants:4	cd14730, LodA_like, L-lysine epsilon-oxidase from Marinomonas mediterranea and similar proteins.  L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is also called marinocine, ...
CDD:269831	587	PRK	Bacteria:34,nodiv:1	cd14731, LodA_like_1, Uncharacterized proteins similar to L-lysine epsilon-oxidase from Marinomonas mediterranea.  L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is known for ...
CDD:269832	639	PRK	Bacteria:26	cd14732, LodA, L-lysine epsilon-oxidase from Marinomonas mediterranea and similar proteins.  L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is also called marinocine, for its ...
CDD:269807	63	EUK	Invertebrates:22,Plants:6,Primates:1,Vertebrates:3	cd14734, SPOP_C, BACK-like Domain C-terminal to BTB in speckle-type POZ protein (SPOP) and similar proteins.  SPOP is an adaptor protein that forms a complex with Cul3, a cullin-3 E3 ubiquitin ligase, and is involved in ubiquitination of BMI1, H2AFY, and the death-associated protein 6 (DAXX). The C-terminal BACK_like domain of SPOP, characterized  by this model, may be involved in oligomer formation and in recruiting Cul3 ...
CDD:269808	59	EUKprk	Invertebrates:31,Mammals:5,Plants:4,Primates:2,Rodents:4,Vertebrates:11,Viruses:1	cd14735, BACK_Kelch, BTB-And-C-terminal-Kelch (BACK) domain of Kelch-like proteins.  This domain is found in architectures C-terminal to a BTB domain and N-terminal to a Kelch domain, in Kelch, Ectoderm-neural cortex protein 1 and 2 (Enc1 and Enc2), cytosolic inhibitor of Nrf2 (INrf2), Kainate receptor-interacting protein for GluR6 (KRIP6), the cytoskeletal BTB/Kelch repeat family gigaxonin, ...
CDD:269809	64	EUK	Plants:17	cd14736, SPOP_C_like_plant, BACK-like Domain C-terminal to BTB in plant proteins similar to speckle-type POZ protein (SPOP).  SPOP is an adaptor protein that forms a complex with Cul3, a cullin-3 E3 ubiquitin ligase, and is involved in ubiquitination of BMI1, H2AFY, and the death-associated protein 6 (DAXX). The C-terminal BACK_like domain of SPOP may be involved in oligomer formation and in recruiting Cul3 (together with the adjacent BTB domain), whereas the ...
CDD:269822	94	PRK	Bacteria:30,Phages:2	cd14737, PAAR_1, proline-alanine-alanine-arginine (PAAR) domain.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The ...
CDD:269823	94	PRK	Bacteria:29	cd14738, PAAR_2, proline-alanine-alanine-arginine (PAAR) domain.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip ...
CDD:269824	90	PRK	Bacteria:12	cd14739, PAAR_3, proline-alanine-alanine-arginine (PAAR) domain.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip ...
CDD:269825	121	PRK	Bacteria:27	cd14740, PAAR_4, proline-alanine-alanine-arginine (PAAR) domain.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as ...
CDD:269826	95	PRK	Bacteria:12	cd14741, PAAR_5, proline-alanine-alanine-arginine (PAAR) domain.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family in bacteria as well as some archaea, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as ...
CDD:269827	86	PRK	Bacteria:32	cd14742, PAAR_RHS, proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement hotspot (Rhs) extensions.  This PAAR (proline-alanine-alanine-arginine) repeat subfamily, which forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS), contains C- and N-terminal domain extensions. These include Rearrangement hotspot (Rhs) protein repeats and conserved Rhs ...
CDD:269828	78	PRK	Bacteria:19	cd14743, PAAR_CT_1, proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Some members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs ...
CDD:269829	78	PRK	Bacteria:161,Environmental:2	cd14744, PAAR_CT_2, proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension.  This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several ...
CDD:270613	331	PRK	Bacteria:40,Environmental:5	cd14745, GH66, Glycoside Hydrolase Family 66.  Glycoside Hydrolase Family 66 contains proteins characterized as cycloisomaltooligosaccharide glucanotransferase (CITase) and dextranases from a variety of bacteria. CITase cyclizes part of a (1-6)-alpha-D-glucan (dextrans) chain by formation of a (1-6)-alpha-D-glucosidic bond. Dextranases catalyze the endohydrolysis of (1-6)-alpha-D-glucosidic linkages in dextran. Some members contain Carbohydrate ...
CDD:270450	386	PRK	Bacteria:25	cd14747, PBP2_MalE, Maltose-binding protein MalE; possesses type 2 periplasmic binding fold.  This group includes the periplasmic maltose-binding component of an ABC transport system from the phytopathogen Xanthomonas citri and its related bacterial proteins. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between ...
CDD:270451	385	PRK	Bacteria:89	cd14748, PBP2_UgpB, The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold.  This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding ...
CDD:270452	388	PRK	Bacteria:16	cd14749, PBP2_XBP1_like, The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold.  This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two ...
CDD:270453	385	PRK	Bacteria:32	cd14750, PBP2_TMBP, The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold.  This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge ...
CDD:270454	376	PRK	Bacteria:10	cd14751, PBP2_GacH, The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; possesses type 2 periplasmic binding fold.  This group represents the periplasmic component GacH of an ABC import system. GacH is identified as a maltose/maltodextrin-binding protein with a low affinity for acarbose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains ...
CDD:270212	122	EUKprk	Bacteria:189,Environmental:28,Invertebrates:33,Plants:44,Vertebrates:2,nodiv:2	cd14752, GH31_N, N-terminal domain of glycosyl hydrolase family 31 (GH31).  This family is found N-terminal to the glycosyl-hydrolase domain of Glycoside hydrolase family 31 (GH31). GH31 includes the glycoside hydrolases alpha-glucosidase (EC 3.2.1.20), alpha-1,3-glucosidase (EC 3.2.1.84), alpha-xylosidase (EC 3.2.1.177), sucrase-isomaltase (EC 3.2.1.48 and EC 3.2.1.10), as well as alpha-glucan ...
CDD:271288	132	PRK	Bacteria:11	cd14755, GS_BA2291-HK_like, Non-heme globin sensor domain of BA2291 histidine kinase and related domains.  This subfamily includes the sensor domain of Bacillus anthracis BA2291 histidine kinase. BA2291 is one of the most active kinases in promoting sporulation, and is found in most members of the Bacillus cereus subfamily of the genus Bacillae, which includes B. anthracis and Bacillus thuringiensis, but not Bacillus subtilis. This subfamily also includes two ...
CDD:271289	111	miss	miss	cd14756, TrHb, Truncated Mb-fold globins, T family.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed ...
CDD:271290	151	PRK	Bacteria:41	cd14757, GS_EcDosC-like_GGDEF, Globin sensor domain of Escherichia coli Direct Oxygen Sensing Cyclase and related proteins; coupled to a C-terminal GGDEF domain.  Globin-coupled-sensors belonging to this subfamily have a C-terminal diguanylate cyclase (DGC/GGDEF) domain coupled to the globin sensor domain. DGC/GGDEF likely functions as a c-di-GMP cyclase in the synthesis of the second messenger cyclic-di-GMP (c-di-GMP). Members include Escherichia coli DosC (also ...
CDD:271291	148	PRK	Bacteria:11,Environmental:1	cd14758, GS_GGDEF_1, Globin sensor domain, coupled to DGC/GGDEF domains; uncharacterized subgroup.  Globin-coupled-sensors belonging to this subfamily have a sensor domain coupled to a C-terminal diguanylate cyclase (DGC/GGDEF) domain. DGC/GGDEF likely functions as a c-di-GMP cyclase in the synthesis of the second messenger cyclic-di-GMP (c-di-GMP).
CDD:271292	150	PRK	Bacteria:15	cd14759, GS_GGDEF_2, Globin sensor domain, coupled to DGC/GGDEF domains; uncharacterized subgroup.  The majority of globin-coupled-sensors in this subfamily have diguanylate cyclase (DGC/GGDEF) domains N-terminal to the globin sensor domain and/or C-terminal EAL domains, DGC/GGDEF and EAL domains are involved in the synthesis and degradation of the secondary messenger c-di-GMP, respectively. Some members have GAF small-molecule-binding domains in addition.
CDD:271294	149	PRK	Bacteria:16	cd14761, GS_GsGCS_like, Globin sensor domain of Geobacter sulfurreducens globin-coupled-sensor and related proteins.  GsGCS is a GCS of unknown function, comprised of an N-terminal globin sensor domain and a C- terminal transmembrane signal-transduction domain. For GCSs in general, the first signal O2 binds to/dissociates from the heme iron complex inducing a structural change in the globin domain, which is then transduced to the functional domain, switching on (or ...
CDD:271295	143	PRK	Bacteria:6	cd14762, GS_STAS, Globin sensor domain; coupled to a STAS domain.  Globin-coupled-sensors in this subfamily have a C-terminal sulphate transporter and anti-sigma factor antagonist (STAT) domain coupled to the globin sensor domain.
CDD:271296	142	PRK	Bacteria:10	cd14763, SSDgbs_1, Sensor single-domain globins; uncharacterized bacterial subgroup.  This subfamily of sensor single-domain globins, belongs to a family that includes GCSs (globin-coupled-sensors) and single-domain protoglobins (Pgbs). For GCSs, an N-terminal heme-bound oxygen-sensing/binding globin domain is coupled to a C-terminal functional/signaling domain. The first signal O2 binds to/dissociates from the heme in its sensor domain inducing a conformational ...
CDD:271297	145	PRK	Bacteria:6	cd14764, SSDgbs_2, Sensor single-domain globins; uncharacterized subgroup.  This subfamily of sensor single-domain globins, belongs to a family that includes GCSs (globin-coupled-sensors) and single-domain protoglobins (Pgbs). For GCSs, an N-terminal heme-bound oxygen-sensing/binding globin domain is coupled to a C-terminal functional/signaling domain. The first signal O2 binds to/dissociates from the heme in its sensor domain inducing a conformational change in ...
CDD:271298	134	miss	miss	cd14765, Hb, Hemoglobins.  Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors ...
CDD:271299	136	EUK	Invertebrates:7	cd14766, CeGLB25_like, Caenorhabditis elegans globin GLB-25, and related globins.  The C. elegans genome contains 33 genes encoding globins that are all transcribed. These are very diverse in gene and protein structure and are localized in a variety of cells. The C. elegans globin GLB-25 (locus tag T06A1.3), like the majority of them, was expressed in neuronal cells in the head and tail portions of the body and in the nerve cord.
CDD:271304	119	PRK	Bacteria:17	cd14771, TrHb2_Mt-trHbO-like_O, Truncated hemoglobins, group 2 (O); Mycobacterium tuberculosis hemoglobin O like.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications ...
CDD:271305	116	PRK	Bacteria:12	cd14772, TrHb2_Bs-trHb-like_O, Truncated hemoglobins, group 2 (O); Bacillus subtilis TrHb like.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical ...
CDD:271306	119	PRK	Bacteria:82,Environmental:1	cd14773, TrHb2_PhHbO-like_O, Truncated hemoglobins, group 2 (O); Pseudoalteromonas haloplanktis PhHbO like.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex ...
CDD:271307	118	PRK	Bacteria:17	cd14774, TrHb2_O_1, Truncated hemoglobins, group 2 (O); uncharacterized subgroup.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 ...
CDD:271308	119	PRK	Bacteria:30	cd14775, TrHb2_O_2, Truncated hemoglobins, group 2 (O); uncharacterized subgroup.  The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 ...
CDD:271310	140	EUKprk	Bacteria:10,Plants:1	cd14777, Yhb1-globin_like, Globin domain of Saccharomyces cerevisiae flavohemoglobin (Yhb1p) and related domains.  FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect ...
CDD:271315	143	EUKprk	Bacteria:9,Plants:1	cd14782, FHb-globin_2, Globin domain of flavohemoglobins (flavoHbs); uncharacterized subgroup.  FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress ...
CDD:270211	368	EUK	Invertebrates:41,Mammals:1,Plants:52,Rodents:1,Vertebrates:4	cd14785, V-ATPase_C, Subunit C of vacuolar H+-ATPase (V-ATPase).  This family contains subunit C of vacuolar H+-ATPase (V-ATPase), a protein that plays a crucial role in the vacuolar system of eukaryotic cells. The main function of V-ATPase is to generate a proton-motive force at the expense of ATP and to cause limited acidification in the internal space (lumen) of several organelles of the vacuolar system. V-ATPases ...
CDD:269892	299	EUKprk	Bacteria:198,Environmental:27,Invertebrates:2,Plants:10	cd14791, GH36, glycosyl hydrolase family 36 (GH36).  GH36 enzymes occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-galactosidase, alpha-N-acetylgalactosaminidase, stachyose synthase, and raffinose synthase. All GH36 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch ...
CDD:269893	271	EUKprk	Bacteria:72,Environmental:10,Invertebrates:27,Plants:41,Primates:1,Vertebrates:3	cd14792, GH27, glycosyl hydrolase family 27 (GH27).  GH27 enzymes occur in eukaryotes, prokaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-N-acetylgalactosaminidase, and 3-alpha-isomalto-dextranase. All GH27 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, ...
CDD:269817	90	PRK	Bacteria:12	cd14794, RNLA_N_1, N-terminal repeat domain of toxin RnlA; first out of two repeats.  The Escherichia coli toxin RnlA functions as an mRNA endoribonuclease and is part of a two-component toxin-antitoxin system that promotes resistance to phage infections, together with the antitoxin RnlB. RNAse activity is located in the C-terminal domain. This N-terminal domain appears to participate in homodimerization and is the first out of two repeats.
CDD:269818	87	PRK	Bacteria:1	cd14795, RNLA_N_2, N-terminal repeat domain of toxin RnlA; second out of two repeats.  The Escherichia coli toxin RnlA functions as an mRNA endoribonuclease and is part of a two-component toxin-antitoxin system that promotes resistance to phage infections, together with the antitoxin RnlB. RNAse activity is located in the C-terminal domain. This N-terminal domain appears to participate in homodimerization and is the second out of two repeats.
CDD:269819	66	PRK	Bacteria:34,Environmental:2	cd14796, RNAse_HIII_N, N-terminal domain of ribonuclease H3.  RNAse H3 (HIII) is a bacterial type 2 ribonuclease, which endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, and plays a role in DNA replication and repair. The N-terminal domain characterized by this model has been shown to be important in substrate binding; it might form initial contacts with the substrate ...
CDD:269820	124	EUKprk	Bacteria:380,Environmental:9,Invertebrates:1,Plants:3,nodiv:1	cd14797, DUF302, Uncharacterized domain family DUF302.  These domains are mostly found in bacterial single-domain proteins and have been shown to form homodimers; they may also bind zinc. Also characterized as COG3439.
CDD:271353	124	EUK	Plants:29	cd14798, RX-CC_like, Coiled-coil domain of the potato virux X resistance protein and similar proteins.  The potato virus X resistance protein (RX) confers resistance against potato virus X. It is a member of a family of resistance proteins with a domain architecture that includes an N-terminal coiled-coil domain (modeled here), a nucleotide-binding domain, and leucine-rich repeats (CC-NB-LRR). These intracellular resistance proteins recognize pathogen effector ...
CDD:271351	122	PRK	Bacteria:14	cd14804, Tra_M, TraM mediates signalling between transferosome and relaxosome.  TraM is a plasmid encoded DNA-binding protein that is essential for conjugative transfer of F-like plasmids (e.g. F, R1, R100 and pED208) between bacterial cells. Bacterial conjugation, a form of horizontal gene transfer between cells, is an important contributor to bacterial genetic diversity, enabling virulence and antibiotics resistance factors to rapidly spread in medically ...
CDD:269813	71	EUK	Invertebrates:7,Mammals:2,Primates:1,Vertebrates:3	cd14806, RAP_D1, Receptor-associated protein (RAP), Domain 1.  This subfamily is the N-terminal domain (D1) of receptor-associated protein, RAP, an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. D1 as well as domain 2 (D2) are essential for blocking low-density ...
CDD:269815	100	EUK	Invertebrates:10,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	cd14808, RAP_D3, C-terminal receptor-associated protein (RAP), Domain 3.  This subfamily is the C-terminal domain (D3) of receptor-associated protein, RAP, an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. D3 is required for folding and trafficking of ...
CDD:269871	52	EUKprk	Invertebrates:1,Plants:12,Viruses:1	cd14809, bZIP_AUREO-like, Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains.  AUREO is a BL-activated transcription factor specific to phototrophic stramenopiles. It has a bZIP and a BL-sensing light-oxygen voltage (LOV) domain. It has been shown to mediate BL-induced branching and regulate the development of the sex organ in Vaucheria frigida. bZIP factors act in networks of homo ...
CDD:269872	52	EUK	Invertebrates:1,Plants:17	cd14810, bZIP_u1, Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily.  Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer ...
CDD:269873	52	EUK	Invertebrates:4,Plants:6	cd14811, bZIP_u2, Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily.  Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer ...
CDD:269874	52	EUK	Plants:22	cd14812, bZIP_u3, Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily.  Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among ...
CDD:269875	52	EUK	Invertebrates:9	cd14813, bZIP_BmCbz-like, Basic leucine zipper (bZIP) domain of Bombyx mori chorion b-ZIP transcription factor and similar bZIP domains.  Bombyx mori chorion b-ZIP transcription factor, is encoded by the Cbz gene. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a ...
CDD:271352	145	PRK	Bacteria:8	cd14815, BA_2398_like, Putative Bacillus anthracis lipoprotein and related proteins.  Uncharacterized protein family found in Bacilli and Gammaproteobacteria.
CDD:271349	206	EUK	Invertebrates:25,Plants:47,Primates:1,Rodents:1,Vertebrates:3	cd14819, Translin, Translin, also known as TB-RBP (testis brain RNA-binding protein).  Translin (also known as TB-RBP for Testis Brain RNA-binding protein, a mouse ortholog), is a paralog of its binding partner protein TRAX (translin-associated factor-X) and together they form oligomeric complexes known as C3PO proteins (for component 3 promoter of  RNA-induced silencing complex or RISC).  DNA damage has been ...
CDD:271350	182	EUKprk	Bacteria:58,Environmental:4,Invertebrates:30,Plants:45,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	cd14820, TRAX, Translin-associated factor-X (TRAX).  TRAX (translin-associated factor-X) is a paralog of its binding partner protein Translin and together they form oligomeric complexes known as C3PO proteins (for component 3 promoter of  RNA-induced silencing complex or RISC). TRAX complexed with Translin is possibly involved in dendritic RNA processing and in DNA ...
CDD:269810	61	EUK	Invertebrates:33,Plants:19,Primates:1,Rodents:1,Vertebrates:6	cd14821, SPOP_C_like, BACK-like Domain C-terminal to BTB in speckle-type POZ protein (SPOP) and similar proteins.  SPOP is an adaptor protein that forms a complex with Cul3, a cullin-3 E3 ubiquitin ligase, and is involved in ubiquitination of BMI1, H2AFY, and the death-associated protein 6 (DAXX). The C-terminal BACK_like domain of SPOP, characterized  by this model, may be involved in oligomer formation and in ...
CDD:269811	59	EUK	Invertebrates:18,Rodents:1,Vertebrates:3	cd14822, BACK_BTBD9_like, BACK-like Domain C-terminal to BTB in BTB/POZ domain-containing protein 9 and similar proteins.  BTBD9 contains BTB/POZ, BACK, and two Coagulation factor 5/8 C-terminal (FA58C) domains. Single-nucleotide polymorphisms in the BTBD9 gene have been associated with a higher risk of Restless Legs Syndrome (RLS), a sensory-motor neurological disorder with a circadian component. BTBD9 may be involved in regulating ...
CDD:271246	185	EUKprk	Bacteria:7,Environmental:2,Invertebrates:22,Mammals:1,Plants:13,Vertebrates:3	cd14867, uS7_Eukaryote, Eukaryota homolog of Ribosomal Protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Eukaryotic RPS7 (also named RPS5) have variable N-terminal regions that affect the efficiency of initiation translation process by impacting small ...
CDD:271247	151	EUK	Plants:46	cd14868, uS7_Mitochondria_Fungi, Fungal Mitochondrial homolog of Ribosomal Protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Fungal and plants mitochondrial RPS7 shows less homology to the mammalian than to bacterial RPS7. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a ...
CDD:271248	138	EUKprk	Bacteria:58,Environmental:4,Invertebrates:2,Plants:4	cd14869, uS7_Bacteria, Bacterial homolog of Ribosomal Protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Prokaryotic RPS7 is lacking the variable N-terminal region of eukaryotic RPS7. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a ...
CDD:271249	199	EUK	Invertebrates:22,Primates:1,Vertebrates:2	cd14870, uS7_Mitochondria_Mammalian, Mammalian Mitochondrial homolog of Ribosomal Protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. MRPS7 shows more homology to bacterial RPS7 than mitochondrial proteins from plants and fungi. The ribosome small subunit is one of the two subunits of ribosome ...
CDD:271250	146	EUK	Plants:12	cd14871, uS7_Chloroplast, Chloroplast homolog of Ribosomal Protein S7.  Chloroplast RPS7 has both general and specific regulatory roles in chloroplast translation process. uS7, also known as Ribosomal protein (RP)S7, is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The chloroplasts of plants and algae have bacterial ancestry, but it has adopted novel mechanisms in order to execute its roles within a eukaryotic cell. Chloroplast ...
CDD:271345	155	EUK	Invertebrates:36,Plants:25,Primates:1,Rodents:2,Vertebrates:3	cd14942, TRAPPC3_bet3, Bet3-TRAPPC3 subunit of the TRAPP complex.  Bet3 (also known as TRAPPC3) subunit of the trafficking protein particle complex (TRAPP). Bet3 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi  and intra-Golgi transport by tethering the vesicle membrane to the target membrane. TRAPPC3 has also been shown to be additionally important for ...
CDD:271346	158	EUK	Invertebrates:31,Plants:38,Primates:1,Vertebrates:3	cd14943, TRAPPC5_Trs31, Trs31 subunit of the TRAPP complex.  TRS31 (also known as TRAPPC5) subunit of the trafficking protein particle complex (TRAPP). TRS31 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi  and intra-Golgi transport by tethering the vesicle membrane to the target membrane.
CDD:271347	167	EUK	Invertebrates:35,Plants:54,Primates:1,Rodents:2,Vertebrates:4	cd14944, TRAPPC6A_Trs33, Trs33 subunit of the TRAPP complex.  TRS33 (also known as TRAPPC6A) subunit of the trafficking protein particle complex (TRAPP). TRS33 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi  and intra-Golgi transport by tethering the vesicle membrane to the target membrane. In mammals, mutations in TRAPPC6a cause mosaic loss of coat pigment.
CDD:271253	288	EUK	Plants:4,Primates:1,Vertebrates:2	cd14945, Myo5-like_CBD, Cargo binding domain of myosin 5 and similar proteins.  Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5 a,b,c) in vertebrates and two (myo2 and myo4) in fungi and related to plant class XI myosins. Their C-terminal cargo binding domains is important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. MyoV-CBDs interact with ...
CDD:271343	112	EUKprk	Bacteria:32,Environmental:2,Invertebrates:18,Plants:87,Primates:1,Rodents:1,Vertebrates:8	cd14947, NBR1_like, Functionally uncharacterized domain in neighbor of Brca1 Gene 1 and related proteins.  NBR1 has been characterized as a specific late endosomal protein, which might play a role in receptor (RTK) trafficking. Specifically, NBR1 was shown to inhibit ligand-mediated receptor internalization from the cell surface. The region covered by this domain model may be involved ...
CDD:271342	83	PRK	Bacteria:211,Environmental:61	cd14948, BACON, Bacteroidetes-Associated Carbohydrate-binding (putative) Often N-terminal (BACON) domain.  The BACON domain is found in diverse domain architectures and accociated with a wide variety of domains, including carbohydrate-active enzymes and proteases. It was named for its suggested function of carbohydrate binding; the latter was inferred from domain architectures, sequence conservation, and phyletic distribution. However, recent ...
CDD:271340	280	PRK	Bacteria:23	cd14949, Asparaginase_2_like_3, Uncharacterized bacterial subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family.  The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and  L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor ...
CDD:271341	251	PRK	Bacteria:26,Environmental:1	cd14950, Asparaginase_2_like_2, Uncharacterized archaebacterial subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family.  The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and  L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and ...
CDD:271321	334	EUKprk	Bacteria:50,Invertebrates:10,Mammals:1,Plants:15,Rodents:2,Vertebrates:7,nodiv:1	cd14951, NHL-2_like, NHL repeat domain of NHL repeat-containing protein 2 and similar proteins.  NHL repeat-containing protein 2 (NHLRC2) and related bacterial proteins; members of this eukaryotic and bacterial family are uncharacterized, the NHL repeat domain is found C-terminally of a thioredoxin domain. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as ...
CDD:271322	247	PRK	Bacteria:21	cd14952, NHL_PKND_like, NHL repeat domain of the protein kinase PknD.  PknD is a mycobacterial transmembrane protein with a cytosolic kinase domain and an extracellular sensor domain that contains NHL repeats. It plays a key role in the development of central nervous system tuberculosis, by mediating the invasion of host brain endothelia. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues ...
CDD:271323	323	PRK	Bacteria:50	cd14953, NHL_like_1, Uncharacterized NHL-repeat domain in bacterial proteins.  This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271324	285	EUKprk	Bacteria:1,Invertebrates:14,Primates:1,Vertebrates:3,nodiv:1	cd14954, NHL_TRIM71_like, NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins.  The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. ...
CDD:271325	279	PRK	Bacteria:14	cd14955, NHL_like_4, Uncharacterized NHL-repeat domain in bacterial and archaeal proteins.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271326	274	PRK	Bacteria:13	cd14956, NHL_like_3, Uncharacterized NHL-repeat domain in bacterial proteins.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271327	280	PRK	Bacteria:5	cd14957, NHL_like_2, Uncharacterized NHL-repeat domain in bacterial and archaeal proteins.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271328	300	EUKprk	Bacteria:30,Invertebrates:20,Mammals:2,Plants:1,Rodents:1,Vertebrates:7	cd14958, NHL_PAL_like, Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5).  PAL catalyzes the N-dealkylation of peptidyl-alpha-hydroxyglycine, which results in an alpha-amidated peptide and glyoxylate. Amidation of the C-terminus is required for the activity of many peptide hormones and neuropeptides. The catalytic residues of PAL are located on several NHL-repeats. The NHL (NCL-1, ...
CDD:271329	274	EUK	Invertebrates:12	cd14959, NHL_brat_like, NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins.  Drosophila brain-tumor (brat) has been identified as a tumor suppressor that negatively regulates cell proliferation during development of the Drosophila larval brain. It appears to be recruited to the 3'-untranslated region of hunchback RNA and regulates its translation by forming a complex with Pumilio (Pum) and Nanos (Nos). The NHL domain of brat ...
CDD:271330	274	EUK	Invertebrates:5,Mammals:2,Rodents:1,Vertebrates:7	cd14960, NHL_TRIM2_like, NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins.  The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L ...
CDD:271331	273	EUK	Invertebrates:4,Mammals:3,Rodents:2,Vertebrates:11	cd14961, NHL_TRIM32_like, NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins.  The E3 ubiquitin-protein ligase TRIM32 (HT2A) is widely expressed and is responsible for ubiquinating a large variety of targets, including dysbindin (DTNBP1), NPHP7/Glis2, TAp73, and others. TRIM32 promotes disassociation of the plakoglobin-PI3K complex and reduces PI3K-Akt-FoxO signaling. Mutations in ...
CDD:271332	271	PRK	Bacteria:14	cd14962, NHL_like_6, Uncharacterized NHL-repeat domain in bacterial proteins.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271333	268	PRK	Bacteria:6	cd14963, NHL_like_5, Uncharacterized NHL-repeat domain in bacterial proteins.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.
CDD:271319	148	EUKprk	Bacteria:364,Environmental:21,Invertebrates:44,Phages:20,Plants:126,Viruses:6	cd15457, NADAR, Escherichia coli swarming motility protein YbiA and related proteins.  This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been ...
CDD:271230	391	PRK	Viruses:7	cd15464, HN_like, Haemagglutinin-neuraminidase (HN) of paramyxoviridae and similar proteins.  Most paramyxoviridae have two membrane-anchored glycoproteins that mediate entry of the virus into the host cell. The protein characterized by this model is called hemagglutinin-neuraminidase (HN), hemagglutinin glycoprotein (H), or glycoprotein (G). Typically it has a variety of functions during viral infection; it participates in virus attachment to host cells, may cleave ...
CDD:271318	159	EUK	Invertebrates:30,Plants:51,Primates:1,Vertebrates:4	cd15466, CLU-central, An uncharacterized central domain of CLU mitochondrial proteins.  Mutations in the mitochondrial CLU proteins have been shown to result in clustered mitochondria. CLU proteins include Saccharomyces cerevisiae clustered mitochondria protein (Clu1p, alias translation initiation factor 31/TIF31p), Dictyostelium discoideum clustered mitochondria protein homolog (CluA), Caenorhabditis elegans clustered ...
CDD:271233	408	PRK	Viruses:27	cd15469, HN, Hemagglutinin-neuraminidase (HN) of parainfluenza virus 5, Newcastle disease virus, and related paramyxoviridiae.  The hemagglutinin-neuraminidase (HN) found in this family of viruses has a variety of functions during viral infection; it participates in virus attachment to host cells, cleaves sialic acid off host oligosaccharides, and has a stimulating effect on membrane fusion during the entry of the virus into the host cell. This model characterizes ...
CDD:271254	332	EUK	Invertebrates:16,Primates:1,Rodents:1,Vertebrates:12	cd15470, Myo5_CBD, Cargo binding domain of myosin 5.  Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5a,b,c) in vertebrates.  Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. The MyoV-CBDs directly interact with several adaptor proteins, in case of Myo5a, melanophilin ...
CDD:271255	322	EUK	Invertebrates:14,Vertebrates:6	cd15471, Myo5p-like_CBD_afadin, cargo binding domain of myosin 5-like of afadin.  Afadin is an actin filament (F-actin) and Rap1 small G protein-binding protein, found in cadherin-based adherens junctions in epithelial cells, endothelial cells, and fibroblasts. It interacts with cell adhesion molecules and signaling molecules and plays a role in the formation of cell junctions, cell polarization, migration, survival, proliferation, and ...
CDD:271256	366	EUK	Invertebrates:2,Mammals:4,Primates:1,Rodents:1,Vertebrates:11	cd15472, Myo5p-like_CBD_Rasip1, cargo binding domain of myosin 5-like of Ras-interacting protein 1.  Ras-interacting protein 1 (Rasip1 or RAIN) is an effector of the small G protein Rap1 and plays an important role in endothelial junction stabilization. Rasip1, like afadin, is a multi domain protein, that contains beside a myosin5-like CBD, a Ras-associated domain and a PDZ domain.
CDD:271257	316	EUK	Plants:53	cd15473, Myo5p-like_CBD_DIL_ANK, cargo binding domain of myosin 5-like of dil and ankyrin domain containing protein.  DIL and ankyrin domain-containing protein are a group of fungal proteins that contain a domain homologous to the cargo binding domain of class V myosins and ankyrin repeats. Their function is unknown.
CDD:271258	352	EUK	Plants:5	cd15474, Myo5p-like_CBD_fungal, cargo binding domain of fungal myosin V -like proteins.  Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V  myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. In case of Myo4 it has been shown to bind to the adapter protein She3p (Swi5p-dependent HO expression 3), ...
CDD:271259	326	EUK	Plants:20	cd15475, MyosinXI_CBD, cargo binding domain of myosin XI.  Class XI myosins are a plant specific group, homologous to class V myosins.  C-terminal domain of Arabidopsis myosin XI has been shown to be homologous  to the cargo-binding domain of yeast myosin V myo2p, which targets myosin to vacuole- and mitochondria, as well as secretory vesicle.
CDD:271264	363	EUK	Plants:39	cd15480, fMyo2p_CBD, cargo binding domain of fungal myosin 2.  Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V  myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. Myo 2 binds to Vac17,  vacuole-specific cargo adaptor, and Mmr1, mitochondria-specific cargo adaptor. Both adaptors bind competitivly ...
CDD:271252	195	EUK	Invertebrates:18,Plants:48,Primates:1,Vertebrates:1	cd15481, SRP68-RBD, RNA-binding domain of signal recognition particle subunit 68.  Signal recognition particles (SRPs) are ribonucleoprotein complexes that target particular nascent pre-secretory proteins to the endoplasmic reticulum. SRP68 is one of the two largest proteins found in SRPs (the other being SRP72), and it forms a heterodimer with SRP72. Heterodimer formation is essential for SRP function. This model ...
CDD:271234	339	EUKprk	Bacteria:193,Environmental:30,Invertebrates:16,Mammals:1,Phages:1,Plants:8,Primates:1,Vertebrates:7	cd15482, Sialidase_non-viral, Non-viral sialidases.  Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates, they play vital roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold with the non-viral sialidases containing 2-5 Asp-box motifs (most commonly ...
CDD:271251	147	EUK	Plants:9	cd15484, uS7_plant, plant ribosomal protein S7.  uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, ...
CDD:271243	27	EUK	Plants:7	cd15485, ZIP_Cat8, Leucine zipper Dimerization domain of transcription factor Cat8 and similar proteins.  Cat8p binds to carbon source-responsive element (CSRE) motifs and activates target genes under conditions of glucose deprivation. It mediates the transcriptional control of at least nine genes (ACS1, FBP1, ICL1, IDP2, JEN1, MLS1, PCK1, SFC1, and SIP4) under non-fermentative growth conditions in yeast. Studies show another 25 genes or open reading frames whose ...
CDD:249497	251	EUKprk	Invertebrates:3,Mammals:2,Primates:1,Rodents:5,Vertebrates:1,Viruses:2	pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).  This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The ...
CDD:249498	239	EUK	Invertebrates:3,Mammals:2,Primates:1,Rodents:2,Vertebrates:3	pfam00002, 7tm_2, 7 transmembrane receptor (Secretin family).  This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognized. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are ...
CDD:249499	238	EUK	Invertebrates:9,Mammals:1,Primates:2,Rodents:2,Vertebrates:8	pfam00003, 7tm_3, 7 transmembrane sweet-taste receptor of 3 GCPR.  This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to ...
CDD:249500	131	EUKprk	Bacteria:32,Invertebrates:8,Phages:2,Plants:15,Primates:1,Rodents:3,Vertebrates:1	pfam00004, AAA, ATPase family associated with various cellular activities (AAA).  AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
CDD:249501	150	EUKprk	Bacteria:7,Mammals:1,Plants:3,Rodents:1	pfam00005, ABC_tran, ABC transporter.  ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong ...
CDD:249502	213	EUKprk	Bacteria:107,Invertebrates:8,Plants:7	pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain.  This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.
CDD:109076	105	EUK	Mammals:2,Primates:2,Rodents:2,Vertebrates:3	pfam00007, Cys_knot, Cystine-knot domain.  The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins. It is believed to be involved in disulfide-linked dimerization.
CDD:249503	32	EUKprk	Invertebrates:4,Mammals:1,Primates:1,Rodents:1,Vertebrates:1,Viruses:1	pfam00008, EGF, EGF-like domain.  There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar ...
CDD:249504	185	EUKprk	Bacteria:50,Invertebrates:11,Plants:19,Primates:1,Rodents:2	pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain.  This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
CDD:249505	52	EUKprk	Invertebrates:11,Plants:7,Primates:1,Rodents:4,Vertebrates:4,Viruses:1,nodiv:1	pfam00010, HLH, Helix-loop-helix DNA-binding domain.  
CDD:249506	101	EUKprk	Bacteria:2,Invertebrates:3,Plants:10,Primates:1,Vertebrates:3	pfam00011, HSP20, Hsp20/alpha crystallin family.  
CDD:249507	598	EUKprk	Bacteria:8,Invertebrates:6,Plants:8,Primates:1	pfam00012, HSP70, Hsp70 protein.  Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
CDD:249508	60	EUKprk	Bacteria:74,Invertebrates:10,Mammals:1,Plants:10,Primates:1,Rodents:3,Vertebrates:2	pfam00013, KH_1, KH domain.  KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
CDD:249509	53	EUK	Invertebrates:9,Mammals:4,Primates:1,Rodents:2,Vertebrates:9	pfam00014, Kunitz_BPTI, Kunitz/Bovine pancreatic trypsin inhibitor domain.  Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP). This is a highly selective inhibitor of factor Xa in the blood ...
CDD:249510	213	PRK	Bacteria:1,nodiv:1	pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP) signalling domain.  This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.
CDD:249511	77	EUKprk	Invertebrates:2,Mammals:3,Plants:1,Primates:1,Rodents:2,Vertebrates:1,Viruses:2	pfam00017, SH2, SH2 domain.  
CDD:249512	48	EUK	Invertebrates:2,Mammals:1,Plants:3,Primates:1,Rodents:1	pfam00018, SH3_1, SH3 domain.  SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
CDD:249513	105	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	pfam00019, TGF_beta, Transforming growth factor beta like domain.  
CDD:249514	39	EUKprk	Primates:1,Rodents:2,Viruses:2	pfam00020, TNFR_c6, TNFR/NGFR cysteine-rich region.  
CDD:249515	77	EUK	Mammals:1,Primates:1,Rodents:3	pfam00021, UPAR_LY6, u-PAR/Ly-6 domain.  This extracellular disulphide bond rich domain is related to pfam00087.
CDD:249516	367	EUK	Invertebrates:7,Mammals:2,Plants:11	pfam00022, Actin, Actin.  
CDD:249517	33	EUKprk	Bacteria:12,Invertebrates:11,Mammals:3,Plants:12,Primates:1,Rodents:2,Vertebrates:4,Viruses:12	pfam00023, Ank, Ankyrin repeat.  Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, ...
CDD:249518	77	EUK	Invertebrates:7,Mammals:2,Plants:2,Primates:1,Rodents:2,Vertebrates:3	pfam00024, PAN_1, PAN domain.  The PAN domain contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.
CDD:249519	174	EUK	Invertebrates:3,Plants:4,Primates:1,Rodents:2	pfam00025, Arf, ADP-ribosylation factor family.  Pfam combines a number of different Prosite families together.
CDD:249520	316	EUK	Invertebrates:1,Mammals:2,Plants:9,Primates:2,Rodents:2,Vertebrates:1	pfam00026, Asp, Eukaryotic aspartyl protease.  Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
CDD:249521	91	EUKprk	Bacteria:98,Invertebrates:14,Plants:17,Primates:2,Rodents:2,Vertebrates:1,nodiv:1	pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.  
CDD:249522	92	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:1	pfam00028, Cadherin, Cadherin domain.  
CDD:143818	107	EUK	Invertebrates:2,Mammals:2,Primates:2,Rodents:2,Vertebrates:6	pfam00029, Connexin, Connexin.  
CDD:249523	82	EUKprk	Bacteria:8,Mammals:5,Primates:2,Rodents:3,Vertebrates:10	pfam00030, Crystall, Beta/Gamma crystallin.  The alignment comprises two Greek key motifs since the similarity between them is very low.
CDD:249524	92	EUK	Mammals:2,Plants:2,Primates:1,Rodents:2,Vertebrates:3	pfam00031, Cystatin, Cystatin domain.  Very diverse family. Attempts to define separate sub-families failed. Typically, either the N-terminal or C-terminal end is very divergent. But splitting into two domains would make very short families. pfam00666 are related to this family but have not been included.
CDD:249525	102	EUKprk	Bacteria:27,Environmental:1,Invertebrates:55,Plants:19,Rodents:1,Vertebrates:4	pfam00032, Cytochrom_B_C, Cytochrome b(C-terminal)/b6/petD.  
CDD:249526	181	EUKprk	Bacteria:78,Mammals:1,Plants:3,Vertebrates:1	pfam00033, Cytochrom_B_N, Cytochrome b(N-terminal)/b6/petB.  
CDD:249527	86	EUKprk	Bacteria:174,Environmental:2,Invertebrates:1,Plants:2	pfam00034, Cytochrom_C, Cytochrome c.  The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, pfam06181, has now been merged into this family.
CDD:249528	66	EUKprk	Bacteria:16,Invertebrates:7,Mammals:1,Phages:1,Plants:8,Primates:1,Rodents:1,Vertebrates:3,Viruses:10	pfam00035, dsrm, Double-stranded RNA binding motif.  Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced ...
CDD:249529	29	EUKprk	Bacteria:1,Invertebrates:52,Mammals:5,Plants:33,Primates:1,Rodents:6,Vertebrates:17,Viruses:1,nodiv:1	pfam00036, EF-hand_1, EF hand.  The EF-hands can be divided into two classes: signaling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The ...
CDD:249530	24	EUKprk	Bacteria:98,Invertebrates:6,Plants:5,Rodents:1	pfam00037, Fer4, 4Fe-4S binding domain.  Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.
CDD:200948	312	EUKprk	Invertebrates:1,Mammals:2,Primates:1,Rodents:2,Synthetic:1,Vertebrates:4	pfam00038, Filament, Intermediate filament protein.  
CDD:249531	39	EUK	Mammals:1,Primates:1,Rodents:2	pfam00039, fn1, Fibronectin type I domain.  
CDD:249532	42	EUK	Invertebrates:2,Mammals:10,Primates:1,Rodents:2,Vertebrates:11	pfam00040, fn2, Fibronectin type II domain.  
CDD:249533	84	EUK	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:1	pfam00041, fn3, Fibronectin type III domain.  
CDD:249534	108	EUKprk	Bacteria:2,Invertebrates:11,Mammals:4,Plants:3,Rodents:1,Vertebrates:11	pfam00042, Globin, Globin.  
CDD:249535	92	EUKprk	Bacteria:4,Invertebrates:6,Mammals:1,Plants:5,Primates:1,Rodents:3,Vertebrates:1	pfam00043, GST_C, Glutathione S-transferase, C-terminal domain.  GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in Escherichia coli are also included in the alignment but are not known to have ...
CDD:249536	150	EUKprk	Bacteria:54,Environmental:1,Invertebrates:9,Plants:18,Primates:1	pfam00044, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain.  GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.
CDD:249537	45	EUK	Primates:1,Rodents:1	pfam00045, Hemopexin, Hemopexin.  Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metallopeptidases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).
CDD:249538	57	EUK	Invertebrates:27,Mammals:1,Plants:10,Primates:2,Rodents:3,Vertebrates:5,nodiv:1	pfam00046, Homeobox, Homeobox domain.  
CDD:249539	62	EUKprk	Mammals:1,Primates:2,Rodents:2,Vertebrates:2,Viruses:2	pfam00047, ig, Immunoglobulin domain.  Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.
CDD:249540	64	EUKprk	Mammals:7,Primates:2,Rodents:5,Vertebrates:23,Viruses:9	pfam00048, IL8, Small cytokines (intecrine/chemokine), interleukin-8 like.  Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.
CDD:249541	77	EUK	Invertebrates:2,Mammals:2,Primates:2,Rodents:1,Vertebrates:6	pfam00049, Insulin, Insulin/IGF/Relaxin family.  Superfamily includes insulins; relaxins; insulin-like growth factor; and bombyxin. All are secreted regulatory hormones. Disulfide rich, all-alpha fold. Alignment includes B chain, linker (which is processed out of the final product), and A chain.
CDD:249542	48	EUK	Mammals:3,Primates:1,Rodents:1,Vertebrates:5	pfam00050, Kazal_1, Kazal-type serine protease inhibitor domain.  Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. Alignment also includes a single domain from transporters in the OATP/PGT family.
CDD:249543	79	EUK	Mammals:1,Primates:1,Rodents:1	pfam00051, Kringle, Kringle domain.  Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.
CDD:249544	49	EUK	Invertebrates:1,Primates:1,Rodents:1	pfam00053, Laminin_EGF, Laminin EGF-like (Domains III and V).  This family is like pfam00008 but has 8 conserved cysteines instead of six.
CDD:249545	131	EUK	Primates:1,Rodents:1,Vertebrates:1	pfam00054, Laminin_G_1, Laminin G domain.  
CDD:249547	140	EUKprk	Bacteria:13,Mammals:1,Plants:3,Rodents:1,Vertebrates:2	pfam00056, Ldh_1_N, lactate/malate dehydrogenase, NAD binding domain.  L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate ...
CDD:249548	37	EUK	Invertebrates:2,Mammals:1,Primates:1,Rodents:3,Vertebrates:1	pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain class A.  
CDD:249549	41	EUK	Primates:1	pfam00058, Ldl_recept_b, Low-density lipoprotein receptor repeat class B.  This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
CDD:249550	106	EUKprk	Invertebrates:10,Mammals:5,Primates:1,Rodents:2,Vertebrates:6,Viruses:17	pfam00059, Lectin_C, Lectin C-type domain.  This family includes both long and short form C-type.
CDD:249551	268	EUK	Invertebrates:4,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam00060, Lig_chan, Ligand-gated ion channel.  This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
CDD:249552	140	EUK	Invertebrates:17,Mammals:11,Primates:2,Rodents:5,Vertebrates:18,nodiv:1	pfam00061, Lipocalin, Lipocalin / cytosolic fatty-acid binding protein family.  Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and ...
CDD:249553	125	EUK	Invertebrates:1,Mammals:4,Primates:2,Rodents:2,Vertebrates:3	pfam00062, Lys, C-type lysozyme/alpha-lactalbumin family.  Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.
CDD:249554	679	EUK	Invertebrates:3,Mammals:1,Plants:3,Primates:1,Vertebrates:1	pfam00063, Myosin_head, Myosin head (motor domain).  
CDD:249555	38	EUK	Invertebrates:12,Plants:1,Primates:2,Rodents:2,Vertebrates:2,nodiv:1	pfam00066, Notch, LNR domain.  The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
CDD:249556	461	EUKprk	Bacteria:1,Invertebrates:4,Mammals:2,Plants:4,Primates:1,Rodents:2,Vertebrates:2	pfam00067, p450, Cytochrome P450.  Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is ...
CDD:249557	116	EUK	Primates:1,Rodents:1,Vertebrates:20	pfam00068, Phospholip_A2_1, Phospholipase A2.  Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee ...
CDD:249558	260	EUKprk	Bacteria:1,Invertebrates:2,Mammals:1,Plants:4,Primates:2,Rodents:2,Viruses:4	pfam00069, Pkinase, Protein kinase domain.  
CDD:249559	80	EUKprk	Bacteria:57,Invertebrates:5,Plants:7,Primates:1,Rodents:1,Vertebrates:1	pfam00070, Pyr_redox, Pyridine nucleotide-disulphide oxidoreductase.  This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
CDD:249560	162	EUK	Invertebrates:5,Mammals:1,Plants:7,Primates:1,Rodents:2,Vertebrates:1	pfam00071, Ras, Ras family.  Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
CDD:249561	111	EUKprk	Bacteria:15,Invertebrates:1,Plants:1,Primates:1,Rodents:1	pfam00072, Response_reg, Response regulator receiver domain.  This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
CDD:249562	172	PRK	Viruses:21	pfam00073, Rhv, picornavirus capsid protein.  CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an ...
CDD:249563	121	EUK	Mammals:11,Primates:14,Rodents:23,Vertebrates:7	pfam00074, RnaseA, Pancreatic ribonuclease.  Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices.
CDD:249564	127	EUKprk	Bacteria:1,Invertebrates:3,Primates:1,Rodents:1,Viruses:27	pfam00075, RNase_H, RNase H.  RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.
CDD:249565	70	EUK	Invertebrates:1,Mammals:1,Plants:5,Primates:1,Rodents:1,Vertebrates:1	pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain).  The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure ...
CDD:249566	99	EUKprk	Invertebrates:1,Primates:1,Synthetic:1,Viruses:18	pfam00077, RVP, Retroviral aspartyl protease.  Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).
CDD:249567	196	EUKprk	Bacteria:9,Invertebrates:11,Mammals:1,Plants:11,Primates:1,Rodents:1,Vertebrates:3,Viruses:27	pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase).  A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.
CDD:249568	369	EUKprk	Bacteria:36,Invertebrates:24,Mammals:6,Plants:4,Primates:3,Rodents:4,Vertebrates:9,Viruses:2	pfam00079, Serpin, Serpin (serine protease inhibitor).  Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.
CDD:249569	140	EUKprk	Bacteria:65,Environmental:1,Invertebrates:19,Mammals:1,Plants:15,Primates:1,Viruses:9,nodiv:1	pfam00080, Sod_Cu, Copper/zinc superoxide dismutase (SODC).  superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's ...
CDD:249570	82	EUKprk	Bacteria:17,Invertebrates:3,Plants:2,Primates:1	pfam00081, Sod_Fe_N, Iron/manganese superoxide dismutases, alpha-hairpin domain.  superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel ...
CDD:249571	272	EUKprk	Bacteria:20,Invertebrates:2,Plants:3,Primates:1,Rodents:2,nodiv:1	pfam00082, Peptidase_S8, Subtilase family.  Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
CDD:249572	449	EUKprk	Bacteria:2,Invertebrates:2,Plants:4,Primates:1,Rodents:1	pfam00083, Sugar_tr, Sugar (and other) transporter.  
CDD:249573	56	EUKprk	Invertebrates:11,Mammals:2,Primates:4,Rodents:3,Vertebrates:8,Viruses:2	pfam00084, Sushi, Sushi domain (SCR repeat).  
CDD:249574	104	EUKprk	Bacteria:5,Invertebrates:1,Plants:9,Rodents:3,Vertebrates:1	pfam00085, Thioredoxin, Thioredoxin.  Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.
CDD:249575	66	EUK	Mammals:1,Primates:1	pfam00086, Thyroglobulin_1, Thyroglobulin type-1 repeat.  Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.
CDD:249576	63	EUK	Vertebrates:22	pfam00087, Toxin_1, Snake toxin.  A family of venomous neurotoxins and cytotoxins. Structure is small, disulfide-rich, nearly all beta sheet.
CDD:249577	42	EUK	Invertebrates:7,Mammals:6,Plants:1,Primates:2,Rodents:3,Vertebrates:15	pfam00088, Trefoil, Trefoil (P-type) domain.  
CDD:249578	219	EUKprk	Bacteria:9,Invertebrates:6,Mammals:2,Plants:2,Primates:1,Rodents:3,Vertebrates:3	pfam00089, Trypsin, Trypsin.  
CDD:249579	48	EUK	Invertebrates:7,Primates:1,Rodents:2	pfam00090, TSP_1, Thrombospondin type 1 domain.  
CDD:249580	200	EUKprk	Bacteria:34,Environmental:2,Invertebrates:16,Plants:3,Primates:1	pfam00091, Tubulin, Tubulin/FtsZ family, GTPase domain.  This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell ...
CDD:249581	177	EUKprk	Bacteria:11,Invertebrates:17,Mammals:9,Plants:1,Primates:2,Rodents:4,Vertebrates:6	pfam00092, VWA, von Willebrand factor type A domain.  
CDD:249582	57	EUK	Invertebrates:1,Primates:1,Rodents:1,Vertebrates:1	pfam00093, VWC, von Willebrand factor type C domain.  The high cutoff was used to prevent overlap with pfam00094.
CDD:249583	157	EUK	Invertebrates:10,Mammals:3,Primates:1,Rodents:2,Vertebrates:6	pfam00094, VWD, von Willebrand factor type D domain.  Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
CDD:249584	42	EUK	Invertebrates:10,Mammals:4,Primates:1,Rodents:3,Vertebrates:7,nodiv:1	pfam00095, WAP, WAP-type (Whey Acidic Protein) 'four-disulfide core'.  
CDD:249585	23	EUKprk	Invertebrates:3,Plants:4,Primates:1,Rodents:2,Vertebrates:6,Viruses:3	pfam00096, zf-C2H2, Zinc finger, C2H2 type.  The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the ...
CDD:249586	40	EUKprk	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:2,Viruses:3	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger).  The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.
CDD:189387	18	EUKprk	Invertebrates:12,Mammals:1,Plants:10,Primates:1,Rodents:2,Vertebrates:1,Viruses:25	pfam00098, zf-CCHC, Zinc knuckle.  The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
CDD:249587	251	EUK	Invertebrates:14,Mammals:5,Primates:1,Rodents:3,Vertebrates:18	pfam00100, Zona_pellucida, Zona pellucida-like domain.  
CDD:201001	99	EUKprk	Bacteria:12,Plants:22	pfam00101, RuBisCO_small, Ribulose bisphosphate carboxylase, small chain.  
CDD:249588	232	EUKprk	Bacteria:2,Invertebrates:6,Plants:2,Primates:1,Rodents:2,Vertebrates:1	pfam00102, Y_phosphatase, Protein-tyrosine phosphatase.  
CDD:249589	198	EUK	Mammals:1,Primates:1,Vertebrates:3	pfam00103, Hormone_1, Somatotropin hormone family.  
CDD:249590	203	EUK	Invertebrates:14,Primates:2,Rodents:1,Vertebrates:5	pfam00104, Hormone_recep, Ligand-binding domain of nuclear hormone receptor.  This all helical domain is involved in binding the hormone in these receptors.
CDD:249591	70	EUKprk	Invertebrates:2,Mammals:1,Primates:1,Vertebrates:1,Viruses:1	pfam00105, zf-C4, Zinc finger, C4 type (two domains).  In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
CDD:249592	167	EUKprk	Bacteria:48,Invertebrates:6,Plants:5,Primates:1,Rodents:1	pfam00106, adh_short, short chain dehydrogenase.  This family contains a wide variety of dehydrogenases.
CDD:249593	131	EUKprk	Bacteria:31,Invertebrates:1,Mammals:1,Plants:12,Rodents:1	pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.  
CDD:249594	262	EUKprk	Bacteria:5,Plants:1,Primates:1,Rodents:1	pfam00108, Thiolase_N, Thiolase, N-terminal domain.  Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase.
CDD:249595	241	EUKprk	Bacteria:44,Invertebrates:3,Plants:6,Primates:1	pfam00109, ketoacyl-synt, Beta-ketoacyl synthase, N-terminal domain.  The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine.
CDD:249596	308	EUK	Invertebrates:24,Primates:2,Rodents:1,Vertebrates:4,nodiv:1	pfam00110, wnt, wnt family.  Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and ...
CDD:249597	77	EUKprk	Bacteria:59,Invertebrates:4,Mammals:2,Plants:16	pfam00111, Fer2, 2Fe-2S iron-sulfur cluster binding domain.  
CDD:249598	213	EUKprk	Bacteria:1,Invertebrates:43,Mammals:1,Plants:23,Primates:1,Rodents:2,Vertebrates:2,Viruses:5	pfam00112, Peptidase_C1, Papain family cysteine protease.  
CDD:249599	107	PRK	Bacteria:81	pfam00114, Pilin, Pilin (bacterial filament).  Proteins with only the short N-terminal methylation site are not separated from the noise. The Prosite pattern detects those better.
CDD:249600	444	EUKprk	Bacteria:69,Invertebrates:12,Mammals:1,Plants:4	pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I.  
CDD:201014	120	EUKprk	Bacteria:7,Invertebrates:14,Mammals:1,Plants:4,Primates:1,Vertebrates:1	pfam00116, COX2, Cytochrome C oxidase subunit II, periplasmic domain.  
CDD:249601	187	EUKprk	Bacteria:33,Invertebrates:7,Plants:8,Primates:1,Rodents:2,Vertebrates:1	pfam00117, GATase, Glutamine amidotransferase class-I.  
CDD:249602	480	EUKprk	Bacteria:30,Environmental:2,Invertebrates:19,Plants:9,Primates:1,Rodents:1	pfam00118, Cpn60_TCP1, TCP-1/cpn60 chaperonin family.  This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family.
CDD:249603	217	EUKprk	Bacteria:8,Invertebrates:7,Mammals:1,Plants:5,Vertebrates:2	pfam00119, ATP-synt_A, ATP synthase A chain.  
CDD:249604	259	EUKprk	Bacteria:49,Invertebrates:3,Plants:9,Primates:1,Vertebrates:1	pfam00120, Gln-synt_C, Glutamine synthetase, catalytic domain.  
CDD:249605	243	EUKprk	Bacteria:34,Invertebrates:6,Plants:2	pfam00121, TIM, Triosephosphate isomerase.  
CDD:249606	222	EUKprk	Bacteria:78,Invertebrates:10,Plants:13,Viruses:1,nodiv:1	pfam00122, E1-E2_ATPase, E1-E2 ATPase.  
CDD:249607	28	EUKprk	Mammals:2,Primates:2,Rodents:4,Synthetic:1,Vertebrates:24	pfam00123, Hormone_2, Peptide hormone.  This family contains glucagon, GIP, secretin and VIP.
CDD:249608	257	EUKprk	Bacteria:34,Environmental:3,Plants:6	pfam00124, Photo_RC, Photosynthetic reaction centre protein.  
CDD:249609	75	EUK	Invertebrates:22,Mammals:1,Plants:12,Primates:1,Rodents:1,Vertebrates:3	pfam00125, Histone, Core histone H2A/H2B/H3/H4.  
CDD:249610	60	EUKprk	Bacteria:207,Plants:6,nodiv:1	pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein, lysR family.  
CDD:249611	99	EUKprk	Bacteria:14,Plants:10	pfam00127, Copper-bind, Copper binding proteins, plastocyanin/azurin family.  
CDD:249612	314	EUKprk	Bacteria:10,Invertebrates:2,Plants:3	pfam00128, Alpha-amylase, Alpha amylase, catalytic domain.  Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.
CDD:249613	179	EUK	Mammals:3,Primates:4,Rodents:2	pfam00129, MHC_I, Class I Histocompatibility antigen, domains alpha 1 and 2.  
CDD:249614	50	EUK	Invertebrates:4,Mammals:1,Plants:1,Primates:1,Rodents:1	pfam00130, C1_1, Phorbol esters/diacylglycerol binding domain (C1 domain).  This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
CDD:109198	62	EUK	Invertebrates:9,Mammals:3,Rodents:1,Vertebrates:7	pfam00131, Metallothio, Metallothionein.  
CDD:249615	36	EUKprk	Bacteria:57,Plants:5,Primates:1	pfam00132, Hexapep, Bacterial transferase hexapeptide (six repeats).  
CDD:249616	606	EUKprk	Bacteria:2,Primates:1	pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).  Other tRNA synthetase sub-families are too dissimilar to be included.
CDD:249617	127	EUKprk	Invertebrates:9,Plants:19,Primates:1,Rodents:2,Vertebrates:4,Viruses:4	pfam00134, Cyclin_N, Cyclin, N-terminal domain.  Cyclins regulate cyclin dependent kinases (CDKs). Human cyclin-O is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.
CDD:249618	514	EUKprk	Bacteria:4,Invertebrates:27,Mammals:2,Plants:4,Primates:1,Rodents:4,Vertebrates:4	pfam00135, COesterase, Carboxylesterase family.  
CDD:249619	455	EUKprk	Bacteria:7,Invertebrates:2,Phages:2,Plants:4,Rodents:1,Viruses:36	pfam00136, DNA_pol_B, DNA polymerase family B.  This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
CDD:249620	66	EUKprk	Bacteria:106,Environmental:1,Invertebrates:17,Plants:20	pfam00137, ATP-synt_C, ATP synthase subunit C.  
CDD:249621	231	EUKprk	Bacteria:2,Plants:16	pfam00139, Lectin_legB, Legume lectin domain.  
CDD:249622	37	EUKprk	Bacteria:122,Environmental:1,Plants:7	pfam00140, Sigma70_r1_2, Sigma-70 factor, region 1.2.  
CDD:249623	181	EUKprk	Bacteria:21,Invertebrates:1,Plants:50	pfam00141, peroxidase, Peroxidase.  
CDD:249625	162	EUK	Mammals:2,Primates:1,Rodents:1	pfam00143, Interferon, Interferon alpha/beta domain.  
CDD:249626	327	EUKprk	Bacteria:60,Invertebrates:1,Plants:2	pfam00144, Beta-lactamase, Beta-lactamase.  This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
CDD:249627	319	PRK	Bacteria:2	pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.  
CDD:109212	309	EUKprk	Bacteria:4,Invertebrates:7,Mammals:2,Plants:4,Primates:1,Vertebrates:3	pfam00146, NADHdh, NADH dehydrogenase.  
CDD:249628	221	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:1	pfam00147, Fibrinogen_C, Fibrinogen beta and gamma chains, C-terminal globular domain.  
CDD:249629	397	EUKprk	Bacteria:77,Plants:3	pfam00148, Oxidored_nitro, Nitrogenase component 1 type Oxidoreductase.  
CDD:249630	186	EUKprk	Bacteria:48,Invertebrates:10,Mammals:1,Phages:6,Plants:14,Primates:1,Rodents:2,Vertebrates:1	pfam00149, Metallophos, Calcineurin-like phosphoesterase.  This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.
CDD:249631	267	EUKprk	Bacteria:37,Invertebrates:2,Plants:11	pfam00150, Cellulase, Cellulase (glycosyl hydrolase family 5).  
CDD:249632	329	EUK	Invertebrates:4,Mammals:3,Primates:1,Rodents:2	pfam00151, Lipase, Lipase.  
CDD:249633	345	EUKprk	Bacteria:48,Invertebrates:2,Plants:7,Primates:1,Rodents:1	pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).  
CDD:249634	96	EUK	Invertebrates:9,Mammals:2,Plants:17,Primates:1,Rodents:3	pfam00153, Mito_carr, Mitochondrial carrier protein.  
CDD:249635	322	PRK	Bacteria:18,nodiv:1	pfam00154, RecA, recA bacterial DNA recombination protein.  RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.
CDD:249636	351	EUKprk	Bacteria:9,Mammals:1,Plants:9,Primates:1,Vertebrates:1	pfam00155, Aminotran_1_2, Aminotransferase class I and II.  
CDD:249637	123	EUKprk	Bacteria:48,Environmental:1,Invertebrates:4,Plants:1,Rodents:1	pfam00156, Pribosyltran, Phosphoribosyl transferase domain.  This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1. Amidophosphoribosyltransferase EC:2.4.2.14. ...
CDD:249638	75	EUK	Invertebrates:7,Mammals:2,Rodents:2,Vertebrates:3	pfam00157, Pou, Pou domain - N-terminal to homeobox domain.  
CDD:249639	168	PRK	Bacteria:102	pfam00158, Sigma54_activat, Sigma-54 interaction domain.  
CDD:201044	36	EUK	Invertebrates:3,Mammals:1,Primates:1,Rodents:1,Vertebrates:7	pfam00159, Hormone_3, Pancreatic hormone peptide.  
CDD:249640	143	EUKprk	Bacteria:74,Environmental:1,Invertebrates:21,Plants:21,Vertebrates:1	pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD.  The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerization during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilized in the cis ...
CDD:249641	207	EUKprk	Bacteria:5,Phages:1,Plants:45	pfam00161, RIP, Ribosome inactivating protein.  
CDD:249642	383	EUKprk	Bacteria:92,Environmental:2,Invertebrates:20,Mammals:1,Plants:10,Primates:1	pfam00162, PGK, Phosphoglycerate kinase.  
CDD:249643	94	EUKprk	Bacteria:2,Invertebrates:1,Plants:5,Primates:1	pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain.  This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.
CDD:201049	122	EUKprk	Bacteria:7,Invertebrates:1,Plants:6,Rodents:1	pfam00164, Ribosom_S12_S23, Ribosomal protein S12/S23.  This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.
CDD:249644	42	PRK	Bacteria:20	pfam00165, HTH_AraC, Bacterial regulatory helix-turn-helix proteins, AraC family.  In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a ...
CDD:249645	92	EUKprk	Bacteria:24,Invertebrates:8,Phages:5,Plants:5	pfam00166, Cpn10, Chaperonin 10 Kd subunit.  This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis.
CDD:249646	122	EUKprk	Invertebrates:8,Mammals:2,Primates:1,Rodents:2,Vertebrates:7,Viruses:13	pfam00167, FGF, Fibroblast growth factor.  Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organisms, from nematodes to humans. Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerization of their ...
CDD:249647	85	EUK	Invertebrates:15,Mammals:2,Plants:22,Primates:2,Rodents:2,Vertebrates:3,nodiv:1	pfam00168, C2, C2 domain.  
CDD:249648	101	EUK	Invertebrates:4,Mammals:2,Plants:5,Primates:2,Rodents:3	pfam00169, PH, PH domain.  PH stands for pleckstrin homology.
CDD:249649	59	EUK	Mammals:1,Plants:5,Primates:1	pfam00170, bZIP_1, bZIP transcription factor.  The Pfam entry includes the basic region and the leucine zipper region.
CDD:249650	459	EUKprk	Bacteria:62,Environmental:1,Invertebrates:3,Plants:7,Primates:1,Vertebrates:1,nodiv:1	pfam00171, Aldedh, Aldehyde dehydrogenase family.  This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. ...
CDD:201056	39	EUK	Plants:5	pfam00172, Zn_clus, Fungal Zn(2)-Cys(6) binuclear cluster domain.  
CDD:249651	74	EUKprk	Bacteria:4,Invertebrates:9,Mammals:4,Plants:72,Primates:2,Rodents:3,Vertebrates:3,nodiv:1	pfam00173, Cyt-b5, Cytochrome b5-like Heme/Steroid binding domain.  This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some ...
CDD:249652	155	EUKprk	Bacteria:97,Environmental:2,Invertebrates:4,Mammals:1,Plants:11,nodiv:1	pfam00174, Oxidored_molyb, Oxidoreductase molybdopterin binding domain.  This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity.
CDD:249653	108	EUKprk	Bacteria:16,Plants:8,Primates:1,Rodents:1,nodiv:1	pfam00175, NAD_binding_1, Oxidoreductase NAD-binding domain.  Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.
CDD:249654	286	EUKprk	Bacteria:1,Invertebrates:3,Plants:4,Primates:1,Rodents:1,Vertebrates:1,Viruses:2	pfam00176, SNF2_N, SNF2 family N-terminal domain.  This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
CDD:249655	149	EUKprk	Bacteria:82,Environmental:2,Invertebrates:12,Plants:35	pfam00177, Ribosomal_S7, Ribosomal protein S7p/S5e.  This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.
CDD:249656	85	EUK	Invertebrates:1,Primates:1,Rodents:1	pfam00178, Ets, Ets-domain.  
CDD:249657	139	EUK	Invertebrates:6,Plants:9,Primates:1,Rodents:3	pfam00179, UQ_con, Ubiquitin-conjugating enzyme.  Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
CDD:249658	348	EUKprk	Bacteria:13,Mammals:1,Plants:7	pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.  
CDD:249659	77	EUKprk	Bacteria:14,Invertebrates:10,Plants:15,Rodents:1	pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding domain.  
CDD:249660	231	EUK	Plants:7	pfam00182, Glyco_hydro_19, Chitinase class I.  
CDD:249662	79	EUK	Invertebrates:7,Mammals:2,Vertebrates:18	pfam00184, Hormone_5, Neurohypophysial hormones, C-terminal Domain.  N-terminal Domain is in hormone5.
CDD:249663	152	EUKprk	Bacteria:88,Environmental:4,Invertebrates:6,Plants:4,Viruses:1	pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain.  
CDD:249664	156	PRK	Bacteria:84	pfam00186, DHFR_1, Dihydrofolate reductase.  
CDD:143950	38	EUK	Plants:5	pfam00187, Chitin_bind_1, Chitin recognition protein.  
CDD:249665	123	EUKprk	Bacteria:27,Invertebrates:19,Plants:5,Primates:1,Vertebrates:1	pfam00188, CAP, Cysteine-rich secretory protein family.  This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis ...
CDD:249666	85	EUKprk	Bacteria:52,Environmental:2,Invertebrates:15,Plants:38	pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-terminal domain.  This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.
CDD:249667	139	EUKprk	Bacteria:7,Invertebrates:1,Plants:68	pfam00190, Cupin_1, Cupin.  This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
CDD:249668	66	EUK	Invertebrates:7,Mammals:2,Plants:11,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	pfam00191, Annexin, Annexin.  This family of annexins also includes giardin that has been shown to function as an annexin.
CDD:109258	91	EUK	Mammals:2,Primates:2,Rodents:1	pfam00193, Xlink, Extracellular link domain.  
CDD:249669	238	EUK	Mammals:3,Primates:1,Rodents:1	pfam00194, Carb_anhydrase, Eukaryotic-type carbonic anhydrase.  
CDD:201072	227	EUK	Plants:15	pfam00195, Chal_sti_synt_N, Chalcone and stilbene synthases, N-terminal domain.  The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase.  The differences in activity are accounted for by differences in this N-terminal domain.
CDD:109261	58	PRK	Bacteria:3	pfam00196, GerE, Bacterial regulatory proteins, luxR family.  
CDD:249670	177	EUK	Plants:7	pfam00197, Kunitz_legume, Trypsin and protease inhibitor.  
CDD:249671	212	EUKprk	Bacteria:57,Environmental:2,Invertebrates:11,Plants:6,Vertebrates:1	pfam00198, 2-oxoacid_dh, 2-oxoacid dehydrogenases acyltransferase (catalytic domain).  These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.
CDD:249672	383	EUKprk	Bacteria:70,Invertebrates:4,Mammals:1,Plants:20,Vertebrates:1	pfam00199, Catalase, Catalase.  
CDD:249673	76	EUK	Invertebrates:6,Mammals:4,Plants:15,Primates:4,Rodents:3,Vertebrates:25	pfam00200, Disintegrin, Disintegrin.  
CDD:201077	500	EUK	Mammals:1,Plants:2,Primates:1,Rodents:1	pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase.  
CDD:249674	338	EUKprk	Bacteria:5,Invertebrates:1,Plants:1,Primates:1	pfam00202, Aminotran_3, Aminotransferase class-III.  
CDD:201079	81	EUKprk	Bacteria:4,Plants:12,Rodents:1	pfam00203, Ribosomal_S19, Ribosomal protein S19.  
CDD:249675	167	EUKprk	Bacteria:47,Environmental:2,Invertebrates:9,Phages:4,Plants:10,Viruses:4	pfam00204, DNA_gyraseB, DNA gyrase B.  This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
CDD:249676	137	EUKprk	Bacteria:165,Environmental:3,Invertebrates:4,Mammals:1,Plants:14,Primates:1,Vertebrates:1	pfam00205, TPP_enzyme_M, Thiamine pyrophosphate enzyme, central domain.  The central domain of TPP enzymes contains a 2-fold Rossman fold.
CDD:249677	312	EUKprk	Bacteria:6,Plants:2,Primates:1,Vertebrates:1	pfam00206, Lyase_1, Lyase.  
CDD:249678	92	EUKprk	Bacteria:30,Invertebrates:23,Mammals:1,Primates:2,Rodents:1,Vertebrates:16	pfam00207, A2M, Alpha-2-macroglobulin family.  This family includes the C-terminal region of the alpha-2-macroglobulin family.
CDD:249679	236	EUKprk	Bacteria:69,Environmental:1,Invertebrates:5,Plants:18	pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine dehydrogenase.  
CDD:249680	506	EUK	Invertebrates:1,Mammals:2,Primates:1,Rodents:2	pfam00209, SNF, Sodium:neurotransmitter symporter family.  
CDD:249681	142	EUKprk	Bacteria:149,Invertebrates:20,Plants:4,Rodents:1,Vertebrates:2,nodiv:2	pfam00210, Ferritin, Ferritin-like domain.  This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.
CDD:249682	184	EUKprk	Bacteria:1,Invertebrates:2,Mammals:1,Primates:1,Rodents:2	pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic domain.  
CDD:249683	33	EUK	Mammals:2,Primates:1,Rodents:3,Vertebrates:18	pfam00212, ANP, Atrial natriuretic peptide.  
CDD:249684	171	EUKprk	Bacteria:162,Environmental:1,Invertebrates:9,Plants:14,Primates:1	pfam00213, OSCP, ATP synthase delta (OSCP) subunit.  The ATP D subunit from Escherichia coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family pfam00401.
CDD:249685	129	EUK	Mammals:3,Primates:1,Rodents:3,Vertebrates:4	pfam00214, Calc_CGRP_IAPP, Calcitonin / CGRP / IAPP family.  
CDD:249686	218	EUKprk	Bacteria:25,Invertebrates:3,Plants:18,Primates:1	pfam00215, OMPdecase, Orotidine 5'-phosphate decarboxylase / HUMPS family.  This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to pfam00834.
CDD:249687	90	EUKprk	Bacteria:104,Invertebrates:2,Phages:1,Plants:3,nodiv:1	pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein.  
CDD:249688	243	EUKprk	Bacteria:25,Invertebrates:45,Primates:1,Rodents:1,Vertebrates:3	pfam00217, ATP-gua_Ptrans, ATP:guanido phosphotransferase, C-terminal catalytic domain.  The substrate binding site is located in the cleft between N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain.
CDD:249689	254	EUKprk	Bacteria:8,Plants:1	pfam00218, IGPS, Indole-3-glycerol phosphate synthase.  
CDD:249690	53	EUK	Mammals:2,Primates:1,Rodents:2,Vertebrates:6,nodiv:1	pfam00219, IGFBP, Insulin-like growth factor binding protein.  
CDD:249692	477	EUKprk	Bacteria:88,Invertebrates:4,Plants:23,Rodents:1	pfam00221, Lyase_aromatic, Aromatic amino acid lyase.  This family includes proteins with phenylalanine ammonia-lyase, EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and tyrosine aminomutase, EC:5.4.3.6, activities.
CDD:249693	683	EUKprk	Bacteria:8,Invertebrates:1,Plants:9	pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein.  
CDD:249694	348	EUKprk	Bacteria:1,Plants:3,Primates:1	pfam00224, PK, Pyruvate kinase, barrel domain.  This domain of the is actually a small beta-barrel domain nested within a larger TIM barrel. The active site is found in a cleft between the two domains.
CDD:249695	324	EUK	Invertebrates:8,Plants:9,Primates:1,Rodents:2	pfam00225, Kinesin, Kinesin motor domain.  
CDD:249696	63	EUKprk	Bacteria:21,Invertebrates:10,Plants:8,Primates:1,Rodents:2,Viruses:5	pfam00226, DnaJ, DnaJ domain.  DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature.
CDD:249697	188	EUKprk	Bacteria:20,Invertebrates:11,Plants:9,Rodents:2,Vertebrates:5	pfam00227, Proteasome, Proteasome subunit.  The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is ...
CDD:249698	25	EUK	Plants:20	pfam00228, Bowman-Birk_leg, Bowman-Birk serine protease inhibitor family.  
CDD:249699	127	EUK	Invertebrates:2,Mammals:5,Primates:2,Rodents:2,Vertebrates:7	pfam00229, TNF, TNF(tumor Necrosis Factor) family.  
CDD:249700	223	EUKprk	Bacteria:1,Mammals:1,Plants:1,Primates:1	pfam00230, MIP, Major intrinsic protein.  MIP (Major Intrinsic Protein) family proteins exhibit essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators.
CDD:249701	288	EUKprk	Bacteria:127,Environmental:1,Invertebrates:9,Plants:12,Primates:1	pfam00231, ATP-synt, ATP synthase.  
CDD:249702	454	EUKprk	Bacteria:6,Mammals:1,Plants:2,Primates:1	pfam00232, Glyco_hydro_1, Glycosyl hydrolase family 1.  
CDD:249703	75	EUK	Plants:50	pfam00234, Tryp_alpha_amyl, Protease inhibitor/seed storage/LTP family.  This family is composed of trypsin-alpha amylase inhibitors, seed storage proteins and lipid transfer proteins from plants.
CDD:249704	121	EUKprk	Invertebrates:17,Mammals:1,Plants:32,Primates:1,Rodents:1,Vertebrates:2,Viruses:1	pfam00235, Profilin, Profilin.  
CDD:249705	105	EUKprk	Bacteria:83,Environmental:2,Invertebrates:8,Mammals:1,Plants:17,Vertebrates:1	pfam00237, Ribosomal_L22, Ribosomal protein L22p/L17e.  This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.
CDD:249706	122	EUKprk	Bacteria:44,Environmental:1,Invertebrates:17,Plants:35,Rodents:1	pfam00238, Ribosomal_L14, Ribosomal protein L14p/L23e.  
CDD:249707	139	EUKprk	Bacteria:145,Phages:4,Plants:1	pfam00239, Resolvase, Resolvase, N terminal domain.  The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.
CDD:249708	69	EUKprk	Invertebrates:4,Mammals:1,Plants:4,Primates:1,Rodents:1,Vertebrates:3,Viruses:3,nodiv:1	pfam00240, ubiquitin, Ubiquitin family.  This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to ...
CDD:143992	127	EUK	Invertebrates:3,Plants:1,Primates:1	pfam00241, Cofilin_ADF, Cofilin/tropomyosin-type actin-binding protein.  Severs actin filaments and binds to actin monomers.
CDD:249711	236	EUK	Invertebrates:22,Plants:20,Rodents:1,Vertebrates:3,nodiv:1	pfam00244, 14-3-3, 14-3-3 protein.  
CDD:249712	421	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Primates:1,Rodents:1	pfam00245, Alk_phosphatase, Alkaline phosphatase.  
CDD:249713	277	EUKprk	Bacteria:20,Invertebrates:11,Mammals:2,Plants:3,Primates:2,Rodents:2,Vertebrates:5	pfam00246, Peptidase_M14, Zinc carboxypeptidase.  
CDD:249714	273	EUKprk	Bacteria:28,Invertebrates:4,Plants:14,Rodents:1	pfam00248, Aldo_ket_red, Aldo/keto reductase family.  This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity.
CDD:249715	47	EUK	Invertebrates:4,Mammals:1,Plants:20,Primates:1,Rodents:2,Vertebrates:2	pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain.  This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
CDD:189470	96	EUK	Invertebrates:2,Primates:1,Rodents:2,Vertebrates:1	pfam00250, Fork_head, Fork head domain.  
CDD:249716	304	EUKprk	Bacteria:39,Invertebrates:1,Plants:36	pfam00251, Glyco_hydro_32N, Glycosyl hydrolases family 32 N-terminal domain.  This domain corresponds to the N-terminal domain of glycosyl hydrolase family 32 which forms a five bladed beta propeller structure.
CDD:249717	131	EUKprk	Bacteria:65,Environmental:1,Invertebrates:14,Plants:34,Rodents:1,Vertebrates:2	pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.  
CDD:249718	53	EUKprk	Bacteria:88,Environmental:1,Invertebrates:25,Plants:44,nodiv:1	pfam00253, Ribosomal_S14, Ribosomal protein S14p/S29e.  This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
CDD:249719	94	EUKprk	Bacteria:41,Invertebrates:9,Mammals:1,Plants:8,Primates:2,Rodents:2,Vertebrates:2	pfam00254, FKBP_C, FKBP-type peptidyl-prolyl cis-trans isomerase.  
CDD:249720	108	EUK	Invertebrates:2,Mammals:1,Plants:2,Primates:2	pfam00255, GSHPx, Glutathione peroxidase.  
CDD:249721	137	EUK	Plants:16	pfam00257, Dehydrin, Dehydrin.  
CDD:249722	141	EUKprk	Bacteria:31,Invertebrates:5,Plants:11,Primates:1,Vertebrates:2	pfam00258, Flavodoxin_1, Flavodoxin.  
CDD:189476	237	EUK	Invertebrates:24,Mammals:2,Primates:2,Rodents:1,Vertebrates:4	pfam00261, Tropomyosin, Tropomyosin.  
CDD:249724	359	EUK	Invertebrates:22,Mammals:2,Plants:19,Primates:2,Rodents:1,Vertebrates:1	pfam00262, Calreticulin, Calreticulin family.  
CDD:249725	166	PRK	Bacteria:115,Phages:2	pfam00263, Secretin, Bacterial type II and III secretion system protein.  
CDD:249726	210	EUKprk	Bacteria:23,Invertebrates:14,Plants:32,Rodents:1,Vertebrates:2	pfam00264, Tyrosinase, Common central domain of tyrosinase.  This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
CDD:249727	175	EUKprk	Phages:1,Vertebrates:1,Viruses:9	pfam00265, TK, Thymidine kinase.  
CDD:249728	371	EUKprk	Bacteria:18,Plants:1,Primates:1	pfam00266, Aminotran_5, Aminotransferase class-V.  This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.
CDD:249729	334	PRK	Bacteria:9	pfam00267, Porin_1, Gram-negative porin.  
CDD:249730	280	EUKprk	Bacteria:1,Plants:1,Primates:1,Viruses:5	pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.  
CDD:249731	61	PRK	Bacteria:42	pfam00269, SASP, Small, acid-soluble spore proteins, alpha/beta type.  
CDD:249732	167	EUKprk	Bacteria:26,Environmental:1,Invertebrates:7,Plants:6,Primates:1,Rodents:1,Viruses:4	pfam00270, DEAD, DEAD/DEAH box helicase.  Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
CDD:249733	78	EUKprk	Bacteria:40,Invertebrates:12,Mammals:3,Phages:4,Plants:12,Primates:1,Rodents:2,Vertebrates:1,Viruses:22	pfam00271, Helicase_C, Helicase conserved C-terminal domain.  The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
CDD:249734	30	EUK	Invertebrates:23	pfam00272, Cecropin, Cecropin family.  
CDD:201127	178	EUK	Mammals:4,Primates:2,Rodents:1,Vertebrates:3	pfam00273, Serum_albumin, Serum albumin family.  
CDD:249735	348	EUKprk	Bacteria:6,Invertebrates:24,Plants:10,Vertebrates:2,nodiv:1	pfam00274, Glycolytic, Fructose-bisphosphate aldolase class-I.  
CDD:249736	415	PRK	Bacteria:7	pfam00275, EPSP_synthase, EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase).  
CDD:144021	90	EUKprk	Bacteria:4,Plants:7	pfam00276, Ribosomal_L23, Ribosomal protein L23.  
CDD:249737	103	EUKprk	Bacteria:1,Invertebrates:2,Mammals:4,Primates:1,Rodents:3,Vertebrates:4	pfam00277, SAA, Serum amyloid A protein.  
CDD:249738	110	EUKprk	Bacteria:50,Environmental:3,Invertebrates:8,Plants:8,Primates:1,Rodents:1,Viruses:1,nodiv:1	pfam00278, Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase, C-terminal sheet domain.  These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates.
CDD:201130	63	EUK	Invertebrates:3,Plants:26	pfam00280, potato_inhibit, Potato inhibitor I family.  
CDD:109342	56	EUKprk	Bacteria:8,Invertebrates:2,Plants:5	pfam00281, Ribosomal_L5, Ribosomal protein L5.  
CDD:249739	373	EUK	Invertebrates:2,Mammals:1,Plants:1	pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase conserved domain.  
CDD:144025	40	EUKprk	Bacteria:13,Plants:12	pfam00284, Cytochrom_B559a, Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit.  This family is the lumenal portion of cytochrome b559 alpha chain, matches to this family should be accompanied by a match to the pfam00283 family also. The Prosite pattern pattern matches the transmembrane region of the cytochrome b559 alpha and beta subunits.
CDD:249740	352	EUKprk	Bacteria:64,Environmental:1,Invertebrates:8,Plants:9	pfam00285, Citrate_synt, Citrate synthase.  
CDD:249741	140	PRK	Viruses:17	pfam00286, Flexi_CP, Viral coat protein.  Family includes coat proteins from Potexviruses and carlaviruses.
CDD:249742	289	EUK	Invertebrates:1,Mammals:1,Primates:1,Vertebrates:3	pfam00287, Na_K-ATPase, Sodium / potassium ATPase beta chain.  
CDD:249743	67	EUKprk	Bacteria:196,Environmental:2,Invertebrates:10,Phages:1,Plants:27,Primates:2,Rodents:1,Vertebrates:2	pfam00288, GHMP_kinases_N, GHMP kinases N terminal domain.  This family includes homoserine kinases, galactokinases and mevalonate kinases.
CDD:249744	108	EUKprk	Bacteria:96,Invertebrates:9,Mammals:1,Plants:14,Primates:1,Vertebrates:1	pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain, N-terminal domain.  Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a ...
CDD:249745	258	EUKprk	Bacteria:7,Plants:1	pfam00290, Trp_syntA, Tryptophan synthase alpha chain.  
CDD:249746	249	EUKprk	Bacteria:91,Environmental:1,Invertebrates:9,Plants:12	pfam00291, PALP, Pyridoxal-phosphate dependent enzyme.  Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.
CDD:249747	133	EUKprk	Bacteria:40,Invertebrates:2,Mammals:1,Phages:1,Plants:9,Primates:1,Rodents:2,Vertebrates:1,Viruses:7	pfam00293, NUDIX, NUDIX domain.  
CDD:249748	298	EUKprk	Bacteria:22,Invertebrates:3,Mammals:1,Plants:1,Primates:1,Rodents:1	pfam00294, PfkB, pfkB family carbohydrate kinase.  This family includes a variety of carbohydrate and pyrimidine kinases.
CDD:249749	325	EUKprk	Bacteria:2,Plants:11	pfam00295, Glyco_hydro_28, Glycosyl hydrolases family 28.  Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolizm.
CDD:249750	260	EUKprk	Bacteria:84,Plants:1	pfam00296, Bac_luciferase, Luciferase-like monooxygenase.  
CDD:144036	199	EUKprk	Bacteria:4,Invertebrates:1,Mammals:1,Plants:3,Primates:1	pfam00297, Ribosomal_L3, Ribosomal protein L3.  
CDD:249751	69	EUKprk	Bacteria:109,Environmental:3,Invertebrates:12,Plants:17,Primates:1,Vertebrates:1	pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding domain.  
CDD:249753	155	EUKprk	Bacteria:37,Invertebrates:6,Plants:8,Primates:1,Rodents:2,Vertebrates:2,nodiv:1	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1).  The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His ...
CDD:249754	47	PRK	Bacteria:18	pfam00301, Rubredoxin, Rubredoxin.  
CDD:249755	206	PRK	Bacteria:9	pfam00302, CAT, Chloramphenicol acetyltransferase.  
CDD:249756	262	EUKprk	Bacteria:76,Invertebrates:17,Phages:5,Plants:17,Rodents:1,Viruses:15	pfam00303, Thymidylat_synt, Thymidylate synthase.  
CDD:109365	47	EUK	Invertebrates:1,Plants:26	pfam00304, Gamma-thionin, Gamma-thionin family.  
CDD:249757	667	EUK	Plants:8,Primates:1,Rodents:1	pfam00305, Lipoxygenase, Lipoxygenase.  
CDD:249758	109	EUKprk	Bacteria:36,Invertebrates:8,Plants:23,Primates:1	pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal domain.  
CDD:249759	104	EUK	Invertebrates:14,Mammals:1,Plants:7,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	pfam00307, CH, Calponin homology (CH) domain.  The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most member proteins have from two to four copies of the CH domain, however some proteins ...
CDD:144046	219	PRK	Bacteria:7	pfam00308, Bac_DnaA, Bacterial dnaA protein.  
CDD:249760	49	PRK	Bacteria:133,Environmental:3	pfam00309, Sigma54_AID, Sigma-54 factor, Activator interacting domain (AID).  The sigma-54 holoenzyme is an enhancer dependent form of the RNA polymerase. The AID is necessary for activator interaction. In addition, the AID also inhibits transcription initiation in the sigma-54 holoenzyme prior to interaction with the activator.
CDD:249761	215	EUKprk	Bacteria:29,Invertebrates:2,Plants:8,Rodents:1	pfam00310, GATase_2, Glutamine amidotransferases class-II.  
CDD:249762	794	EUKprk	Bacteria:43,Invertebrates:1,Plants:8	pfam00311, PEPcase, Phosphoenolpyruvate carboxylase.  
CDD:109373	83	EUKprk	Bacteria:4,Invertebrates:1,Plants:2	pfam00312, Ribosomal_S15, Ribosomal protein S15.  
CDD:201147	66	EUKprk	Bacteria:17,Invertebrates:4,Primates:1,Rodents:1,Vertebrates:1	pfam00313, CSD, 'Cold-shock' DNA-binding domain.  
CDD:249763	212	EUK	Invertebrates:6,Plants:50	pfam00314, Thaumatin, Thaumatin family.  
CDD:249764	325	EUKprk	Bacteria:3,Plants:1,Primates:1	pfam00316, FBPase, Fructose-1-6-bisphosphatase.  
CDD:249765	79	EUKprk	Bacteria:79,Environmental:3,Invertebrates:3,Phages:12,Plants:3,Viruses:31	pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha domain.  
CDD:249766	205	EUKprk	Bacteria:83,Invertebrates:18,Plants:34,Vertebrates:1	pfam00318, Ribosomal_S2, Ribosomal protein S2.  
CDD:249767	36	EUK	Invertebrates:7,Plants:13,Primates:1,Rodents:1,Vertebrates:1	pfam00320, GATA, GATA zinc finger.  This domain uses four cysteine residues to coordinate a zinc ion. This domain binds to DNA. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain.
CDD:201152	46	EUK	Plants:17	pfam00321, Thionin, Plant thionin.  
CDD:249768	29	EUK	Mammals:1,Primates:1,Rodents:2	pfam00323, Defensin_1, Mammalian defensin.  
CDD:249769	472	EUKprk	Bacteria:6,Invertebrates:1,Mammals:1,Plants:1,Primates:1,Rodents:1	pfam00324, AA_permease, Amino acid permease.  
CDD:249770	32	PRK	Bacteria:5	pfam00325, Crp, Bacterial regulatory proteins, crp family.  
CDD:249771	212	EUKprk	Bacteria:34,Environmental:2,Invertebrates:5,Mammals:1,Plants:6,Rodents:2	pfam00326, Peptidase_S9, Prolyl oligopeptidase family.  
CDD:249772	52	EUKprk	Bacteria:68,Environmental:2,Invertebrates:8,Mammals:1,Plants:17,Rodents:1,Vertebrates:2	pfam00327, Ribosomal_L30, Ribosomal protein L30p/L7e.  This family includes prokaryotic L30 and eukaryotic L7.
CDD:249773	331	EUKprk	Bacteria:4,Invertebrates:4,Plants:18,Primates:1,Rodents:1	pfam00328, His_Phos_2, Histidine phosphatase superfamily (branch 2).  The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and ...
CDD:249774	103	EUKprk	Bacteria:92,Environmental:4,Invertebrates:2,Plants:4	pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30 Kd subunit.  
CDD:249775	464	EUKprk	Bacteria:3,Invertebrates:1,Mammals:1,Plants:1	pfam00330, Aconitase, Aconitase family (aconitate hydratase).  
CDD:249776	308	EUKprk	Bacteria:26,Invertebrates:1,Plants:15	pfam00331, Glyco_hydro_10, Glycosyl hydrolase family 10.  
CDD:249777	310	EUK	Plants:8	pfam00332, Glyco_hydro_17, Glycosyl hydrolases family 17.  
CDD:144065	67	EUKprk	Bacteria:8,Invertebrates:1,Plants:2,Rodents:1	pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain.  
CDD:249778	135	EUKprk	Bacteria:93,Invertebrates:22,Mammals:1,Plants:9,Rodents:1,Vertebrates:5,Viruses:1,nodiv:1	pfam00334, NDK, Nucleoside diphosphate kinase.  
CDD:249779	221	EUK	Invertebrates:24,Mammals:2,Plants:5,Primates:2,Rodents:2,Vertebrates:7	pfam00335, Tetraspannin, Tetraspanin family.  
CDD:249780	129	EUKprk	Invertebrates:10,Mammals:1,Plants:4,Primates:1,Rodents:2,Vertebrates:6,Viruses:1	pfam00337, Gal-bind_lectin, Galactoside-binding lectin.  This family contains galactoside binding lectins.   The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5).
CDD:249781	97	EUKprk	Bacteria:83,Environmental:3,Invertebrates:27,Plants:44,Primates:2,Vertebrates:2	pfam00338, Ribosomal_S10, Ribosomal protein S10p/S20e.  This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.
CDD:249782	148	EUK	Invertebrates:6,Mammals:1,Plants:2,Rodents:1,Vertebrates:4	pfam00339, Arrestin_N, Arrestin (or S-antigen), N-terminal domain.  Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain.
CDD:144072	120	EUK	Mammals:2,Primates:2,Rodents:2	pfam00340, IL1, Interleukin-1 / 18.  This family includes interleukin-1 and interleukin-18.
CDD:249783	81	EUKprk	Invertebrates:7,Mammals:3,Primates:2,Rodents:2,Vertebrates:17,Viruses:5	pfam00341, PDGF, PDGF/VEGF domain.  
CDD:249786	342	EUKprk	Bacteria:95,Environmental:2,Invertebrates:6,Plants:21	pfam00344, SecY, SecY translocase.  
CDD:249787	119	PRK	Bacteria:90,nodiv:1	pfam00345, PapD_N, Pili and flagellar-assembly chaperone, PapD N-terminal domain.  C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly.
CDD:249789	76	EUKprk	Bacteria:35,Invertebrates:8,Plants:13,Rodents:1	pfam00347, Ribosomal_L6, Ribosomal protein L6.  
CDD:249790	260	EUKprk	Bacteria:2,Plants:3,Primates:1	pfam00348, polyprenyl_synt, Polyprenyl synthetase.  
CDD:249791	205	EUK	Invertebrates:1,Mammals:1,Plants:1,Primates:1	pfam00349, Hexokinase_1, Hexokinase.  Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam03727. Some members of the family have two copies of each of these domains.
CDD:249792	168	EUKprk	Bacteria:5,Invertebrates:1,Mammals:2,Plants:4,Rodents:2,Vertebrates:2	pfam00350, Dynamin_N, Dynamin family.  
CDD:249794	86	EUKprk	Bacteria:25,Environmental:1,Invertebrates:25,Plants:11,Rodents:1,Vertebrates:3	pfam00352, TBP, Transcription factor TFIID (or TATA-binding protein, TBP).  
CDD:109413	18	PRK	Bacteria:39	pfam00353, HemolysinCabind, Hemolysin-type calcium-binding repeat (2 copies).  
CDD:249796	99	EUKprk	Bacteria:65,Invertebrates:3,Plants:10,Primates:1,nodiv:1	pfam00355, Rieske, Rieske [2Fe-2S] domain.  The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.
CDD:249797	46	PRK	Bacteria:3	pfam00356, LacI, Bacterial regulatory proteins, lacI family.  
CDD:249798	15	EUKprk	Invertebrates:3,Primates:1,Rodents:1,Synthetic:1,Vertebrates:2	pfam00357, Integrin_alpha, Integrin alpha cytoplasmic region.  This family contains the short intracellular region of integrin alpha chains.
CDD:109418	133	PRK	Bacteria:2	pfam00358, PTS_EIIA_1, phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1.  
CDD:249799	141	PRK	Bacteria:103,Environmental:1	pfam00359, PTS_EIIA_2, Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2.  
CDD:249800	183	EUKprk	Bacteria:34,Plants:30	pfam00360, PHY, Phytochrome region.  Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain ...
CDD:201180	270	EUKprk	Bacteria:2,Invertebrates:9,Mammals:1,Plants:7,Vertebrates:1	pfam00361, Oxidored_q1, NADH-Ubiquinone/plastoquinone (complex I), various chains.  This family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.
CDD:249801	424	EUK	Invertebrates:17,Mammals:1,Primates:1,Rodents:1,Vertebrates:7	pfam00362, Integrin_beta, Integrin, beta chain.  Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF.
CDD:249802	84	EUK	Mammals:4,Primates:1,Rodents:3	pfam00363, Casein, Casein.  
CDD:249803	73	EUKprk	Bacteria:7,Invertebrates:1,Mammals:1,Plants:1,Primates:1	pfam00364, Biotin_lipoyl, Biotin-requiring enzyme.  This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognize the Glycine cleavage system H proteins.
CDD:109426	69	EUKprk	Bacteria:7,Plants:5,Rodents:1	pfam00366, Ribosomal_S17, Ribosomal protein S17.  
CDD:249804	35	PRK	Bacteria:99	pfam00367, PTS_EIIB, phosphotransferase system, EIIB.  
CDD:249805	370	EUKprk	Bacteria:50,Environmental:1,Invertebrates:16,Plants:19,Primates:1,Rodents:1,Vertebrates:1	pfam00368, HMG-CoA_red, Hydroxymethylglutaryl-coenzyme A reductase.  The HMG-CoA reductases catalyse the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, ...
CDD:249806	245	PRK	Bacteria:3	pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal domain.  This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain.
CDD:249807	278	EUK	Invertebrates:8	pfam00372, Hemocyanin_M, Hemocyanin, copper containing domain.  This family includes arthropod hemocyanins and insect larval storage proteins.
CDD:249808	114	EUK	Invertebrates:12,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	pfam00373, FERM_M, FERM central domain.  This domain is the central structural domain of the FERM domain.
CDD:249809	505	PRK	Bacteria:10	pfam00374, NiFeSe_Hases, Nickel-dependent hydrogenase.  
CDD:249810	388	EUKprk	Bacteria:114,Invertebrates:5,Vertebrates:1	pfam00375, SDF, Sodium:dicarboxylate symporter family.  
CDD:249811	38	PRK	Bacteria:126,nodiv:1	pfam00376, MerR, MerR family regulatory protein.  
CDD:249813	245	EUKprk	Bacteria:4,Primates:1,Rodents:1	pfam00378, ECH, Enoyl-CoA hydratase/isomerase family.  This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA delta-isomerase.
CDD:249814	51	EUK	Invertebrates:31	pfam00379, Chitin_bind_4, Insect cuticle protein.  Many insect cuticular proteins include a 35-36 amino acid motif known as the R&R consensus. The extensive conservation of this region led to the suggestion that it functions to bind chitin. Provocatively, it has no sequence similarity to the well-known cysteine-containing chitin-binding domain found in chitinases and some peritrophic membrane proteins. Chitin binding has been shown experimentally for this ...
CDD:249815	121	EUKprk	Bacteria:94,Environmental:2,Invertebrates:16,Plants:30,Primates:1,Vertebrates:2	pfam00380, Ribosomal_S9, Ribosomal protein S9/S16.  This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.
CDD:249816	83	PRK	Bacteria:127,Environmental:1	pfam00381, PTS-HPr, PTS HPr component phosphorylation site.  
CDD:109440	71	EUK	Invertebrates:1,Plants:2	pfam00382, TFIIB, Transcription factor TFIIB repeat.  
CDD:249817	104	EUKprk	Bacteria:15,Invertebrates:2,Phages:2,Plants:4,Primates:1,Viruses:1	pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase zinc-binding region.  
CDD:249818	358	EUKprk	Bacteria:7,Invertebrates:1,Plants:3,Primates:1	pfam00384, Molybdopterin, Molybdopterin oxidoreductase.  
CDD:249819	54	EUK	Invertebrates:15,Plants:31,Primates:3,Rodents:2,Vertebrates:3	pfam00385, Chromo, Chromo (CHRromatin Organisation MOdifier) domain.  
CDD:249820	125	EUK	Invertebrates:3,Mammals:3,Primates:1,Rodents:2,Vertebrates:10	pfam00386, C1q, C1q domain.  C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
CDD:249821	117	EUK	Invertebrates:11,Plants:20,Primates:2,Rodents:1,Vertebrates:3	pfam00387, PI-PLC-Y, Phosphatidylinositol-specific phospholipase C, Y domain.  This associates with pfam00388 to form a single structural unit.
CDD:249822	145	EUKprk	Bacteria:8,Invertebrates:14,Mammals:1,Plants:19,Primates:1,Rodents:3	pfam00388, PI-PLC-X, Phosphatidylinositol-specific phospholipase C, X domain.  This associates with pfam00387 to form a single structural unit.
CDD:249823	312	EUKprk	Bacteria:37,Invertebrates:4,Plants:2,Primates:1,Rodents:1,Viruses:1	pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain.  This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.
CDD:249824	182	EUKprk	Bacteria:21,Invertebrates:5,Plants:4,Primates:1,Vertebrates:1	pfam00390, malic, Malic enzyme, N-terminal domain.  
CDD:249825	73	EUKprk	Bacteria:127,Environmental:4,Invertebrates:2	pfam00391, PEP-utilizers, PEP-utilizing enzyme, mobile domain.  This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it.
CDD:201202	64	PRK	Bacteria:7	pfam00392, GntR, Bacterial regulatory proteins, gntR family.  This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction ...
CDD:249826	290	EUKprk	Bacteria:31,Invertebrates:7,Mammals:1,Plants:10	pfam00393, 6PGD, 6-phosphogluconate dehydrogenase, C-terminal domain.  This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase.   The domain contains two structural repeats of 5 helices each.
CDD:249827	142	EUKprk	Bacteria:7,Plants:31,Primates:1	pfam00394, Cu-oxidase, Multicopper oxidase.  Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
CDD:249828	44	PRK	Bacteria:53	pfam00395, SLH, S-layer homology domain.  
CDD:249829	43	EUKprk	Bacteria:1,Invertebrates:7,Mammals:2,Plants:10,Primates:3,Rodents:3,Vertebrates:5	pfam00396, Granulin, Granulin.  
CDD:249830	30	EUK	Invertebrates:57,Mammals:5,Plants:68,Primates:5,Rodents:3,Vertebrates:4	pfam00397, WW, WW domain.  The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
CDD:249831	258	EUKprk	Bacteria:13,Plants:3	pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.  
CDD:144114	18	EUK	Plants:2	pfam00399, PIR, Yeast PIR protein repeat.  
CDD:249832	39	EUKprk	Bacteria:3,Invertebrates:21,Mammals:2,Plants:32,Primates:1,Rodents:4,Vertebrates:3,nodiv:1	pfam00400, WD40, WD domain, G-beta repeat.  
CDD:249833	46	EUKprk	Bacteria:120,Invertebrates:1,Plants:33,Primates:1,Vertebrates:1	pfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long alpha-helix domain.  Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213).
CDD:249834	62	EUKprk	Bacteria:37,Environmental:1,Invertebrates:4,Mammals:1,Plants:13,nodiv:1	pfam00403, HMA, Heavy-metal-associated domain.  
CDD:249835	21	PRK	Bacteria:16	pfam00404, Dockerin_1, Dockerin type I repeat.  The dockerin repeat is the binding partner of the cohesin domain pfam00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome. The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium.
CDD:249837	186	EUKprk	Bacteria:5,Invertebrates:1,Mammals:1,Plants:2,Primates:1,Vertebrates:1	pfam00406, ADK, Adenylate kinase.  
CDD:249838	150	EUK	Plants:15	pfam00407, Bet_v_1, Pathogenesis-related protein Bet v I family.  This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several ...
CDD:249839	71	EUKprk	Bacteria:87,Environmental:1,Invertebrates:2,Plants:5	pfam00408, PGM_PMM_IV, Phosphoglucomutase/phosphomannomutase, C-terminal domain.  
CDD:249840	127	EUKprk	Bacteria:73,Environmental:2,Invertebrates:6,Plants:31	pfam00410, Ribosomal_S8, Ribosomal protein S8.  
CDD:189537	109	EUKprk	Bacteria:4,Invertebrates:1,Plants:8	pfam00411, Ribosomal_S11, Ribosomal protein S11.  
CDD:249841	58	EUK	Invertebrates:1,Plants:2,Primates:1,Rodents:1,Vertebrates:2	pfam00412, LIM, LIM domain.  This family represents two copies of the LIM structural domain.
CDD:249842	158	EUKprk	Invertebrates:5,Mammals:5,Plants:4,Primates:1,Rodents:2,Vertebrates:5,Viruses:7,nodiv:1	pfam00413, Peptidase_M10, Matrixin.  The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
CDD:249843	50	EUKprk	Bacteria:5,Invertebrates:17,Plants:17,Primates:3,Rodents:2,Vertebrates:2	pfam00415, RCC1, Regulator of chromosome condensation (RCC1) repeat.  
CDD:249844	107	EUKprk	Bacteria:5,Invertebrates:2,Plants:6,Rodents:1	pfam00416, Ribosomal_S13, Ribosomal protein S13/S18.  This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
CDD:249845	143	PRK	Bacteria:112,nodiv:1	pfam00419, Fimbrial, Fimbrial protein.  
CDD:249846	95	EUKprk	Bacteria:42,Invertebrates:39,Mammals:17,Plants:18,Primates:6,Rodents:14,Vertebrates:32	pfam00420, Oxidored_q2, NADH-ubiquinone/plastoquinone oxidoreductase chain 4L.  
CDD:249848	545	PRK	Viruses:13	pfam00423, HN, Haemagglutinin-neuraminidase.  
CDD:249850	255	EUKprk	Bacteria:137,Environmental:1,Plants:6	pfam00425, Chorismate_bind, chorismate binding enzyme.  This family includes the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase.
CDD:201220	131	EUKprk	Bacteria:32,Plants:7	pfam00427, PBS_linker_poly, Phycobilisome Linker polypeptide.  
CDD:249851	88	EUKprk	Bacteria:10,Environmental:1,Invertebrates:34,Mammals:1,Plants:23,Rodents:2	pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein.  This family includes archaebacterial L12, eukaryotic P0, P1 and P2.
CDD:249852	560	PRK	Viruses:9	pfam00429, TLV_coat, ENV polyprotein (coat polyprotein).  
CDD:109486	132	EUKprk	Bacteria:10,Plants:7	pfam00430, ATP-synt_B, ATP synthase B/B' CF(0).  Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006.
CDD:249853	110	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:1	pfam00431, CUB, CUB domain.  
CDD:109488	44	EUKprk	Bacteria:2,Mammals:1,Plants:2,Primates:1,Rodents:1	pfam00432, Prenyltrans, Prenyltransferase and squalene oxidase repeat.  
CDD:249854	47	EUK	Invertebrates:16,Mammals:2,Plants:24,Primates:1,Rodents:2,Vertebrates:3,nodiv:1	pfam00433, Pkinase_C, Protein kinase C terminal domain.  
CDD:249855	105	EUK	Primates:1	pfam00435, Spectrin, Spectrin repeat.  Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin domain- repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position ...
CDD:249856	102	EUKprk	Bacteria:38,Environmental:1,Invertebrates:2,Phages:4,Plants:3,Rodents:1,Unassigned:1	pfam00436, SSB, Single-strand binding protein family.  This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.
CDD:249857	273	PRK	Bacteria:10	pfam00437, T2SE, Type II/IV secretion system protein.  This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection.
CDD:249858	100	EUKprk	Bacteria:83,Invertebrates:8,Mammals:1,Plants:3,Primates:1	pfam00438, S-AdoMet_synt_N, S-adenosylmethionine synthetase, N-terminal domain.  The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.
CDD:249859	84	EUK	Invertebrates:16,Plants:17,Primates:1,Vertebrates:1	pfam00439, Bromodomain, Bromodomain.  Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
CDD:249860	47	PRK	Bacteria:43	pfam00440, TetR_N, Bacterial regulatory proteins, tetR family.  
CDD:249861	150	EUKprk	Bacteria:28,Invertebrates:1,Plants:2	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain.  C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.
CDD:249862	311	EUK	Invertebrates:2,Mammals:2,Plants:4,Primates:2,Rodents:1	pfam00443, UCH, Ubiquitin carboxyl-terminal hydrolase.  
CDD:249863	38	EUKprk	Bacteria:68,Environmental:1,Invertebrates:8,Plants:25,Primates:1,Rodents:1,Vertebrates:1	pfam00444, Ribosomal_L36, Ribosomal protein L36.  
CDD:249864	183	EUKprk	Bacteria:40,Invertebrates:10,Plants:40,Rodents:1,Vertebrates:1,nodiv:1	pfam00445, Ribonuclease_T2, Ribonuclease T2 family.  
CDD:249865	96	EUK	Invertebrates:7,Plants:33,Primates:1,Rodents:1,Vertebrates:3	pfam00447, HSF_DNA-bind, HSF-type DNA-binding.  
CDD:249866	195	EUKprk	Bacteria:19,Invertebrates:1,Plants:5,Primates:1	pfam00448, SRP54, SRP54-type protein, GTPase domain.  This family includes relatives of the G-domain of the SRP54 family of proteins.
CDD:249867	121	EUKprk	Bacteria:88,Invertebrates:1,Plants:15	pfam00449, Urease_alpha, Urease alpha-subunit, N-terminal domain.  The N-terminal domain is a composite domain and plays a major trimer stabilizing role by contacting the catalytic domain of the symmetry related alpha-subunit.
CDD:249868	410	EUKprk	Bacteria:1,Invertebrates:3,Plants:22,Primates:1,Rodents:1	pfam00450, Peptidase_S10, Serine carboxypeptidase.  
CDD:249869	32	EUK	Invertebrates:24,Plants:1	pfam00451, Toxin_2, Scorpion short toxin, BmKK2.  Members of this family, which are found in various scorpion toxins, confer potassium channel blocking activity.
CDD:249870	100	EUKprk	Invertebrates:8,Mammals:3,Primates:2,Rodents:3,Vertebrates:6,Viruses:9,nodiv:1	pfam00452, Bcl-2, Apoptosis regulator proteins, Bcl-2 family.  
CDD:249871	107	EUKprk	Bacteria:73,Environmental:2,Invertebrates:4,Plants:23,Rodents:1	pfam00453, Ribosomal_L20, Ribosomal protein L20.  
CDD:249872	232	EUKprk	Bacteria:1,Invertebrates:4,Mammals:1,Plants:3,Primates:1,Rodents:2	pfam00454, PI3_PI4_kinase, Phosphatidylinositol 3- and 4-kinase.  Some members of this family probably do not have lipid kinase activity and are protein kinases.
CDD:249873	162	PRK	Bacteria:55,nodiv:1	pfam00455, DeoRC, DeoR C terminal sensor domain.  The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site. DeorC senses diverse sugar derivatives such as deoxyribose nucleoside (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR),,.
CDD:249874	333	EUKprk	Bacteria:3,Plants:2,Primates:1	pfam00456, Transketolase_N, Transketolase, thiamine diphosphate binding domain.  This family includes transketolase enzymes EC:2.2.1.1. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit EC:1.2.4.4. Both these enzymes utilize thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.
CDD:249876	56	EUK	Invertebrates:11,Mammals:2,Plants:2,Primates:2,Rodents:2,Vertebrates:5	pfam00458, WHEP-TRS, WHEP-TRS domain.  
CDD:249877	269	EUKprk	Bacteria:19,Invertebrates:2,Mammals:2,Plants:5,Primates:1,Rodents:1	pfam00459, Inositol_P, Inositol monophosphatase family.  
CDD:109515	31	PRK	Bacteria:4	pfam00460, Flg_bb_rod, Flagella basal body rod protein.  
CDD:249878	60	EUKprk	Bacteria:96,Environmental:1,Invertebrates:15,Mammals:1,Phages:4,Plants:20,Primates:3,Rodents:1,Vertebrates:2,Viruses:2,nodiv:2	pfam00462, Glutaredoxin, Glutaredoxin.  
CDD:249880	323	EUKprk	Bacteria:134,Environmental:1,Invertebrates:6,Plants:6	pfam00465, Fe-ADH, Iron-containing alcohol dehydrogenase.  
CDD:249881	100	EUKprk	Bacteria:81,Environmental:6,Invertebrates:13,Plants:12	pfam00466, Ribosomal_L10, Ribosomal protein L10.  
CDD:249882	32	EUKprk	Bacteria:43,Invertebrates:10,Mammals:2,Plants:19,Primates:2,Rodents:1,Vertebrates:2	pfam00467, KOW, KOW motif.  This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.
CDD:249883	44	EUKprk	Bacteria:104,Invertebrates:1,Plants:22,Primates:1	pfam00468, Ribosomal_L34, Ribosomal protein L34.  
CDD:249884	220	PRK	Viruses:21	pfam00469, F-protein, Negative factor, (F-Protein) or Nef.  Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src kinase family.
CDD:249885	48	EUKprk	Bacteria:80,Invertebrates:5,Plants:19	pfam00471, Ribosomal_L33, Ribosomal protein L33.  
CDD:249886	114	EUKprk	Bacteria:64,Environmental:1,Invertebrates:12,Plants:4,Rodents:1	pfam00472, RF-1, RF-1 domain.  This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.
CDD:109527	406	EUKprk	Bacteria:1,Primates:1	pfam00474, SSF, Sodium:solute symporter family.  Membership of this family is supported by a significant blast score.
CDD:249887	145	EUKprk	Bacteria:65,Environmental:2,Plants:5,nodiv:1	pfam00475, IGPD, Imidazoleglycerol-phosphate dehydratase.  
CDD:249888	383	PRK	Bacteria:3,Phages:3	pfam00476, DNA_pol_A, DNA polymerase family A.  
CDD:249889	467	EUKprk	Bacteria:36,Invertebrates:6,Plants:5,Primates:1,Rodents:3	pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain.  This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family.
CDD:249890	183	EUKprk	Bacteria:63,Invertebrates:8,Mammals:1,Plants:18,Primates:1,Vertebrates:2	pfam00479, G6PD_N, Glucose-6-phosphate dehydrogenase, NAD binding domain.  
CDD:249891	181	PRK	Bacteria:11	pfam00480, ROK, ROK family.  
CDD:249892	253	EUKprk	Bacteria:1,Invertebrates:3,Plants:5,Primates:1	pfam00481, PP2C, Protein phosphatase 2C.  Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.
CDD:249893	125	PRK	Bacteria:104	pfam00482, T2SF, Type II secretion system (T2SS), protein F.  The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella. This domain seems to show some similarity to PF00664 but this may just be due ...
CDD:249894	247	EUKprk	Bacteria:28,Plants:7	pfam00483, NTP_transferase, Nucleotidyl transferase.  This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars.
CDD:249895	152	EUKprk	Bacteria:311,Environmental:3,Invertebrates:8,Plants:43	pfam00484, Pro_CA, Carbonic anhydrase.  This family includes carbonic anhydrases as well as a family of non-functional homologues related to YbcF.
CDD:249896	196	EUKprk	Bacteria:5,Invertebrates:1,Plants:2	pfam00485, PRK, Phosphoribulokinase / Uridine kinase family.  In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
CDD:249897	77	EUKprk	Bacteria:119,Plants:3	pfam00486, Trans_reg_C, Transcriptional regulatory protein, C terminal.  
CDD:249898	251	EUKprk	Bacteria:70,Environmental:2,Invertebrates:6,Plants:11,Primates:1	pfam00487, FA_desaturase, Fatty acid desaturase.  
CDD:249899	235	EUKprk	Bacteria:11,Invertebrates:1,Plants:3,Primates:1	pfam00488, MutS_V, MutS domain V.  This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair ...
CDD:249901	322	EUKprk	Bacteria:90,Environmental:3,Invertebrates:9,Plants:9,Rodents:1	pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.  
CDD:249902	274	EUKprk	Bacteria:158,Environmental:2,Invertebrates:4,Plants:13,Primates:1,Rodents:1,Vertebrates:4	pfam00491, Arginase, Arginase family.  
CDD:249903	330	EUKprk	Bacteria:9,Invertebrates:11,Plants:6,Rodents:2	pfam00493, MCM, MCM2/3/5 family.  
CDD:249904	262	EUKprk	Bacteria:96,Environmental:7,Invertebrates:7,Plants:15	pfam00494, SQS_PSY, Squalene/phytoene synthase.  
CDD:249905	361	PRK	Bacteria:88,nodiv:1	pfam00496, SBP_bac_5, Bacterial extracellular solute-binding proteins, family 5 Middle.  The borders of this family are based on the PDBSum definitions of the domain edges for Salmonella typhimurium oppA.
CDD:249906	220	PRK	Bacteria:254,Environmental:1,nodiv:1	pfam00497, SBP_bac_3, Bacterial extracellular solute-binding proteins, family 3.  
CDD:249907	67	EUKprk	Bacteria:38,Invertebrates:6,Mammals:1,Plants:11,Primates:1,Rodents:2,Vertebrates:3	pfam00498, FHA, FHA domain.  The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
CDD:249908	139	EUKprk	Bacteria:22,Invertebrates:57,Plants:10,Primates:1,Vertebrates:4	pfam00499, Oxidored_q3, NADH-ubiquinone/plastoquinone oxidoreductase chain 6.  
CDD:249909	500	PRK	Viruses:19	pfam00500, Late_protein_L1, L1 (late) protein.  
CDD:249910	398	EUKprk	Bacteria:58,Invertebrates:10,Mammals:1,Plants:13,Primates:1,Rodents:2	pfam00501, AMP-binding, AMP-binding enzyme.  
CDD:249911	157	EUKprk	Bacteria:7,Plants:3	pfam00502, Phycobilisome, Phycobilisome protein.  
CDD:249912	317	EUK	Invertebrates:9,Mammals:1,Plants:13,Primates:3,Rodents:2	pfam00503, G-alpha, G-protein alpha subunit.  G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the ...
CDD:249913	134	EUK	Invertebrates:1,Plants:45,nodiv:1	pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein.  
CDD:189580	69	EUKprk	Invertebrates:4,Plants:6,Primates:2,Rodents:1,Vertebrates:1,Viruses:1,nodiv:1	pfam00505, HMG_box, HMG (high mobility group) box.  
CDD:249915	101	EUKprk	Bacteria:20,Invertebrates:60,Plants:12,Rodents:1,Vertebrates:1	pfam00507, Oxidored_q4, NADH-ubiquinone/plastoquinone oxidoreductase, chain 3.  
CDD:249916	201	PRK	Viruses:83	pfam00508, PPV_E2_N, E2 (early) protein, N terminal.  
CDD:249917	550	PRK	Viruses:15	pfam00509, Hemagglutinin, Haemagglutinin.  Hemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalises the virus by endocytosis. The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion.
CDD:249918	258	EUK	Invertebrates:3,Mammals:2,Plants:5	pfam00510, COX3, Cytochrome c oxidase subunit III.  
CDD:249919	81	PRK	Viruses:46	pfam00511, PPV_E2_C, E2 (early) protein, C terminal.  
CDD:249920	66	EUKprk	Bacteria:64,Invertebrates:1,Plants:8	pfam00512, HisKA, His Kinase A (phospho-acceptor) domain.  Dimerization and phospho-acceptor domain of histidine kinases.
CDD:249921	466	PRK	Viruses:29	pfam00513, Late_protein_L2, Late Protein L2.  
CDD:249922	41	EUK	Invertebrates:5,Mammals:1,Plants:5,Primates:2,Rodents:2,Vertebrates:1,nodiv:1	pfam00514, Arm, Armadillo/beta-catenin-like repeat.  Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.
CDD:249923	34	EUKprk	Bacteria:26,Invertebrates:10,Mammals:3,Plants:28,Primates:1,Rodents:4,Vertebrates:1	pfam00515, TPR_1, Tetratricopeptide repeat.  
CDD:249924	493	PRK	Viruses:20	pfam00516, GP120, Envelope glycoprotein GP120.  The entry of HIV requires interaction of viral GP120 with CD4 and a chemokine receptor on the cell surface.
CDD:249925	204	EUKprk	Primates:1,Viruses:2	pfam00517, GP41, Retroviral envelope protein.  This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein ...
CDD:109569	110	PRK	Viruses:25,nodiv:1	pfam00518, E6, Early Protein (E6).  
CDD:249926	432	PRK	Viruses:65	pfam00519, PPV_E1_C, Papillomavirus helicase.  This protein is a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508.
CDD:249927	195	EUKprk	Bacteria:1,Invertebrates:22,Mammals:4,Plants:6,Primates:1,Rodents:3,Vertebrates:7	pfam00520, Ion_trans, Ion transport protein.  This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial ...
CDD:249928	427	EUKprk	Bacteria:50,Environmental:1,Invertebrates:12,Phages:3,Plants:5,Primates:1,Rodents:1,Viruses:3	pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.  
CDD:249929	468	PRK	Viruses:12	pfam00523, Fusion_gly, Fusion glycoprotein F0.  
CDD:249930	130	PRK	Viruses:32	pfam00524, PPV_E1_N, E1 Protein, N terminal domain.  
CDD:109577	24	EUK	Invertebrates:2	pfam00526, Dicty_CTDC, Dictyostelium (slime mold) repeat.  
CDD:249932	92	PRK	Viruses:75	pfam00527, E7, E7 protein, Early protein.  
CDD:144205	183	PRK	Bacteria:4	pfam00528, BPD_transp_1, Binding-protein-dependent transport system inner membrane component.  The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.
CDD:249933	303	PRK	Bacteria:23	pfam00529, HlyD, HlyD family secretion protein.  
CDD:249934	99	EUK	Invertebrates:13,Mammals:4,Primates:4,Rodents:2,Vertebrates:6	pfam00530, SRCR, Scavenger receptor cysteine-rich domain.  These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
CDD:249935	81	EUK	Invertebrates:6,Mammals:2,Primates:3,Rodents:2,Vertebrates:8	pfam00531, Death, Death domain.  
CDD:249937	75	EUKprk	Bacteria:2,Invertebrates:3,Mammals:1,Plants:7,Primates:1,Rodents:1,Vertebrates:2	pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain.  The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT ...
CDD:249938	158	EUKprk	Bacteria:28,Invertebrates:1,Plants:1	pfam00534, Glycos_transf_1, Glycosyl transferases group 1.  Mutations in this domain of human PIGA lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family.
CDD:249939	168	EUKprk	Bacteria:76,Invertebrates:4,Phages:2,Plants:1,Primates:1,Rodents:2,Viruses:1	pfam00535, Glycos_transf_2, Glycosyl transferase family 2.  Diverse family, transferring sugar from UDP-glucose, UDP-N-acetyl- galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.
CDD:249940	64	EUK	Invertebrates:4,Plants:1,Primates:1,Rodents:2,Vertebrates:3	pfam00536, SAM_1, SAM domain (Sterile alpha motif).  It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.
CDD:201290	54	EUK	Invertebrates:14,Plants:2	pfam00537, Toxin_3, Scorpion toxin-like domain.  This family contains both neurotoxins and plant defensins. The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activity against aphids. Brazzein is plant defensin-like protein. It is pH-stable, heat-stable and intensely sweet protein. The scorpion toxin (a neurotoxin) binds ...
CDD:249941	77	EUK	Invertebrates:3,Plants:2,Primates:1,Vertebrates:1	pfam00538, Linker_histone, linker histone H1 and H5 family.  Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.
CDD:249942	68	PRK	Viruses:19	pfam00539, Tat, Transactivating regulatory protein (Tat).  The retroviral Tat protein binds to the Tar RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.
CDD:249944	170	PRK	Viruses:47	pfam00541, Adeno_knob, Adenoviral fibre protein (knob domain).  Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, termed the carboxy-terminal knob domain.
CDD:249945	68	EUKprk	Bacteria:135,Environmental:3,Invertebrates:5,Plants:8,Primates:1,Vertebrates:3	pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal domain.  
CDD:201295	102	EUKprk	Bacteria:58,Plants:3	pfam00543, P-II, Nitrogen regulatory protein P-II.  P-II modulates the activity of glutamine synthetase.
CDD:249946	200	EUKprk	Bacteria:4,Plants:3	pfam00544, Pec_lyase_C, Pectate lyase.  This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and soft rotting of plant tissue.
CDD:249947	83	EUKprk	Bacteria:52,Plants:19	pfam00545, Ribonuclease, ribonuclease.  This enzyme hydrolyses RNA and oligoribonucleotides.
CDD:249948	99	EUKprk	Bacteria:66,Environmental:1,Plants:7	pfam00547, Urease_gamma, Urease, gamma subunit.  Urease is a nickel-binding enzyme that catalyses the hydrolysis of urea to carbon dioxide and ammonia.
CDD:249949	170	PRK	Viruses:16	pfam00548, Peptidase_C3, 3C cysteine protease (picornain 3C).  Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.
CDD:249950	128	EUKprk	Bacteria:9,Invertebrates:2,Mammals:1	pfam00549, Ligase_CoA, CoA-ligase.  This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilize ATP others use GTP.
CDD:249951	67	EUKprk	Bacteria:87,Environmental:1,Invertebrates:2,Plants:21	pfam00550, PP-binding, Phosphopantetheine attachment site.  A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional ...
CDD:249952	181	EUKprk	Bacteria:1,Plants:1,Rodents:1	pfam00551, Formyl_trans_N, Formyl transferase.  This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the ...
CDD:144223	53	EUKprk	Mammals:1,Primates:1,Rodents:1,Vertebrates:1,Viruses:6	pfam00552, IN_DBD_C, Integrase DNA binding domain.  Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.
CDD:249953	101	PRK	Bacteria:7	pfam00553, CBM_2, Cellulose binding domain.  Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.
CDD:249954	169	EUK	Invertebrates:4,Mammals:1,Rodents:1,Vertebrates:3	pfam00554, RHD, Rel homology domain (RHD).  Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
CDD:249955	205	PRK	Bacteria:11	pfam00555, Endotoxin_M, delta endotoxin.  This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading ...
CDD:249956	40	PRK	Bacteria:12	pfam00556, LHC, Antenna complex alpha/beta subunit.  
CDD:249957	208	EUKprk	Bacteria:315,Environmental:7,Invertebrates:29,Plants:36,Rodents:1,Vertebrates:2,nodiv:1	pfam00557, Peptidase_M24, Metallopeptidase family M24.  This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module.
CDD:109608	81	PRK	Viruses:2	pfam00558, Vpu, Vpu protein.  The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.
CDD:249958	22	EUKprk	Bacteria:28,Invertebrates:28,Mammals:5,Phages:1,Plants:61,Primates:2,Rodents:3,Vertebrates:7,Viruses:2	pfam00560, LRR_1, Leucine Rich Repeat.  CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein. Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units ...
CDD:249959	225	EUKprk	Bacteria:18,Invertebrates:2,Plants:3,Primates:1,nodiv:1	pfam00561, Abhydrolase_1, alpha/beta hydrolase fold.  This catalytic domain is found in a very wide range of enzymes.
CDD:249960	373	EUKprk	Bacteria:43,Environmental:1,Invertebrates:16,Plants:19,Primates:1,Rodents:1,Viruses:13	pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6.  RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / ...
CDD:249961	231	PRK	Bacteria:109	pfam00563, EAL, EAL domain.  This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site.
CDD:249962	84	EUK	Invertebrates:1,Plants:2,Primates:1,Rodents:1	pfam00564, PB1, PB1 domain.  
CDD:249963	106	EUKprk	Bacteria:5,Invertebrates:1,Plants:3	pfam00565, SNase, Staphylococcal nuclease homologue.  Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.
CDD:249964	206	EUK	Invertebrates:21,Mammals:1,Plants:13,Primates:2,Rodents:2,Vertebrates:2	pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain.  Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases.
CDD:249965	118	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:2,Vertebrates:1	pfam00567, TUDOR, Tudor domain.  
CDD:144236	46	EUK	Invertebrates:1,Primates:1,Rodents:1	pfam00569, ZZ, Zinc finger, ZZ type.  Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
CDD:249966	68	EUKprk	Bacteria:91,Environmental:1,Invertebrates:7,Plants:8,Rodents:1	pfam00570, HRDC, HRDC domain.  The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
CDD:249967	57	EUKprk	Bacteria:123,Environmental:4,Invertebrates:6,Plants:16,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	pfam00571, CBS, CBS domain.  CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other ...
CDD:249968	128	EUKprk	Bacteria:52,Environmental:2,Invertebrates:12,Plants:17,Rodents:1	pfam00572, Ribosomal_L13, Ribosomal protein L13.  
CDD:249969	190	EUKprk	Bacteria:107,Environmental:3,Invertebrates:15,Plants:16,Primates:1,Synthetic:1	pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family.  This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA.
CDD:249970	182	EUKprk	Bacteria:20,Invertebrates:2,Phages:4,Plants:8,Rodents:1	pfam00574, CLP_protease, Clp protease.  The Clp protease has an active site catalytic triad. In Escherichia coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Cyanophora parodoxa clpP-B has lost all of these active site residues and is therefore inactive. Some members contain one or two large insertions.
CDD:249971	74	EUKprk	Bacteria:5,Invertebrates:1,Plants:2,Rodents:1,Viruses:1	pfam00575, S1, S1 RNA binding domain.  The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
CDD:249972	111	EUKprk	Bacteria:6,Invertebrates:1,Mammals:2,Plants:1,Rodents:1,Vertebrates:4	pfam00576, Transthyretin, HIUase/Transthyretin family.  This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU. HIU hydrolysis ...
CDD:249973	552	PRK	Bacteria:10	pfam00577, Usher, Outer membrane usher protein.  In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher'. The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of ...
CDD:249974	124	EUKprk	Bacteria:79,Environmental:1,Invertebrates:10,Mammals:1,Plants:9	pfam00578, AhpC-TSA, AhpC/TSA family.  This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).
CDD:249975	290	EUKprk	Bacteria:6,Invertebrates:1,Plants:4,Primates:1	pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).  
CDD:249976	267	EUKprk	Bacteria:19,Plants:1	pfam00580, UvrD-helicase, UvrD/REP helicase N-terminal domain.  The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Some members have large insertions near to the carboxy-terminus relative to other members of the family.
CDD:249977	106	EUKprk	Bacteria:86,Environmental:3,Invertebrates:8,Plants:12,Primates:1,Rodents:1,Vertebrates:1	pfam00581, Rhodanese, Rhodanese-like domain.  Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
CDD:249978	139	EUKprk	Bacteria:58,Invertebrates:1,Plants:3,nodiv:1	pfam00582, Usp, Universal stress protein family.  The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that ...
CDD:249979	80	EUKprk	Bacteria:76,Invertebrates:5,Phages:1,Plants:6,Primates:1,Rodents:1,Vertebrates:1	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family.  This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.
CDD:249980	56	EUKprk	Bacteria:141,Environmental:2,Invertebrates:7,Plants:5	pfam00584, SecE, SecE/Sec61-gamma subunits of protein translocation complex.  SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha translocates protein from the cytoplasm to the ER. Archaea have a similar complex.
CDD:109635	91	EUKprk	Bacteria:1,Plants:1	pfam00585, Thr_dehydrat_C, C-terminal regulatory domain of Threonine dehydratase.  Threonine dehydratases pfam00291 all contain a carboxy terminal region. This region may have a regulatory role. Some members contain two copies of this region. This family is homologous to the pfam01842 domain.
CDD:249981	94	EUKprk	Bacteria:323,Environmental:7,Invertebrates:9,Mammals:1,Phages:1,Plants:12,Primates:2,Vertebrates:2	pfam00586, AIRS, AIR synthase related protein, N-terminal domain.  This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain.
CDD:249982	171	EUKprk	Bacteria:17,Invertebrates:2,Plants:5,Primates:1	pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G, H, P, S and T).  Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases.
CDD:249983	142	EUKprk	Bacteria:79,Environmental:3,Invertebrates:2,Plants:3,Primates:1	pfam00588, SpoU_methylase, SpoU rRNA Methylase family.  This family of proteins probably use S-AdoMet.
CDD:249984	170	PRK	Bacteria:8,Phages:8,Viruses:1,nodiv:1	pfam00589, Phage_integrase, Phage integrase family.  Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.
CDD:249985	198	EUKprk	Bacteria:100,Environmental:1,Plants:4	pfam00590, TP_methylase, Tetrapyrrole (Corrin/Porphyrin) Methylases.  This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase.
CDD:249986	253	EUKprk	Bacteria:11,Primates:1	pfam00591, Glycos_transf_3, Glycosyl transferase family, a/b domain.  This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.
CDD:249987	257	PRK	Bacteria:103,Environmental:2,nodiv:1	pfam00593, TonB_dep_Rec, TonB dependent receptor.  This model now only covers the conserved part of the barrel structure.
CDD:109643	42	EUK	Mammals:4,Primates:1,Rodents:2,Vertebrates:4	pfam00594, Gla, Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain.  This domain is responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).
CDD:249988	80	EUKprk	Bacteria:5,Invertebrates:1,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF).  PDZ domains are found in diverse signaling proteins.
CDD:249989	179	EUKprk	Bacteria:244,Environmental:3,Invertebrates:10,Plants:22,Rodents:1,Vertebrates:2	pfam00596, Aldolase_II, Class II Aldolase and Adducin N-terminal domain.  This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
CDD:249991	110	EUK	Invertebrates:2,Mammals:2,Primates:2,Rodents:1,Vertebrates:5	pfam00605, IRF, Interferon regulatory factor transcription factor.  This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.
CDD:249992	711	PRK	Viruses:39	pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B.  This family of proteins contains a transmembrane region.
CDD:249993	197	EUKprk	Primates:1,Viruses:11	pfam00607, Gag_p24, gag gene protein p24 (core nucleocapsid protein).  p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.
CDD:109656	30	PRK	Viruses:10	pfam00608, Adeno_shaft, Adenoviral fibre protein (repeat/shaft region).  There is no separation between signal and noise. Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, rather than the 'shaft' region represented by this family. The alignment of this family contains two copies of a fifteen residue ...
CDD:249994	157	EUK	Invertebrates:12,Plants:5,Primates:1,Rodents:1,Vertebrates:1	pfam00609, DAGK_acc, Diacylglycerol kinase accessory domain.  Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
CDD:249995	74	EUKprk	Bacteria:3,Invertebrates:11,Mammals:1,Plants:34,Primates:1,Rodents:2,Vertebrates:5,nodiv:1	pfam00610, DEP, Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP).  The DEP domain is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting. New findings in ...
CDD:249996	91	EUKprk	Invertebrates:11,Mammals:2,Plants:29,Primates:2,Rodents:1,Vertebrates:4,Viruses:1	pfam00611, FCH, Fes/CIP4, and EFC/F-BAR homology domain.  Alignment extended from. Highly alpha-helical. The cytosolic endocytic adaptor proteins in fungi carry this domain at the N-terminus; several of these have been referred to as muniscin proteins. These N-terminal BAR, N-BAR, and EFC/F-BAR domains are found in proteins that regulate membrane trafficking events by inducing membrane ...
CDD:249997	21	EUKprk	Bacteria:1,Invertebrates:8,Mammals:6,Plants:8,Primates:1,Rodents:2,Vertebrates:5	pfam00612, IQ, IQ calmodulin-binding motif.  Calmodulin-binding motif.
CDD:144268	185	EUK	Mammals:1,Primates:1	pfam00613, PI3Ka, Phosphoinositide 3-kinase family, accessory domain (PIK domain).  PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation.
CDD:216022	28	EUKprk	Bacteria:3,Plants:3,Viruses:6	pfam00614, PLDc, Phospholipase D Active site motif.  Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, ...
CDD:249998	117	EUK	Invertebrates:8,Mammals:1,Plants:4,Primates:1,Rodents:2,Vertebrates:4	pfam00615, RGS, Regulator of G protein signaling domain.  RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
CDD:249999	183	EUK	Invertebrates:11,Plants:26,Primates:1,Rodents:2	pfam00616, RasGAP, GTPase-activator protein for Ras-like GTPase.  All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position.
CDD:250000	186	EUK	Invertebrates:9,Mammals:1,Plants:25,Primates:4,Rodents:3,Vertebrates:2	pfam00617, RasGEF, RasGEF domain.  Guanine nucleotide exchange factor for Ras-like small GTPases.
CDD:250001	94	EUK	Invertebrates:4,Mammals:1,Plants:6,Primates:2,Rodents:2	pfam00618, RasGEF_N, RasGEF N-terminal motif.  A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.
CDD:250002	85	EUKprk	Invertebrates:3,Mammals:4,Primates:1,Rodents:5,Vertebrates:3,Viruses:2	pfam00619, CARD, Caspase recruitment domain.  Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
CDD:250003	152	EUK	Invertebrates:4,Plants:7,Primates:1,Rodents:2	pfam00620, RhoGAP, RhoGAP domain.  GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
CDD:250004	180	EUK	Invertebrates:16,Mammals:1,Plants:15,Primates:4,Rodents:2,Vertebrates:4	pfam00621, RhoGEF, RhoGEF domain.  Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that pfam00169 domains invariably occur C-terminal to RhoGEF/DH domains.
CDD:250005	123	EUK	Invertebrates:2,Mammals:3,Plants:1,Rodents:2	pfam00622, SPRY, SPRY domain.  SPRY Domain is named from SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
CDD:250006	165	EUKprk	Bacteria:3,Invertebrates:5,Plants:6,Primates:1,Viruses:2	pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2.  RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
CDD:250007	44	EUK	Plants:5	pfam00624, Flocculin, Flocculin repeat.  This short repeat is rich in serine and threonine residues.
CDD:250008	183	EUKprk	Bacteria:1,Invertebrates:1,Mammals:1,Plants:1,Primates:1	pfam00625, Guanylate_kin, Guanylate kinase.  
CDD:250009	76	EUK	Invertebrates:3,Plants:4,Primates:1,Vertebrates:1	pfam00626, Gelsolin, Gelsolin repeat.  
CDD:250010	37	EUKprk	Bacteria:10,Invertebrates:4,Plants:13,Primates:1,Rodents:2	pfam00627, UBA, UBA/TS-N domain.  This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N ...
CDD:250011	51	EUK	Invertebrates:2,Plants:7,Primates:1,Rodents:1,Vertebrates:1	pfam00628, PHD, PHD-finger.  PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
CDD:250012	159	EUKprk	Bacteria:1,Invertebrates:3,Mammals:3,Primates:5,Rodents:2,Vertebrates:2	pfam00629, MAM, MAM domain.  An extracellular domain found in many receptors.
CDD:250013	91	EUK	Invertebrates:17,Mammals:1,Plants:4,Primates:2,Rodents:2,Vertebrates:3	pfam00630, Filamin, Filamin/ABP280 repeat.  
CDD:250014	66	EUK	Invertebrates:9,Plants:18,Primates:4,Rodents:3	pfam00631, G-gamma, GGL domain.  G-protein gamma like domains (GGL) are found in the gamma subunit of the heterotrimeric G protein complex and in regulators of G protein signaling (RGS) proteins. It is also found fused to an inactive Galpha in the Dictyostelium protein gbqA. G-gamma likely shares a common origin with the helical N-terminal unit of G-beta. All organisms that posses a G-beta possess a G-gamma.
CDD:250015	303	EUK	Invertebrates:20,Plants:18,Primates:1,Rodents:1,Vertebrates:3	pfam00632, HECT, HECT-domain (ubiquitin-transferase).  The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
CDD:250016	30	EUKprk	Bacteria:41,Invertebrates:1,Plants:4,Primates:1,Rodents:1,nodiv:1	pfam00633, HHH, Helix-hairpin-helix motif.  The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
CDD:201361	34	EUK	Mammals:1,Plants:1,Primates:2,Rodents:3	pfam00634, BRCA2, BRCA2 repeat.  The alignment covers only the most conserved region of the repeat.
CDD:250017	109	EUK	Invertebrates:7,Plants:5,Primates:1,Rodents:2	pfam00635, Motile_Sperm, MSP (Major sperm protein) domain.  Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
CDD:250018	90	EUKprk	Bacteria:108,Environmental:3,Invertebrates:11,Plants:40,Primates:1,Rodents:1,Vertebrates:1,Viruses:5	pfam00636, Ribonuclease_3, Ribonuclease III domain.  
CDD:250019	138	EUK	Invertebrates:26,Mammals:1,Plants:26,Primates:1,Rodents:1,Vertebrates:1	pfam00637, Clathrin, Region in Clathrin and VPS.  Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
CDD:250020	95	EUKprk	Bacteria:72,Environmental:1,Invertebrates:2,Plants:4	pfam00639, Rotamase, PPIC-type PPIASE domain.  Rotamases increase the rate of protein folding by catalyzing the interconversion of cis-proline and trans-proline.
CDD:250021	133	EUK	Invertebrates:2,Primates:1,Rodents:2	pfam00640, PID, Phosphotyrosine interaction domain (PTB/PID).  
CDD:250022	29	EUK	Invertebrates:1,Plants:1,Primates:1,Rodents:1	pfam00641, zf-RanBP, Zn-finger in Ran binding protein and others.  
CDD:250023	27	EUK	Invertebrates:5,Plants:5,Primates:1,Rodents:1,Vertebrates:2	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
CDD:250024	42	EUK	Invertebrates:19,Mammals:1,Plants:4,Primates:2,Rodents:3,Vertebrates:4	pfam00643, zf-B_box, B-box zinc finger.  
CDD:250025	206	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:1,Vertebrates:4	pfam00644, PARP, Poly(ADP-ribose) polymerase catalytic domain.  Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. ...
CDD:250026	81	EUK	Invertebrates:10,Mammals:1,Plants:13,Primates:1,Vertebrates:2	pfam00645, zf-PARP, Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region.  Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
CDD:250027	48	EUKprk	Invertebrates:3,Plants:12,Primates:1,Rodents:2,Vertebrates:1,Viruses:2	pfam00646, F-box, F-box domain.  This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, ...
CDD:250028	105	EUK	Invertebrates:16,Plants:12,Primates:1,Rodents:1,Vertebrates:3	pfam00647, EF1G, Elongation factor 1 gamma, conserved domain.  
CDD:144300	39	EUK	Plants:21	pfam00649, Copper-fist, Copper fist DNA binding domain.  
CDD:250030	156	EUK	Invertebrates:19,Mammals:1,Plants:28,Primates:1,Rodents:1,Vertebrates:1	pfam00650, CRAL_TRIO, CRAL/TRIO domain.  
CDD:250031	107	EUKprk	Invertebrates:4,Mammals:1,Plants:1,Primates:2,Rodents:2,Vertebrates:1,Viruses:6	pfam00651, BTB, BTB/POZ domain.  The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerization and in some instances heteromeric dimerization. The ...
CDD:250032	124	EUKprk	Bacteria:15,Environmental:1,Invertebrates:9,Plants:8,Primates:2,Rodents:1	pfam00652, Ricin_B_lectin, Ricin-type beta-trefoil lectin domain.  
CDD:250033	69	EUKprk	Invertebrates:10,Plants:17,Primates:2,Rodents:3,Synthetic:1,Vertebrates:4,Viruses:41	pfam00653, BIR, Inhibitor of Apoptosis domain.  BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are ...
CDD:250034	345	EUKprk	Bacteria:84,Environmental:4,Invertebrates:5,Plants:4,Rodents:2,Vertebrates:2	pfam00654, Voltage_CLC, Voltage gated chloride channel.  This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 is involved in ...
CDD:250035	229	EUKprk	Bacteria:12,Invertebrates:10,Mammals:1,Plants:10,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	pfam00656, Peptidase_C14, Caspase domain.  
CDD:250036	219	EUKprk	Bacteria:15,Invertebrates:1,Plants:11,Rodents:1	pfam00657, Lipase_GDSL, GDSL-like Lipase/Acylhydrolase.  
CDD:250037	71	EUK	Invertebrates:11,Plants:18,Primates:1,Rodents:1	pfam00658, PABP, Poly-adenylate binding protein, unique domain.  The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, ...
CDD:144309	64	EUK	Invertebrates:5,Mammals:1,Plants:7,Primates:1,Rodents:2	pfam00659, POLO_box, POLO box duplicated region.  
CDD:144310	104	EUK	Plants:6	pfam00660, SRP1_TIP1, Seripauperin and TIP1 family.  
CDD:250038	347	PRK	Viruses:14	pfam00661, Matrix, Viral matrix protein.  Found in Morbillivirus and paramyxovirus, pneumovirus.
CDD:109709	62	EUKprk	Bacteria:2,Invertebrates:6,Mammals:2,Plants:10,Rodents:2,Vertebrates:4	pfam00662, Oxidored_q1_N, NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus.  This sub-family represents an amino terminal extension of pfam00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across ...
CDD:250039	274	EUKprk	Bacteria:3,Invertebrates:2,Plants:1,Primates:1,Rodents:4,Vertebrates:1	pfam00664, ABC_membrane, ABC transporter transmembrane region.  This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
CDD:250040	119	EUKprk	Bacteria:78,Invertebrates:7,Phages:2,Plants:12,Rodents:1,Vertebrates:1,Viruses:9	pfam00665, rve, Integrase core domain.  Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an ...
CDD:250041	217	EUKprk	Bacteria:1,Mammals:1,Plants:3,Rodents:1	pfam00667, FAD_binding_1, FAD binding domain.  This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase.
CDD:250042	300	PRK	Bacteria:1	pfam00668, Condensation, Condensation domain.  This domain is found in many multi-domain enzymes which synthesize peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pfam00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site.
CDD:250043	139	PRK	Bacteria:22	pfam00669, Flagellin_N, Bacterial flagellin N-terminal helical region.  Flagellins polymerize to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with pfam00700.
CDD:250044	70	PRK	Bacteria:12	pfam00672, HAMP, HAMP domain.  
CDD:250045	95	EUKprk	Bacteria:75,Environmental:2,Invertebrates:11,Plants:23	pfam00673, Ribosomal_L5_C, ribosomal L5P family C-terminus.  This region is found associated with pfam00281.
CDD:250046	108	EUK	Plants:6	pfam00674, DUP, DUP family.  This family consists of several yeast proteins of unknown functions. Swiss-prot annotates these as belonging to the DUP family. Several members of this family contain an internal duplication of this region.
CDD:250047	149	EUKprk	Bacteria:4,Invertebrates:3,Mammals:1,Plants:4,Primates:1,Rodents:1	pfam00675, Peptidase_M16, Insulinase (Peptidase family M16).  
CDD:250048	300	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Primates:1	pfam00676, E1_dh, Dehydrogenase E1 component.  This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase.
CDD:250049	86	PRK	Bacteria:6	pfam00677, Lum_binding, Lumazine binding domain.  This domain binds to derivatives of lumazine in some proteins. Some proteins have lost the residues involved in binding lumazine.
CDD:250050	89	EUKprk	Bacteria:89,Invertebrates:16,Plants:13,Vertebrates:1	pfam00679, EFG_C, Elongation factor G C-terminus.  This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
CDD:250051	479	PRK	Phages:4,Viruses:17	pfam00680, RdRP_1, RNA dependent RNA polymerase.  
CDD:201389	45	EUK	Invertebrates:5,Primates:1,Rodents:3,Vertebrates:2	pfam00681, Plectin, Plectin repeat.  This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen.
CDD:201390	236	EUKprk	Bacteria:5,Primates:1	pfam00682, HMGL-like, HMGL-like.  This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.
CDD:250052	42	EUK	Primates:1	pfam00683, TB, TB domain.  This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
CDD:250053	66	EUKprk	Bacteria:18,Environmental:1,Invertebrates:8,Plants:9,Viruses:1	pfam00684, DnaJ_CXXCXGXG, DnaJ central domain.  The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ ...
CDD:250054	253	EUKprk	Bacteria:1,Invertebrates:3,Mammals:2,Plants:4,Primates:2,Rodents:3,Vertebrates:2	pfam00685, Sulfotransfer_1, Sulfotransferase domain.  
CDD:250055	96	EUKprk	Bacteria:28,Invertebrates:3,Plants:26,Rodents:1	pfam00686, CBM_20, Starch binding domain.  
CDD:250056	201	EUKprk	Bacteria:109,Environmental:3,Invertebrates:32,Mammals:1,Plants:53,Primates:1,Rodents:1,Vertebrates:1	pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family.  This family includes prokaryotic L1 and eukaryotic L10.
CDD:250057	230	EUK	Invertebrates:18,Mammals:2,Primates:1,Rodents:2,Vertebrates:17,nodiv:1	pfam00688, TGFb_propeptide, TGF-beta propeptide.  This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
CDD:250058	175	EUKprk	Bacteria:76,Environmental:2,Invertebrates:11,Plants:10,Primates:1,Viruses:1	pfam00689, Cation_ATPase_C, Cation transporting ATPase, C-terminus.  Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices.
CDD:250059	69	EUKprk	Bacteria:70,Environmental:1,Invertebrates:22,Plants:19,Rodents:1,Vertebrates:1,Viruses:1	pfam00690, Cation_ATPase_N, Cation transporter/ATPase, N-terminus.  Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.
CDD:250060	95	PRK	Bacteria:66	pfam00691, OmpA, OmpA family.  The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.
CDD:201398	129	EUKprk	Bacteria:1,Plants:2,Primates:1,Viruses:14	pfam00692, dUTPase, dUTPase.  dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
CDD:250061	279	PRK	Viruses:14	pfam00693, Herpes_TK, Thymidine kinase from herpesvirus.  
CDD:250062	131	EUKprk	Bacteria:2,Mammals:1,Plants:2,Primates:1	pfam00694, Aconitase_C, Aconitase C-terminal domain.  Members of this family usually also match to pfam00330. This domain undergoes conformational change in the enzyme mechanism.
CDD:250064	232	EUKprk	Bacteria:95,Environmental:4,Invertebrates:2,Plants:5	pfam00696, AA_kinase, Amino acid kinase family.  This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase EC:2.7.2.4. Acetylglutamate kinase EC:2.7.2.8. Glutamate 5-kinase EC:2.7.2.11. Uridylate kinase EC:2.7.4.-. Carbamate kinase EC:2.7.2.2.
CDD:250065	195	EUKprk	Bacteria:3,Plants:4	pfam00697, PRAI, N-(5'phosphoribosyl)anthranilate (PRA) isomerase.  
CDD:144338	319	EUK	Plants:2	pfam00698, Acyl_transf_1, Acyl transferase domain.  
CDD:250066	100	EUKprk	Bacteria:120,Environmental:1,Plants:7	pfam00699, Urease_beta, Urease beta subunit.  This subunit is known as alpha in Heliobacter.
CDD:144340	84	PRK	Bacteria:7	pfam00700, Flagellin_C, Bacterial flagellin C-terminal helical region.  Flagellins polymerize to form bacterial flagella.   #=GF CC   There is some similarity between this family and pfam00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate and this is shown to be correct as structurally this family forms an extended helix that interacts with pfam00700.
CDD:250067	289	EUKprk	Bacteria:4,Plants:1	pfam00701, DHDPS, Dihydrodipicolinate synthetase family.  This family has a TIM barrel structure.
CDD:250068	188	EUKprk	Bacteria:61,Invertebrates:4,Plants:5,Primates:1,Rodents:1	pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase.  This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of ...
CDD:250069	109	EUKprk	Bacteria:74,Environmental:1,Invertebrates:2,Plants:12,Vertebrates:1	pfam00703, Glyco_hydro_2, Glycosyl hydrolases family 2.  This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.
CDD:250070	324	EUKprk	Bacteria:27,Invertebrates:16,Mammals:1,Plants:30,Primates:1,Rodents:2,Viruses:9	pfam00704, Glyco_hydro_18, Glycosyl hydrolases family 18.  
CDD:250071	88	EUKprk	Bacteria:120,Environmental:1,Invertebrates:1,Mammals:1,Plants:8,Rodents:1,Vertebrates:2	pfam00707, IF3_C, Translation initiation factor IF-3, C-terminal domain.  
CDD:250072	90	EUKprk	Bacteria:64,Environmental:1,Invertebrates:6,Plants:1	pfam00708, Acylphosphatase, Acylphosphatase.  
CDD:250073	420	EUKprk	Bacteria:72,Environmental:1,Invertebrates:6,Mammals:1,Phages:1,Plants:3,Rodents:1	pfam00709, Adenylsucc_synt, Adenylosuccinate synthetase.  
CDD:250074	318	EUKprk	Bacteria:106,Environmental:1,Invertebrates:7,Plants:11,Synthetic:1,Vertebrates:1	pfam00710, Asparaginase, Asparaginase.  
CDD:250075	35	EUK	Mammals:6,Primates:4,Rodents:3,Vertebrates:4	pfam00711, Defensin_beta, Beta defensin.  The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.
CDD:250076	120	PRK	Bacteria:4,nodiv:1	pfam00712, DNA_pol3_beta, DNA polymerase III beta subunit, N-terminal domain.  A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.
CDD:250079	326	PRK	Viruses:11	pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).  
CDD:250080	69	EUKprk	Bacteria:82,Phages:18,Plants:2,nodiv:1	pfam00717, Peptidase_S24, Peptidase S24-like.  
CDD:250081	156	EUKprk	Bacteria:103,Invertebrates:16,Plants:15,Vertebrates:1	pfam00719, Pyrophosphatase, Inorganic pyrophosphatase.  
CDD:144353	95	PRK	Bacteria:22	pfam00720, SSI, Subtilisin inhibitor-like.  
CDD:250082	146	PRK	Viruses:41	pfam00721, TMV_coat, Virus coat protein (TMV like).  This family contains coat proteins from tobamoviruses, hordeiviruses, Tobraviruses, Furoviruses and Potyviruses.
CDD:250083	174	EUKprk	Bacteria:18,Environmental:3,Plants:31,nodiv:1	pfam00722, Glyco_hydro_16, Glycosyl hydrolases family 16.  
CDD:250084	416	EUKprk	Bacteria:5,Invertebrates:1,Mammals:1,Plants:5,Vertebrates:1	pfam00723, Glyco_hydro_15, Glycosyl hydrolases family 15.  In higher organisms this family is represented by phosphorylase kinase subunits.
CDD:250085	336	EUKprk	Bacteria:3,Plants:2	pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase family.  
CDD:250086	97	EUKprk	Bacteria:25,Invertebrates:3,Mammals:1,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam00725, 3HCDH, 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain.  This family also includes lambda crystallin. Some proteins include two copies of this domain.
CDD:250089	336	EUKprk	Bacteria:24,Invertebrates:4,Mammals:1,Plants:5	pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic domain.  This domain has a TIM barrel fold.
CDD:250090	197	PRK	Viruses:11	pfam00729, Viral_coat, Viral coat protein (S domain).  
CDD:250091	145	EUKprk	Bacteria:24,Plants:3,Primates:1	pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein.  This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also ...
CDD:250092	150	EUKprk	Bacteria:187,Environmental:1,Invertebrates:5,Plants:13	pfam00731, AIRC, AIR carboxylase.  Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain.
CDD:250093	218	EUKprk	Bacteria:6,Invertebrates:1,Plants:6	pfam00732, GMC_oxred_N, GMC oxidoreductase.  This family of proteins bind FAD as a cofactor.
CDD:250094	195	EUKprk	Bacteria:59,Environmental:1,Invertebrates:4,Plants:4,Primates:1,Rodents:1,Vertebrates:1	pfam00733, Asn_synthase, Asparagine synthase.  This family is always found associated with pfam00310. Members of this family catalyse the conversion of aspartate to asparagine.
CDD:250095	29	EUKprk	Plants:53,Viruses:1	pfam00734, CBM_1, Fungal cellulose binding domain.  
CDD:250096	273	EUK	Invertebrates:1,Plants:4,Rodents:1	pfam00735, Septin, Septin.  Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in ...
CDD:250097	88	EUKprk	Bacteria:30,Invertebrates:27,Mammals:2,Plants:10,Primates:1	pfam00736, EF1_GNE, EF-1 guanine nucleotide exchange domain.  This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains.
CDD:250098	521	PRK	Viruses:23	pfam00740, Parvo_coat, Parvovirus coat protein VP2.  This protein, together with VP1 forms a capsomer. Both of these proteins are formed from the same transcript using alternative splicing.   As a result, VP1 and VP2 differ only in the N-terminal region of VP1.   VP2 is involved in packaging the viral DNA.
CDD:144370	39	PRK	Bacteria:33	pfam00741, Gas_vesicle, Gas vesicle protein.  
CDD:250099	179	EUKprk	Bacteria:111,Invertebrates:1,Plants:5	pfam00742, Homoserine_dh, Homoserine dehydrogenase.  
CDD:250100	101	EUKprk	Bacteria:145,Plants:2	pfam00745, GlutR_dimer, Glutamyl-tRNAGlu reductase, dimerization domain.  
CDD:250101	39	EUKprk	Bacteria:41,Primates:1	pfam00746, Gram_pos_anchor, Gram positive anchor.  
CDD:250102	1111	PRK	Viruses:11	pfam00747, Viral_DNA_bp, ssDNA binding protein.  This protein is found in herpesviruses and is needed for replication.
CDD:250103	131	EUK	Mammals:4,Primates:2,Rodents:2,Vertebrates:3	pfam00748, Calpain_inhib, Calpain inhibitor.  This region is found multiple times in calpain inhibitor proteins.
CDD:250104	314	EUKprk	Bacteria:3,Plants:2	pfam00749, tRNA-synt_1c, tRNA synthetases class I (E and Q), catalytic domain.  Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).
CDD:250106	47	EUK	Invertebrates:8,Mammals:1,Primates:1,Vertebrates:3	pfam00751, DM, DM DNA binding domain.  The DM domain is named after dsx and mab-3. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4. The dsx DM domain has been shown to dimerise and bind palindromic DNA.
CDD:250107	100	EUK	Primates:1	pfam00752, XPG_N, XPG N-terminal domain.  
CDD:250108	148	EUKprk	Bacteria:72,Environmental:2,Invertebrates:2,Plants:4,Primates:1,Rodents:1,nodiv:1	pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily.  
CDD:250109	129	EUKprk	Bacteria:26,Invertebrates:8,Mammals:4,Plants:2,Primates:2,Rodents:1,Vertebrates:5,Viruses:1	pfam00754, F5_F8_type_C, F5/8 type C domain.  This domain is also known as the discoidin (DS) domain family.
CDD:250110	592	EUK	Invertebrates:2,Mammals:1,Plants:2,Primates:1,Rodents:2,Vertebrates:1	pfam00755, Carn_acyltransf, Choline/Carnitine o-acyltransferase.  
CDD:250111	246	EUKprk	Bacteria:9,Environmental:1,Plants:1,Primates:1	pfam00756, Esterase, Putative esterase.  This family contains Esterase D. However it is not clear if all members of the family have the same function. This family is related to the pfam00135 family.
CDD:250112	143	EUK	Invertebrates:7,Mammals:2,Primates:1,Vertebrates:7	pfam00757, Furin-like, Furin-like cysteine rich region.  
CDD:250113	436	EUKprk	Bacteria:10,Invertebrates:3,Plants:9	pfam00759, Glyco_hydro_9, Glycosyl hydrolase family 9.  
CDD:250115	314	EUKprk	Bacteria:165,Environmental:1,Invertebrates:6,Plants:8,Primates:1,Rodents:1	pfam00762, Ferrochelatase, Ferrochelatase.  
CDD:250116	117	EUKprk	Bacteria:84,Invertebrates:6,Plants:6,Primates:1,Vertebrates:1	pfam00763, THF_DHG_CYH, Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.  
CDD:250117	387	EUKprk	Bacteria:2,Mammals:1,Plants:1,Primates:1	pfam00764, Arginosuc_synth, Arginosuccinate synthase.  This family contains a PP-loop motif.
CDD:144386	182	PRK	Bacteria:12	pfam00765, Autoind_synth, Autoinducer synthetase.  
CDD:189709	86	EUKprk	Bacteria:23,Environmental:1,Plants:3,Primates:1,nodiv:1	pfam00766, ETF_alpha, Electron transfer flavoprotein FAD-binding domain.  This domain found at the C-terminus of electron transfer flavoprotein alpha chain and binds to FAD. The fold consists of a five-stranded parallel beta sheet as the core of the domain, flanked by alternating helices. A small part of this domain is donated by the beta chain.
CDD:109810	237	PRK	Viruses:26	pfam00767, Poty_coat, Potyvirus coat protein.  
CDD:250118	241	PRK	Bacteria:9,nodiv:1	pfam00768, Peptidase_S11, D-alanyl-D-alanine carboxypeptidase.  
CDD:250119	244	EUK	Invertebrates:3,Mammals:1,Primates:1	pfam00769, ERM, Ezrin/radixin/moesin family.  This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins.
CDD:250120	183	PRK	Viruses:13	pfam00770, Peptidase_C5, Adenovirus endoprotease.  This family of adenovirus thiol endoproteases specifically cleave Gly-Ala peptides in viral precursor peptides.
CDD:250121	658	PRK	Bacteria:143,Environmental:1	pfam00771, FHIPEP, FHIPEP family.  
CDD:250122	103	EUKprk	Bacteria:125,Environmental:1,Phages:8,Plants:4	pfam00772, DnaB, DnaB-like helicase N terminal domain.  The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the ...
CDD:250123	321	EUKprk	Bacteria:43,Environmental:2,Invertebrates:9,Plants:13	pfam00773, RNB, RNB domain.  This domain is the catalytic domain of ribonuclease II.
CDD:250124	181	PRK	Bacteria:13	pfam00775, Dioxygenase_C, Dioxygenase.  
CDD:250125	268	EUKprk	Invertebrates:5,Mammals:3,Plants:5,Primates:2,Rodents:2,Vertebrates:11,Viruses:2	pfam00777, Glyco_transf_29, Glycosyltransferase family 29 (sialyltransferase).  Members of this family belong to glycosyltransferase family 29.
CDD:250126	81	EUK	Invertebrates:6,Primates:1,Rodents:2,Vertebrates:1	pfam00778, DIX, DIX domain.  The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerization. It is involved in the homo- oligomerization of mouse axin. The axin DIX domain also interacts with the dishevelled DIX domain. The DIX domain has also been called the DAX domain.
CDD:144394	31	EUK	Invertebrates:3,Mammals:1,Primates:1,Rodents:1,Vertebrates:4	pfam00779, BTK, BTK motif.  Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains. The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
CDD:250127	266	EUK	Invertebrates:6,Plants:17,Primates:2,Rodents:1,Vertebrates:2	pfam00780, CNH, CNH domain.  Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations.
CDD:250128	126	EUKprk	Bacteria:48,Invertebrates:4,Plants:6,Primates:1,Rodents:1,Vertebrates:1	pfam00781, DAGK_cat, Diacylglycerol kinase catalytic domain.  Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel ...
CDD:250129	131	EUKprk	Invertebrates:1,Plants:3,Primates:1,Rodents:1,Viruses:2	pfam00782, DSPc, Dual specificity phosphatase, catalytic domain.  Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
CDD:250130	106	miss	miss	pfam00784, MyTH4, MyTH4 domain.  Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins.
CDD:250131	56	EUK	Invertebrates:4,Plants:8,Primates:1,Rodents:1	pfam00786, PBD, P21-Rho-binding domain.  Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
CDD:250132	106	EUK	Invertebrates:2,Plants:5,Primates:1,Rodents:1	pfam00787, PX, PX domain.  PX domains bind to phosphoinositides.
CDD:250133	87	EUK	Invertebrates:2,Plants:4,Primates:1,Rodents:2	pfam00788, RA, Ras association (RalGDS/AF-6) domain.  RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase.
CDD:250134	78	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:2	pfam00789, UBX, UBX domain.  This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.
CDD:250135	136	EUK	Invertebrates:1,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam00790, VHS, VHS domain.  Domain present in VPS-27, Hrs and STAM.
CDD:189721	103	EUK	Invertebrates:6,Primates:1,Rodents:2,Vertebrates:3,nodiv:2	pfam00791, ZU5, ZU5 domain.  Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
CDD:250136	143	EUK	Invertebrates:1,Plants:2,Primates:1	pfam00792, PI3K_C2, Phosphoinositide 3-kinase C2.  Phosphoinositide 3-kinase region postulated to contain a C2 domain. Outlier of pfam00168 family.
CDD:250137	271	EUKprk	Bacteria:13,Plants:4	pfam00793, DAHP_synth_1, DAHP synthetase I family.  Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54.
CDD:250138	107	EUK	Mammals:1,Primates:1	pfam00794, PI3K_rbd, PI3-kinase family, ras-binding domain.  Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding pfam00788 domains (unpublished observation).
CDD:250139	172	EUKprk	Bacteria:16,Invertebrates:1,Plants:2,Rodents:2,nodiv:1	pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase.  This family contains hydrolases that break carbon-nitrogen bonds. The family includes: Nitrilase EC:3.5.5.1, Aliphatic amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12, Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins.
CDD:201449	25	EUKprk	Bacteria:15,Plants:18	pfam00796, PSI_8, Photosystem I reaction centre subunit VIII.  
CDD:250140	240	EUKprk	Bacteria:19,Mammals:1,Primates:1,Rodents:2,Vertebrates:2	pfam00797, Acetyltransf_2, N-acetyltransferase.  Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to ...
CDD:250141	473	PRK	Viruses:20	pfam00798, Arena_glycoprot, Arenavirus glycoprotein.  
CDD:109839	114	PRK	Viruses:11	pfam00799, Gemini_AL1, Geminivirus Rep catalytic domain.  The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer.
CDD:250142	181	EUKprk	Bacteria:101,Plants:10	pfam00800, PDT, Prephenate dehydratase.  This protein is involved in Phenylalanine biosynthesis. This protein catalyses the decarboxylation of prephenate to phenylpyruvate.
CDD:250143	70	EUKprk	Bacteria:12,Phages:1,Primates:1,Rodents:1,Vertebrates:2	pfam00801, PKD, PKD domain.  This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.
CDD:250144	234	PRK	Viruses:25	pfam00803, 3A, 3A/RNA2 movement protein family.  This family includes movement proteins from various viruses. The 3A protein is found in bromoviruses and Cucumoviruses. The genome of these viruses contain 3 RNA segments. The third segment (RNA 3) contains two proteins, the coat protein and the 3A protein. The function of the 3A protein is uncertain but has been shown to be involved in cell-to- cell movement of the virus. The family also includes movement proteins ...
CDD:250145	97	EUKprk	Bacteria:3,Invertebrates:23,Mammals:3,Plants:39,Primates:1,Rodents:2,Vertebrates:5	pfam00804, Syntaxin, Syntaxin.  Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins (pfam05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A it is found as ...
CDD:109845	40	EUKprk	Bacteria:13,Invertebrates:1,Plants:1	pfam00805, Pentapeptide, Pentapeptide repeats (8 copies).  These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid.
CDD:250146	35	EUK	Invertebrates:1,Plants:2	pfam00806, PUF, Pumilio-family RNA binding repeat.  Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). ...
CDD:250147	65	EUKprk	Bacteria:3,Invertebrates:3,Plants:4,Primates:1	pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor (CBF/NF-Y) and archaeal histone.  This family includes archaebacterial histones and histone like transcription factors from eukaryotes.
CDD:250148	208	EUKprk	Bacteria:23,Invertebrates:2,Plants:3,Rodents:1	pfam00809, Pterin_bind, Pterin binding enzyme.  This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the ...
CDD:144416	143	EUKprk	Bacteria:1,Invertebrates:20,Plants:22,Vertebrates:1	pfam00810, ER_lumen_recept, ER lumen protein retaining receptor.  
CDD:250149	133	EUK	Invertebrates:4,Primates:1,Vertebrates:10	pfam00811, Ependymin, Ependymin.  
CDD:250150	134	EUK	Primates:1,Rodents:1,Vertebrates:3	pfam00812, Ephrin, Ephrin.  
CDD:250151	194	PRK	Bacteria:96	pfam00813, FliP, FliP family.  
CDD:250152	225	EUKprk	Bacteria:75,Invertebrates:2,Plants:4,Rodents:1,Vertebrates:1,nodiv:1	pfam00814, Peptidase_M22, Glycoprotease family.  The Peptidase M22 proteins are part of the HSP70-actin superfamily. The region represented here is an insert into the fold and is not found in the rest of the family (beyond the Peptidase M22 family). Included in this family are the Rhizobial NodU proteins and the HypF regulator. This region also contains the histidine dyad believed to coordinate the metal ...
CDD:250153	413	miss	miss	pfam00815, Histidinol_dh, Histidinol dehydrogenase.  
CDD:250154	92	PRK	Bacteria:100	pfam00816, Histone_HNS, H-NS histone family.  
CDD:250155	148	EUKprk	Bacteria:68,Environmental:2,Invertebrates:12,Plants:12	pfam00817, IMS, impB/mucB/samB family.  These proteins are involved in UV protection.
CDD:250156	586	EUKprk	Bacteria:21,Invertebrates:10,Rodents:2,Vertebrates:3	pfam00821, PEPCK, Phosphoenolpyruvate carboxykinase.  Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate.
CDD:250157	161	EUK	Mammals:2,Primates:1,Rodents:1,Vertebrates:1	pfam00822, PMP22_Claudin, PMP-22/EMP/MP20/Claudin family.  
CDD:250158	159	PRK	Bacteria:37,Phages:1	pfam00823, PPE, PPE family.  This family named after a PPE motif near to the amino terminus of the domain. The PPE family of proteins all contain an amino-terminal region of about 180 amino acids. The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups. The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are ...
CDD:250159	107	EUKprk	Bacteria:130,Plants:1	pfam00825, Ribonuclease_P, Ribonuclease P.  
CDD:144426	192	EUKprk	Bacteria:22,Environmental:1,Invertebrates:18,Mammals:1,Plants:6,Primates:1,Vertebrates:2	pfam00827, Ribosomal_L15e, Ribosomal L15.  
CDD:250160	122	EUKprk	Bacteria:32,Invertebrates:29,Plants:14,Vertebrates:3	pfam00828, Ribosomal_L18e, Ribosomal protein L18e/L15.  This family includes eukaryotic L18 as well as prokaryotic L15.
CDD:201461	96	EUKprk	Bacteria:44,Invertebrates:1,Plants:7,Rodents:1,nodiv:1	pfam00829, Ribosomal_L21p, Ribosomal prokaryotic L21 protein.  
CDD:250161	61	EUKprk	Bacteria:69,Invertebrates:7,Plants:21	pfam00830, Ribosomal_L28, Ribosomal L28 family.  The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts. The L24 protein from yeast also contains a region of similarity to prokaryotic L28 proteins. L24 from yeast is also found in the large ribosomal subunit.
CDD:250162	58	EUKprk	Bacteria:96,Environmental:2,Invertebrates:10,Plants:10	pfam00831, Ribosomal_L29, Ribosomal L29 protein.  
CDD:250163	43	EUKprk	Bacteria:25,Invertebrates:8,Plants:7,Rodents:1	pfam00832, Ribosomal_L39, Ribosomal L39 protein.  
CDD:250164	122	EUKprk	Bacteria:2,Invertebrates:15,Plants:11,Primates:1	pfam00833, Ribosomal_S17e, Ribosomal S17.  
CDD:250165	201	EUKprk	Bacteria:6,Plants:1	pfam00834, Ribul_P_3_epim, Ribulose-phosphate 3 epimerase family.  This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
CDD:250166	57	EUK	Invertebrates:5,Plants:1,Rodents:1,Vertebrates:2	pfam00835, SNAP-25, SNAP-25 family.  SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
CDD:250168	58	EUK	Invertebrates:5,Mammals:1,Primates:1,Rodents:3,Vertebrates:2	pfam00839, Cys_rich_FGFR, Cysteine rich repeat.  This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
CDD:250169	427	EUK	Plants:10	pfam00840, Glyco_hydro_7, Glycosyl hydrolase family 7.  
CDD:250170	125	EUKprk	Bacteria:85,Invertebrates:1	pfam00842, Ala_racemase_C, Alanine racemase, C-terminal domain.  
CDD:250172	244	PRK	Viruses:39	pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family.  It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus.
CDD:144440	276	PRK	Viruses:17	pfam00845, Gemini_BL1, Geminivirus BL1 movement protein.  Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation.
CDD:250173	54	EUKprk	Bacteria:13,Invertebrates:10,Phages:11,Plants:23	pfam00847, AP2, AP2 domain.  This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.
CDD:250174	199	EUKprk	Bacteria:54,Environmental:1,Plants:13	pfam00848, Ring_hydroxyl_A, Ring hydroxylating alpha subunit (catalytic domain).  This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems. The active site contains a non-heme ferrous ion coordinated by three ligands.
CDD:250175	150	EUKprk	Bacteria:33,Invertebrates:10,Mammals:1,Plants:6,Vertebrates:1	pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase.  Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from Escherichia coli converts bases in both rRNA and tRNA.
CDD:250176	303	EUKprk	Bacteria:65,Environmental:3,Invertebrates:15,Mammals:1,Plants:15,Primates:1,Rodents:1	pfam00850, Hist_deacetyl, Histone deacetylase domain.  Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins.
CDD:109889	453	PRK	Viruses:7	pfam00851, Peptidase_C6, Helper component proteinase.  This protein is found in genome polyproteins of potyviruses.
CDD:250177	349	EUK	Invertebrates:8,Mammals:3,Primates:2,Rodents:1,Vertebrates:7	pfam00852, Glyco_transf_10, Glycosyltransferase family 10 (fucosyltransferase).  This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10.
CDD:250179	372	EUKprk	Bacteria:2,Invertebrates:2,Mammals:1,Plants:4,Primates:1,Rodents:1	pfam00854, PTR2, POT family.  The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
CDD:250180	86	EUK	Invertebrates:42,Mammals:2,Plants:66,Primates:4,Rodents:1,Vertebrates:6	pfam00855, PWWP, PWWP domain.  The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In ...
CDD:250181	113	EUKprk	Bacteria:33,Invertebrates:31,Mammals:1,Plants:39,Primates:1,Rodents:1,Vertebrates:4,Viruses:3	pfam00856, SET, SET domain.  SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are ...
CDD:250182	172	EUKprk	Bacteria:48,Invertebrates:4,Plants:6	pfam00857, Isochorismatase, Isochorismatase family.  This family are hydrolase enzymes.
CDD:250183	444	EUK	Invertebrates:8,Mammals:1,Primates:2,Rodents:2,Vertebrates:8,nodiv:1	pfam00858, ASC, Amiloride-sensitive sodium channel.  
CDD:250184	389	EUKprk	Bacteria:4,Invertebrates:1,Rodents:1	pfam00860, Xan_ur_permease, Permease family.  This family includes permeases for diverse substrates such as xanthine, uracil, and vitamin C. However many members of this family are functionally uncharacterized and may transport other substrates. Members of this family have ten predicted transmembrane helices.
CDD:250185	119	EUKprk	Bacteria:11,Plants:4	pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e family.  This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of rat Rpl5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding.
CDD:109901	233	PRK	Viruses:32	pfam00863, Peptidase_C4, Peptidase family C4.  This peptidase is present in the nuclear inclusion protein of potyviruses.
CDD:250186	374	EUK	Invertebrates:2,Plants:1,Primates:1,Rodents:2,Vertebrates:1	pfam00864, P2X_receptor, ATP P2X receptor.  
CDD:250188	145	PRK	Bacteria:25	pfam00866, Ring_hydroxyl_B, Ring hydroxylating beta subunit.  This subunit has a similar structure to NTF-2 and scytalone dehydratase.
CDD:250189	88	EUKprk	Bacteria:11,Environmental:2,Invertebrates:24,Plants:42,Primates:1,Synthetic:1,Vertebrates:2,Viruses:18	pfam00867, XPG_I, XPG I-region.  
CDD:250190	119	EUK	Invertebrates:12,Mammals:1,Primates:2,Rodents:3,Vertebrates:7	pfam00868, Transglut_N, Transglutaminase family.  
CDD:250191	293	PRK	Viruses:35	pfam00869, Flavi_glycoprot, Flavivirus glycoprotein, central and dimerization domains.  
CDD:250192	387	PRK	Bacteria:4	pfam00871, Acetate_kinase, Acetokinase family.  This family includes acetate kinase, butyrate kinase and 2-methylpropanoate kinase.
CDD:250193	381	PRK	Bacteria:9	pfam00872, Transposase_mut, Transposase, Mutator family.  
CDD:201483	1021	PRK	Bacteria:8	pfam00873, ACR_tran, AcrB/AcrD/AcrF family.  Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer.
CDD:250194	90	PRK	Bacteria:42	pfam00874, PRD, PRD domain.  The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal ...
CDD:250195	164	EUKprk	Bacteria:107,Invertebrates:5,Plants:12,Rodents:1,Vertebrates:2,Viruses:4,nodiv:2	pfam00875, DNA_photolyase, DNA photolyase.  This domain binds a light harvesting cofactor.
CDD:250196	342	EUKprk	Invertebrates:19,Viruses:4	pfam00876, Innexin, Innexin.  This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins.
CDD:189752	105	PRK	Bacteria:14,Phages:2	pfam00877, NLPC_P60, NlpC/P60 family.  The function of this domain is unknown. It is found in several lipoproteins.
CDD:109916	145	EUK	Primates:1,Rodents:2	pfam00878, CIMR, Cation-independent mannose-6-phosphate receptor repeat.  The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
CDD:144464	52	EUK	Mammals:2,Primates:4,Rodents:4	pfam00879, Defensin_propep, Defensin propeptide.  
CDD:250197	29	EUK	Invertebrates:1,Mammals:4,Primates:3,Rodents:3,Vertebrates:5	pfam00880, Nebulin, Nebulin repeat.  
CDD:250198	125	EUKprk	Bacteria:117,Environmental:2,Invertebrates:3,Plants:3	pfam00881, Nitroreductase, Nitroreductase family.  The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds.
CDD:250199	174	EUKprk	Bacteria:121,Invertebrates:4,Plants:6,Rodents:1	pfam00882, Zn_dep_PLPC, Zinc dependent phospholipase C.  
CDD:250200	312	EUKprk	Bacteria:4,Invertebrates:1,Plants:2	pfam00883, Peptidase_M17, Cytosol aminopeptidase family, catalytic domain.  The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase.
CDD:250201	299	EUKprk	Bacteria:26,Invertebrates:2,Mammals:2,Plants:3,Primates:1,Rodents:1	pfam00884, Sulfatase, Sulfatase.  
CDD:250202	144	EUKprk	Bacteria:45,Environmental:2,Plants:4,nodiv:1	pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllumazine synthase.  This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function.
CDD:250203	58	EUKprk	Bacteria:108,Invertebrates:2,Plants:29	pfam00886, Ribosomal_S16, Ribosomal protein S16.  
CDD:250204	87	EUKprk	Bacteria:12,Invertebrates:21,Mammals:1,Plants:27,Primates:2,Rodents:2,Vertebrates:5	pfam00887, ACBP, Acyl CoA binding protein.  
CDD:250205	602	EUK	Invertebrates:6,Mammals:1,Plants:9,Primates:1,Rodents:1	pfam00888, Cullin, Cullin family.  
CDD:250206	180	EUKprk	Bacteria:123,Invertebrates:3,Plants:6,Rodents:1	pfam00889, EF_TS, Elongation factor TS.  
CDD:250207	401	EUKprk	Bacteria:38,Invertebrates:5	pfam00890, FAD_binding_2, FAD binding domain.  This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.
CDD:250208	239	EUKprk	Bacteria:7,Mammals:1,Plants:15,Primates:1,Rodents:1,Vertebrates:1	pfam00891, Methyltransf_2, O-methyltransferase.  This family includes a range of O-methyltransferases. These enzymes utilize S-adenosyl methionine.
CDD:250209	126	EUKprk	Bacteria:24,Plants:1	pfam00892, EamA, EamA-like transporter family.  This family includes many hypothetical membrane proteins of unknown function.  Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
CDD:250210	93	PRK	Bacteria:9	pfam00893, Multi_Drug_Res, Small Multidrug Resistance protein.  This family is the Small Multidrug Resistance (SMR) family. Several members have been shown to export a range of toxins, including ethidium bromide and quaternary ammonium compounds, through coupling with proton influx.
CDD:201496	54	EUK	Invertebrates:15,Mammals:15,Primates:4,Rodents:5,Vertebrates:25	pfam00895, ATP-synt_8, ATP synthase protein 8.  
CDD:250211	946	PRK	Viruses:14	pfam00898, Orbi_VP2, Orbivirus outer capsid protein VP2.  VP2 acts as an anchor for VP1 and VP3. VP2 contains a non-specific DNA and RNA binding domain in the N-terminus.
CDD:250212	134	EUKprk	Bacteria:53,Environmental:2,Invertebrates:4,Plants:8,Primates:1,Vertebrates:1	pfam00899, ThiF, ThiF family.  This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family.
CDD:189761	77	EUKprk	Bacteria:17,Environmental:2,Invertebrates:22,Plants:7,Vertebrates:1	pfam00900, Ribosomal_S4e, Ribosomal family S4e.  
CDD:189762	507	PRK	Viruses:14	pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.  cryoelectron microscopy indicates that VP5 is a trimer implying that there are 360 copies of VP5 per virion.
CDD:250213	212	EUKprk	Bacteria:109,Environmental:5,Invertebrates:5,Plants:18	pfam00902, TatC, Sec-independent protein translocase protein (TatC).  The bacterial Tat system has a remarkable ability to transport folded proteins even enzyme complexes across the cytoplasmic membrane. It is structurally and mechanistically similar to the Delta pH-driven thylakoidal protein import pathway. A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, ...
CDD:250214	121	EUKprk	Bacteria:32,Plants:2,Rodents:1	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily.  
CDD:144485	10	EUK	Primates:7	pfam00904, Involucrin, Involucrin repeat.  
CDD:250215	296	PRK	Bacteria:25	pfam00905, Transpeptidase, Penicillin binding protein transpeptidase domain.  The active site serine is conserved in all members of this family.
CDD:250216	182	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:3	pfam00907, T-box, T-box.  The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for ...
CDD:144487	177	EUKprk	Bacteria:15,Invertebrates:1	pfam00908, dTDP_sugar_isom, dTDP-4-dehydrorhamnose 3,5-epimerase.  This family catalyse the isomerization of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.
CDD:250217	399	EUKprk	Bacteria:3,Invertebrates:1,Plants:1,Primates:2	pfam00909, Ammonium_transp, Ammonium Transporter Family.  
CDD:250218	105	EUKprk	Invertebrates:1,Viruses:70	pfam00910, RNA_helicase, RNA helicase.  This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.
CDD:250219	177	EUKprk	Bacteria:143,Environmental:1,Plants:2	pfam00912, Transgly, Transglycosylase.  The penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively. The transglycosylase domain catalyses the polymerization of murein glycan chains.
CDD:250220	370	EUK	Invertebrates:5	pfam00913, Trypan_glycop, Trypanosome variant surface glycoprotein (A-type).  The trypanosome parasite expresses these proteins to evade the immune response. This family includes a variety of surface proteins such as Trypanosoma brucei VSGs such as expression site associated gene (ESAG) 6 and 7.
CDD:201503	293	PRK	Viruses:11	pfam00915, Calici_coat, Calicivirus coat protein.  
CDD:250221	279	EUKprk	Bacteria:3,Plants:3	pfam00916, Sulfate_transp, Sulfate transporter family.  Mutations in human SLC26A2 lead to several human diseases.
CDD:250222	116	EUK	Invertebrates:2,Plants:1,Rodents:1	pfam00917, MATH, MATH domain.  This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans.
CDD:250223	111	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:2,Vertebrates:4	pfam00918, Gastrin, Gastrin/cholecystokinin family.  
CDD:250224	98	EUKprk	Bacteria:116,Environmental:1,Invertebrates:4,Mammals:1,Plants:3	pfam00919, UPF0004, Uncharacterized protein family UPF0004.  This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
CDD:250225	521	EUKprk	Bacteria:64,Environmental:2,Invertebrates:1,Plants:5	pfam00920, ILVD_EDD, Dehydratase family.  
CDD:250226	174	PRK	Bacteria:3	pfam00921, Lipoprotein_2, Borrelia lipoprotein.  This family of lipoproteins is found in Borrelia spirochetes. The function of these proteins is uncertain.
CDD:250228	247	EUKprk	Bacteria:85,Invertebrates:6,Phages:1,Plants:3	pfam00923, Transaldolase, Transaldolase.  
CDD:250229	202	EUKprk	Bacteria:16,Plants:1	pfam00924, MS_channel, Mechanosensitive ion channel.  Two members of this protein family from M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins.
CDD:250230	169	EUKprk	Bacteria:120,Plants:6	pfam00925, GTP_cyclohydro2, GTP cyclohydrolase II.  GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin.
CDD:250231	193	EUKprk	Bacteria:59,Environmental:1,Plants:6	pfam00926, DHBP_synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase.  3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with pfam00925.
CDD:250232	105	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:2,Vertebrates:2	pfam00927, Transglut_C, Transglutaminase family, C-terminal ig like domain.  
CDD:250233	268	EUK	Invertebrates:8,Plants:7,Primates:1,Rodents:2,Vertebrates:4	pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.  This family also contains members which are coatomer subunits.
CDD:250234	161	EUKprk	Bacteria:16,Invertebrates:1,Phages:3,Plants:2,Primates:1	pfam00929, RNase_T, Exonuclease.  This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;.
CDD:250235	348	EUKprk	Bacteria:11,Invertebrates:2,Mammals:1,Plants:5,Primates:1,Rodents:2,Vertebrates:1	pfam00930, DPPIV_N, Dipeptidyl peptidase IV (DPP IV) N-terminal region.  This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry.
CDD:250236	287	EUK	Plants:3	pfam00931, NB-ARC, NB-ARC domain.  
CDD:250237	111	EUKprk	Bacteria:27,Invertebrates:2,Plants:1,Primates:1	pfam00932, LTD, Lamin Tail Domain.  The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies.
CDD:250238	296	EUKprk	Bacteria:20,Environmental:1,Plants:13	pfam00933, Glyco_hydro_3, Glycosyl hydrolase family 3 N terminal domain.  
CDD:250239	94	PRK	Bacteria:38	pfam00934, PE, PE family.  This family named after a PE motif near to the amino terminus of the domain. The PE family of proteins all contain an amino-terminal region of about 110 amino acids. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be ...
CDD:250240	77	EUKprk	Bacteria:12,Environmental:1,Invertebrates:15,Mammals:1,Plants:5	pfam00935, Ribosomal_L44, Ribosomal protein L44.  
CDD:250241	75	PRK	Bacteria:57,Environmental:1	pfam00936, BMC, BMC domain.  Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
CDD:250242	346	PRK	Viruses:20	pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein.  
CDD:189778	87	PRK	Bacteria:2	pfam00938, Lipoprotein_3, Lipoprotein.  This family of lipoproteins is Mycoplasma specific.
CDD:250243	471	PRK	Bacteria:6	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region.  There are also some members in this family that do not match the Prosite motif, and belong to the subfamily SODIT1.
CDD:250244	394	EUKprk	Bacteria:3,Invertebrates:22,Phages:9,Plants:44,Rodents:1,Vertebrates:1,nodiv:1	pfam00940, RNA_pol, DNA-dependent RNA polymerase.  This is a family of single chain RNA polymerases.
CDD:250245	171	EUKprk	Bacteria:32,Environmental:1,Invertebrates:6,Mammals:2,Plants:4,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	pfam00941, FAD_binding_5, FAD binding domain in molybdopterin dehydrogenase.  
CDD:250246	83	PRK	Bacteria:11	pfam00942, CBM_3, Cellulose binding domain.  
CDD:201519	403	PRK	Viruses:20	pfam00943, Alpha_E2_glycop, Alphavirus E2 glycoprotein.  E2 forms a heterodimer with E1. The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus).
CDD:201520	406	PRK	Viruses:13	pfam00945, Rhabdo_ncap, Rhabdovirus nucleocapsid protein.  The Nucleocapsid (N) Protein is said to have a "tight" structure. The carboxyl end of the N-terminal domain possesses an RNA binding domain. Sequence alignments show 2 regions of reasonable conservation, approx. 64-103 and 201-329. A whole functional protein is required for encapsidation to take place.
CDD:250248	1065	PRK	Viruses:37	pfam00946, Mononeg_RNA_pol, Mononegavirales RNA dependent RNA polymerase.  Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P.  This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor.
CDD:189781	355	PRK	Viruses:10	pfam00948, Flavi_NS1, Flavivirus non-structural Protein NS1.  The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.
CDD:250249	144	EUKprk	Bacteria:3,Invertebrates:1,Viruses:16	pfam00949, Peptidase_S7, Peptidase S7, Flavivirus NS3 serine protease.  The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
CDD:109985	258	miss	miss	pfam00950, ABC-3, ABC 3 transport family.  
CDD:109986	179	PRK	Viruses:5	pfam00951, Arteri_Gl, Arterivirus GL envelope glycoprotein.  Arteriviruses encode 4 envelope proteins, Gl, Gs, M and N. Gl envelope protein, is encoded in ORF5, and is 30- 45 kDa in size. Gl is heterogenously glycosylated with N-acetyllactosamine in a cell-type-specific manner. The Gl glycoprotein expresses the neutralization determinants.
CDD:109987	228	PRK	Viruses:16	pfam00952, Bunya_nucleocap, Bunyavirus nucleocapsid (N) protein.  The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The N protein is the major component of the nucleocapsids. This protein is thought to interact with the L protein, virus RNA and/or other N proteins.
CDD:250250	158	EUKprk	Bacteria:68,Invertebrates:3,nodiv:1	pfam00953, Glycos_transf_4, Glycosyl transferase family 4.  
CDD:201524	110	EUK	Plants:10	pfam00954, S_locus_glycop, S-locus glycoprotein family.  In Brassicaceae, self-incompatible plants have a self/non-self recognition system. This is sporophytically controlled by multiple alleles at a single locus (S). S-locus glycoproteins, as well as S-receptor kinases, are in linkage with the S-alleles.
CDD:250251	501	EUK	Invertebrates:4,Mammals:1,Primates:1,Rodents:2,Vertebrates:4	pfam00955, HCO3_cotransp, HCO3- transporter family.  This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
CDD:250252	237	EUK	Invertebrates:25,Mammals:3,Plants:28,Primates:2,Rodents:4,Vertebrates:2	pfam00956, NAP, Nucleosome assembly protein (NAP).  NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity. They affect the transcription of many genes.
CDD:250253	89	EUK	Invertebrates:27,Plants:23,Primates:1,Rodents:1,Vertebrates:3	pfam00957, Synaptobrevin, Synaptobrevin.  
CDD:250254	93	EUKprk	Bacteria:88,Environmental:4,Invertebrates:9,Plants:13	pfam00958, GMP_synt_C, GMP synthase C terminal domain.  GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. This family is the C-terminal domain specific to the GMP synthases EC:6.3.5.2. In prokaryotes this domain mediates dimerization. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains.
CDD:250255	108	PRK	Bacteria:5,Phages:8	pfam00959, Phage_lysozyme, Phage lysozyme.  This family includes lambda phage lysozyme and Escherichia coli endolysin.
CDD:250257	100	EUKprk	Bacteria:1,Invertebrates:3,Plants:22	pfam00961, LAGLIDADG_1, LAGLIDADG endonuclease.  
CDD:250258	329	EUKprk	Bacteria:1,Invertebrates:1,Mammals:1,Plants:2,Primates:1,Rodents:1	pfam00962, A_deaminase, Adenosine/AMP deaminase.  
CDD:250259	136	PRK	Bacteria:10	pfam00963, Cohesin, Cohesin domain.  Cohesin domains interact with a complementary domain, termed the dockerin domain. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome.
CDD:250260	90	EUK	Plants:11	pfam00964, Elicitin, Elicitin.  Elicitins form a novel class of plant necrotic proteins which are secreted by Phytophthora and Pythium fungi, parasites of many economically important crops. These proteins induce leaf necrosis in infected plants and elicit an incompatible hypersensitive-like reaction, leading to the development of a systemic acquired resistance against a range of fungal and bacterial plant pathogens.
CDD:250261	181	EUK	Invertebrates:6,Mammals:1,Primates:1,Rodents:3,Vertebrates:5	pfam00965, TIMP, Tissue inhibitor of metalloproteinase.  Members of this family are common in extracellular regions of vertebrate species.
CDD:250263	75	EUK	Mammals:15,Primates:9,Rodents:10,Vertebrates:11	pfam00969, MHC_II_beta, Class II histocompatibility antigen, beta domain.  
CDD:250264	99	EUKprk	Bacteria:16,Invertebrates:2,Mammals:1,Plants:5,Primates:1	pfam00970, FAD_binding_6, Oxidoreductase FAD-binding domain.  
CDD:250267	501	PRK	Viruses:8	pfam00974, Rhabdo_glycop, Rhabdovirus spike glycoprotein.  Frequently abbreviated to G protein. The glycoprotein spike is made up of a trimer of G proteins. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating.
CDD:250268	224	EUKprk	Bacteria:12,Plants:1,Rodents:1,Vertebrates:1	pfam00975, Thioesterase, Thioesterase domain.  Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, ...
CDD:250269	229	PRK	Bacteria:53	pfam00977, His_biosynth, Histidine biosynthesis protein.  Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel ...
CDD:250270	441	PRK	Viruses:36	pfam00978, RdRP_2, RNA dependent RNA polymerase.  This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins:  2A protein from bromoviruses  putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses.
CDD:144538	488	PRK	Viruses:14	pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).  This protein is also known as NSP1. NS53 is encoded by gene 5. It is made in low levels in the infected cells and is a component of early replication. The protein is known to accumulate on the cytoskeleton of the infected cell. NS53 is an RNA binding protein that contains a characteristic cysteine rich region.
CDD:250271	470	EUKprk	Bacteria:3,Plants:7	pfam00982, Glyco_transf_20, Glycosyltransferase family 20.  Members of this family belong to glycosyl transferase family 20. OtsA (Trehalose-6-phosphate synthase) is homologous to regions in the subunits of yeast trehalose-6-phosphate synthase/phosphate complex,.
CDD:250272	96	EUKprk	Bacteria:16,Invertebrates:2,Plants:1	pfam00984, UDPG_MGDP_dh, UDP-glucose/GDP-mannose dehydrogenase family, central domain.  The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate.
CDD:250273	65	EUKprk	Bacteria:38,Invertebrates:3,Plants:2	pfam00986, DNA_gyraseB_C, DNA gyrase B subunit, carboxyl terminus.  The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyse the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent ...
CDD:250274	131	EUKprk	Bacteria:96,Environmental:1,Invertebrates:2,Plants:7,Vertebrates:1	pfam00988, CPSase_sm_chain, Carbamoyl-phosphate synthase small chain, CPSase domain.  The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The ...
CDD:250275	111	EUKprk	Bacteria:6,Invertebrates:3,Primates:1	pfam00989, PAS, PAS fold.  The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
CDD:250276	159	PRK	Bacteria:10	pfam00990, GGDEF, GGDEF domain.  This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic ...
CDD:250277	117	EUK	Invertebrates:13,Mammals:2,Primates:1,Rodents:1,Vertebrates:11	pfam00992, Troponin, Troponin.  Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin ...
CDD:189794	82	EUK	Mammals:8,Primates:2,Rodents:6,Vertebrates:7	pfam00993, MHC_II_alpha, Class II histocompatibility antigen, alpha domain.  
CDD:250278	141	EUKprk	Bacteria:71,Environmental:4,Invertebrates:1,Plants:3,Vertebrates:1,nodiv:1	pfam00994, MoCF_biosynth, Probable molybdopterin binding domain.  This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerization.
CDD:250279	555	EUK	Invertebrates:28,Plants:31,Primates:1,Rodents:2,Vertebrates:4	pfam00995, Sec1, Sec1 family.  
CDD:250282	486	PRK	Viruses:26	pfam00998, RdRP_3, Viral RNA dependent RNA polymerase.  This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.
CDD:250283	373	EUKprk	Bacteria:38,Invertebrates:2,Plants:4,Primates:1,Rodents:2,Vertebrates:1	pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family.  Na/H antiporters are key transporters in maintaining the pH of actively metabolizing cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other ...
CDD:250284	116	EUKprk	Bacteria:14,Invertebrates:3,Plants:7,Primates:1,Rodents:2	pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.  Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal.
CDD:110033	128	PRK	Viruses:10	pfam01002, Flavi_NS2B, Flavivirus non-structural protein NS2B.  Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.
CDD:250285	117	PRK	Viruses:10	pfam01003, Flavi_capsid, Flavivirus capsid protein C.  Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.
CDD:250286	75	PRK	Viruses:11	pfam01004, Flavi_M, Flavivirus envelope glycoprotein M.  Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
CDD:250287	216	PRK	Viruses:11	pfam01005, Flavi_NS2A, Flavivirus non-structural protein NS2A.  NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex.
CDD:250289	336	EUK	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:1	pfam01007, IRK, Inward rectifier potassium channel.  
CDD:250290	281	EUKprk	Bacteria:3,Invertebrates:1,Mammals:1,Primates:1,Rodents:1	pfam01008, IF-2B, Initiation factor 2 subunit family.  This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- ...
CDD:250291	242	EUKprk	Bacteria:3,Plants:110	pfam01010, Oxidored_q1_C, NADH-Ubiquinone oxidoreductase (complex I) subunit C-terminus.  This sub-family represents a carboxyl terminal extension of pfam00361. It includes subunit 5 from chloroplasts, and bacterial subunit L. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.
CDD:250292	38	PRK	Bacteria:15	pfam01011, PQQ, PQQ enzyme repeat.  The family represent a single repeat of a beta propeller. This propeller has been found in several enzymes which utilize pyrrolo-quinoline quinone as a prosthetic group.
CDD:250293	160	EUKprk	Bacteria:111,Environmental:1,Invertebrates:4,Plants:8	pfam01012, ETF, Electron transfer flavoprotein domain.  This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein.
CDD:250294	143	EUKprk	Bacteria:18,Invertebrates:7,Mammals:1,Plants:35,Primates:1,Vertebrates:5	pfam01014, Uricase, Uricase.  
CDD:250295	195	EUKprk	Bacteria:22,Environmental:3,Invertebrates:22,Plants:11,Rodents:1	pfam01015, Ribosomal_S3Ae, Ribosomal S3Ae family.  
CDD:250296	80	EUKprk	Bacteria:53,Environmental:1,Invertebrates:8,Mammals:1,Plants:13,Synthetic:1,Vertebrates:1	pfam01016, Ribosomal_L27, Ribosomal L27 protein.  
CDD:250297	182	EUK	Invertebrates:4,Primates:3,Rodents:2,Vertebrates:7	pfam01017, STAT_alpha, STAT protein, all-alpha domain.  STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
CDD:250298	506	EUKprk	Bacteria:23,Invertebrates:3,Plants:4,Primates:1,Rodents:1	pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase.  
CDD:250300	47	PRK	Bacteria:15	pfam01022, HTH_5, Bacterial regulatory protein, arsR family.  Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
CDD:250301	44	EUK	Primates:1	pfam01023, S_100, S-100/ICaBP type calcium binding domain.  The S-100 domain is a subfamily of the EF-hand calcium binding proteins.
CDD:144565	187	PRK	Bacteria:6,nodiv:2	pfam01024, Colicin, Colicin pore forming domain.  
CDD:250302	165	EUKprk	Bacteria:74,Environmental:2,Invertebrates:7,Plants:6,Primates:1	pfam01025, GrpE, GrpE.  
CDD:250303	255	EUKprk	Bacteria:53,Invertebrates:3,Plants:3,Primates:1,nodiv:1	pfam01026, TatD_DNase, TatD related DNase.  This family of proteins are related to a large superfamily of metalloenzymes. TatD, a member of this family has been shown experimentally to be a DNase enzyme.
CDD:250304	194	EUKprk	Bacteria:335,Environmental:3,Invertebrates:38,Mammals:1,Plants:36,Primates:1,Rodents:1,Vertebrates:4,Viruses:5	pfam01027, Bax1-I, Inhibitor of apoptosis-promoting Bax1.  Programmed cell-death involves a set of Bcl-2 family proteins, some of which inhibit apoptosis (Bcl-2 and Bcl-XL) and some of which promote it (Bax and Bak). Human Bax inhibitor, BI-1, is an evolutionarily conserved integral membrane protein containing multiple membrane-spanning segments predominantly ...
CDD:250305	244	EUKprk	Bacteria:75,Environmental:1,Invertebrates:15,Plants:15,Primates:1,Rodents:1,Vertebrates:1,Viruses:12	pfam01028, Topoisom_I, Eukaryotic DNA topoisomerase I, catalytic core.  Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.
CDD:250306	126	PRK	Bacteria:90,nodiv:1	pfam01029, NusB, NusB family.  The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.
CDD:250307	113	EUK	Invertebrates:5,Primates:1,Vertebrates:1	pfam01030, Recep_L_domain, Receptor L domain.  The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
CDD:250308	273	EUK	Invertebrates:21,Mammals:5,Plants:13,Primates:1,Rodents:3,Vertebrates:10	pfam01031, Dynamin_M, Dynamin central region.  This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169.
CDD:250309	311	PRK	Bacteria:111	pfam01032, FecCD, FecCD transport family.  This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system.
CDD:250310	44	EUKprk	Bacteria:1,Invertebrates:6,Mammals:2,Plants:1,Primates:2,Rodents:2,Vertebrates:6	pfam01033, Somatomedin_B, Somatomedin B domain.  
CDD:250312	85	EUKprk	Bacteria:55,Environmental:1,Invertebrates:2,Plants:3,Primates:1,Vertebrates:1	pfam01035, DNA_binding_1, 6-O-methylguanine DNA methyltransferase, DNA binding domain.  This domain is a 3 helical bundle.
CDD:250313	223	EUKprk	Bacteria:8,Plants:6	pfam01036, Bac_rhodopsin, Bacteriorhodopsin-like protein.  The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain ...
CDD:250314	73	PRK	Bacteria:101,Environmental:3,nodiv:1	pfam01037, AsnC_trans_reg, AsnC family.  The AsnC family is a family of similar bacterial transcription regulatory proteins.
CDD:250315	487	EUKprk	Bacteria:14,Invertebrates:1,Plants:6,Primates:1	pfam01039, Carboxyl_trans, Carboxyl transferase domain.  All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognized types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in ...
CDD:250316	256	EUKprk	Bacteria:81,Environmental:3,Invertebrates:2,Plants:13,Primates:1	pfam01040, UbiA, UbiA prenyltransferase family.  
CDD:250317	363	PRK	Bacteria:21	pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase family.  The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA, StsC, and StsS. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the ...
CDD:250318	119	EUKprk	Bacteria:9,Invertebrates:1,Plants:1,Rodents:1	pfam01042, Ribonuc_L-PSP, Endoribonuclease L-PSP.  Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including ...
CDD:250319	113	EUKprk	Bacteria:93,Environmental:3,Plants:8	pfam01043, SecA_PP_bind, SecA preprotein cross-linking domain.  The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain.
CDD:250321	59	PRK	Bacteria:17	pfam01047, MarR, MarR family.  The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure ...
CDD:250322	228	EUKprk	Bacteria:102,Environmental:1,Invertebrates:13,Plants:5,Rodents:1,Viruses:1	pfam01048, PNP_UDP_1, Phosphorylase superfamily.  Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase).
CDD:250323	144	EUK	Invertebrates:16,Mammals:2,Rodents:2,Vertebrates:4	pfam01049, Cadherin_C, Cadherin cytoplasmic region.  Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This ...
CDD:144587	151	PRK	Bacteria:2	pfam01050, MannoseP_isomer, Mannose-6-phosphate isomerase.  All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional enzymes. This Pfam entry covers the isomerase domain. The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see pfam00483.
CDD:250324	217	PRK	Bacteria:123,Environmental:1,Phages:1	pfam01051, Rep_3, Initiator Replication protein.  This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene.
CDD:250325	73	PRK	Bacteria:103	pfam01052, SpoA, Surface presentation of antigens (SPOA).  This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, pfam02154.
CDD:250326	381	EUKprk	Bacteria:9,Invertebrates:3,Plants:5,Primates:1	pfam01053, Cys_Met_Meta_PP, Cys/Met metabolizm PLP-dependent enzyme.  This family includes enzymes involved in cysteine and methionine metabolizm. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP ...
CDD:250327	441	EUKprk	Bacteria:23,Invertebrates:3,Plants:16,Primates:1,Rodents:1	pfam01055, Glyco_hydro_31, Glycosyl hydrolases family 31.  Glycosyl hydrolases are key enzymes of carbohydrate metabolizm. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases.
CDD:250329	271	PRK	Viruses:24	pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1.  This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA ...
CDD:250330	124	EUKprk	Bacteria:112,Environmental:1,Vertebrates:1	pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit.  
CDD:144594	110	EUK	Invertebrates:69,Mammals:5,Primates:3,Rodents:2,Vertebrates:36	pfam01059, Oxidored_q5_N, NADH-ubiquinone oxidoreductase chain 4, amino terminus.  
CDD:250331	80	EUK	Invertebrates:4	pfam01060, DUF290, Transthyretin-like family.  This family called family 2 in, has weak similarity to transthyretin (formerly called pre-albumin) which transports thyroid hormones.  The specific function of this protein is unknown.
CDD:250332	210	EUKprk	Bacteria:82,Invertebrates:8,Mammals:1,Plants:24,Rodents:1	pfam01061, ABC2_membrane, ABC-2 type transporter.  
CDD:250333	284	EUKprk	Bacteria:63,Invertebrates:11,Mammals:1,Plants:2,Primates:1,Vertebrates:2	pfam01062, Bestrophin, Bestrophin, RFP-TM, chloride channel.  Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterized by a depressed light peak in the electrooculogram. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which ...
CDD:250334	231	EUKprk	Bacteria:61,Environmental:1,Invertebrates:5,Plants:6	pfam01063, Aminotran_4, Aminotransferase class IV.  The D-amino acid transferases (D-AAT) are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity.
CDD:250335	82	EUK	Invertebrates:8,Primates:2,Rodents:2,Vertebrates:1	pfam01064, Activin_recp, Activin types I and II receptor domain.  This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box.
CDD:250336	488	PRK	Viruses:36	pfam01065, Adeno_hexon, Hexon, adenovirus major coat protein, N-terminal domain.  Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. ...
CDD:250337	97	EUKprk	Bacteria:82,Environmental:3,Invertebrates:12,Plants:7,Rodents:1	pfam01066, CDP-OH_P_transf, CDP-alcohol phosphatidyltransferase.  All of these members have the ability to catalyse the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
CDD:250338	142	EUK	Invertebrates:16,Mammals:2,Plants:5,Primates:1,Rodents:2,Vertebrates:5	pfam01067, Calpain_III, Calpain large subunit, domain III.  The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
CDD:250339	190	EUKprk	Bacteria:4,Phages:3,Plants:1,Viruses:7	pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain.  This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.
CDD:250340	351	EUKprk	Bacteria:95,Environmental:1,Invertebrates:6,Plants:16,Rodents:1,Vertebrates:2	pfam01070, FMN_dh, FMN-dependent dehydrogenase.  
CDD:250341	193	EUKprk	Bacteria:1,Invertebrates:1,Plants:1	pfam01071, GARS_A, Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain.  Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate ...
CDD:250342	280	EUKprk	Bacteria:1,Plants:1,Primates:1,Rodents:3,Vertebrates:1,Viruses:3	pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase family.  The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerization of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones.
CDD:250343	267	EUKprk	Bacteria:20,Invertebrates:4,Mammals:1,Plants:3,Rodents:2	pfam01074, Glyco_hydro_38, Glycosyl hydrolases family 38 N-terminal domain.  Glycosyl hydrolases are key enzymes of carbohydrate metabolizm.
CDD:250344	249	PRK	Bacteria:8	pfam01075, Glyco_transf_9, Glycosyltransferase family 9 (heptosyltransferase).  Members of this family belong to glycosyltransferase family 9. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core.
CDD:250345	196	PRK	Bacteria:16	pfam01076, Mob_Pre, Plasmid recombination enzyme.  With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilisation).
CDD:250346	154	EUKprk	Bacteria:55,Environmental:1,Plants:5	pfam01077, NIR_SIR, Nitrite and sulphite reductase 4Fe-4S domain.  Sulphite and nitrite reductases are vital in the biosynthetic assimilation of sulphur and nitrogen, respectfully. They are also both important for the dissimilation of oxidized anions for energy transduction.
CDD:144608	207	PRK	Bacteria:54,nodiv:1	pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.  Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have ...
CDD:250347	213	EUK	Invertebrates:19,Primates:1,Rodents:2,Vertebrates:10	pfam01079, Hint, Hint module.  This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module.
CDD:250349	128	EUK	Invertebrates:13,Mammals:2,Plants:1,Primates:2,Rodents:2,Vertebrates:3	pfam01082, Cu2_monooxygen, Copper type II ascorbate-dependent monooxygenase, N-terminal domain.  The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
CDD:250350	179	EUKprk	Bacteria:3,Plants:14	pfam01083, Cutinase, Cutinase.  
CDD:250351	54	EUKprk	Bacteria:71,Invertebrates:9,Plants:26,Primates:1,Rodents:1,Vertebrates:1	pfam01084, Ribosomal_S18, Ribosomal protein S18.  
CDD:250353	225	EUK	Invertebrates:3,Mammals:2,Plants:18,Vertebrates:3	pfam01086, Clathrin_lg_ch, Clathrin light chain.  
CDD:250354	170	EUKprk	Bacteria:92,Invertebrates:2,Plants:18,Rodents:1,Vertebrates:2	pfam01087, GalP_UDP_transf, Galactose-1-phosphate uridyl transferase, N-terminal domain.  SCOP reports fold duplication with C-terminal domain. Both involved in Zn and Fe binding.
CDD:250355	211	EUK	Invertebrates:16,Mammals:1,Plants:20,Primates:1,Vertebrates:5	pfam01088, Peptidase_C12, Ubiquitin carboxyl-terminal hydrolase, family 1.  
CDD:250356	140	EUKprk	Bacteria:16,Environmental:1,Invertebrates:19,Plants:9,Rodents:1,Vertebrates:1	pfam01090, Ribosomal_S19e, Ribosomal protein S19e.  
CDD:250358	434	EUK	Mammals:4,Primates:1,Rodents:2,Vertebrates:5	pfam01093, Clusterin, Clusterin.  
CDD:250359	344	EUKprk	Bacteria:11,Invertebrates:8,Mammals:1,Plants:2,Primates:1,Rodents:2,Vertebrates:12	pfam01094, ANF_receptor, Receptor family ligand binding region.  This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
CDD:250360	298	EUK	Plants:13	pfam01095, Pectinesterase, Pectinesterase.  
CDD:250361	39	EUKprk	Bacteria:21,Environmental:1,Invertebrates:20,Plants:19,Rodents:1,Vertebrates:1,Viruses:18	pfam01096, TFIIS_C, Transcription factor S-II (TFIIS).  
CDD:201595	29	EUK	Invertebrates:10	pfam01097, Defensin_2, Arthropod defensin.  
CDD:110122	356	EUKprk	Bacteria:4,Plants:1	pfam01098, FTSW_RODA_SPOVE, Cell cycle protein.  This entry includes the following members; FtsW, RodA, SpoVE.
CDD:201596	67	EUK	Mammals:5,Primates:1,Rodents:4	pfam01099, Uteroglobin, Uteroglobin family.  Uteroglobin is a homodimer of two identical 70 amino acid polypeptides linked by two disulphide bridges. The precise role of uteroglobin has still to be elucidated.
CDD:250362	93	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:4	pfam01101, HMG14_17, HMG14 and HMG17.  
CDD:250364	317	EUKprk	Bacteria:42,Invertebrates:1,Plants:2,Rodents:1	pfam01103, Bac_surface_Ag, Surface antigen.  This entry includes the following surface antigens;  D15 antigen from H.influenzae, OMA87 from P.multocida, OMP85 from N.meningitidis and N.gonorrhoeae. The family also includes a number of eukaryotic proteins that are members of the UPF0140 family. There also appears to be a relationship to pfam03865 (personal obs: C Yeats). In eukaryotes, it appears that these proteins are not ...
CDD:110127	91	PRK	Viruses:24	pfam01104, Bunya_NS-S, Bunyavirus non-structural protein NS-s.  The NS-s protein is encoded by the S RNA. This segment also encodes for the N protein. These two proteins are encoded by overlapping reading frames.
CDD:250365	178	EUK	Invertebrates:34,Mammals:1,Plants:41,Primates:1,Rodents:3,Vertebrates:3	pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD.  Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
CDD:144628	68	EUKprk	Bacteria:14,Invertebrates:1	pfam01106, NifU, NifU-like domain.  This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
CDD:250366	189	PRK	Viruses:17	pfam01107, MP, Viral movement protein (MP).  This family includes a variety of movement proteins (MP)s. The MP is necessary for the initial cell-to-cell movement during the early stages of a viral infection. This movement is active, and it is known that the MP interacts with the plasmodesmata and possesses the ability to bind to RNA to achieve its role. This family also includes consists of virus movement proteins from the caulimovirus family. It has been suggested ...
CDD:201599	106	EUK	Mammals:5,Primates:1,Rodents:3,Vertebrates:6	pfam01108, Tissue_fac, Tissue factor.  This family is found in metazoa, and is very similar to the fibronectin type III domain. The family is found in cytokine receptors, interleukin and interferon receptors and coagulation factor III proteins. It occurs multiple times, as does fn3, family pfam00041.
CDD:144631	70	EUK	Invertebrates:17,Plants:6,Primates:1,Vertebrates:2	pfam01111, CKS, Cyclin-dependent kinase regulatory subunit.  
CDD:250369	124	EUKprk	Bacteria:70,Environmental:1,Plants:1,nodiv:1	pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.  Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.
CDD:250370	240	EUK	Invertebrates:12,Mammals:1,Plants:17,Vertebrates:1	pfam01115, F_actin_cap_B, F-actin capping protein, beta subunit.  
CDD:250371	283	EUKprk	Bacteria:120,Environmental:3,Invertebrates:5,Plants:17	pfam01116, F_bP_aldolase, Fructose-bisphosphate aldolase class-II.  
CDD:250372	359	EUKprk	Bacteria:10,Invertebrates:1,Plants:1	pfam01117, Aerolysin, Aerolysin toxin.  This family represents the pore forming lobe of aerolysin.
CDD:250373	121	EUKprk	Bacteria:131,Environmental:1,Plants:8,nodiv:1	pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding domain.  This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase.
CDD:250374	119	EUKprk	Bacteria:107,Environmental:2,Invertebrates:6,Mammals:1,Plants:10,Vertebrates:1	pfam01119, DNA_mis_repair, DNA mismatch repair protein, C-terminal domain.  This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.
CDD:250375	320	EUKprk	Bacteria:17,Invertebrates:7,Plants:1,Primates:1,Rodents:1,Vertebrates:2	pfam01120, Alpha_L_fucos, Alpha-L-fucosidase.  
CDD:250376	179	EUKprk	Bacteria:5,Invertebrates:1	pfam01121, CoaE, Dephospho-CoA kinase.  This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction.
CDD:250377	305	EUK	Mammals:3,Primates:1,Rodents:1,Vertebrates:2	pfam01122, Cobalamin_bind, Eukaryotic cobalamin-binding protein.  
CDD:250378	85	PRK	Bacteria:7	pfam01123, Stap_Strp_toxin, Staphylococcal/Streptococcal toxin, OB-fold domain.  
CDD:250379	123	EUKprk	Bacteria:154,Environmental:2,Invertebrates:8,Mammals:2,Plants:19,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	pfam01124, MAPEG, MAPEG family.  This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolizm). It includes proteins such as Prostaglandin E synthase. This enzyme catalyses the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, ...
CDD:250380	143	EUK	Invertebrates:12,Plants:14,Rodents:1	pfam01125, G10, G10 protein.  
CDD:250381	204	EUKprk	Bacteria:7,Invertebrates:1,Mammals:1,Plants:1,Primates:1,Vertebrates:1	pfam01126, Heme_oxygenase, Heme oxygenase.  
CDD:250382	123	EUKprk	Bacteria:84,Invertebrates:6,Plants:13,Rodents:1	pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase transmembrane subunit.  This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.
CDD:250384	222	EUKprk	Bacteria:1,Primates:1,Rodents:2,Vertebrates:1	pfam01129, ART, NAD:arginine ADP-ribosyltransferase.  
CDD:250385	461	EUK	Invertebrates:15,Mammals:1,Rodents:1,Vertebrates:4	pfam01130, CD36, CD36 family.  The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.
CDD:250386	404	EUKprk	Bacteria:89,Environmental:3,Invertebrates:7,Plants:2,Vertebrates:1	pfam01131, Topoisom_bac, DNA topoisomerase.  This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
CDD:250387	55	EUKprk	Bacteria:206,Environmental:1,Plants:3	pfam01132, EFP, Elongation factor P (EF-P) OB domain.  
CDD:201616	103	EUK	Invertebrates:7,Plants:3,Rodents:1	pfam01133, ER, Enhancer of rudimentary.  Enhancer of rudimentary is a protein of unknown function that is highly conserved in plants and animals. This protein is found to be an enhancer of the rudimentary gene.
CDD:250388	391	EUKprk	Bacteria:74,Invertebrates:3,Plants:8,nodiv:1	pfam01134, GIDA, Glucose inhibited division protein A.  
CDD:250389	205	EUKprk	Bacteria:1,Invertebrates:2,Mammals:1,Plants:2	pfam01135, PCMT, Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT).  
CDD:250390	233	EUKprk	Bacteria:116,Phages:1,Plants:1	pfam01136, Peptidase_U32, Peptidase family U32.  
CDD:250391	330	EUKprk	Bacteria:2,Plants:1,Primates:1,Rodents:1,nodiv:1	pfam01137, RTC, RNA 3'-terminal phosphate cyclase.  RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain ...
CDD:250392	128	EUKprk	Bacteria:59,Environmental:1,Invertebrates:18,Plants:20,Rodents:1,Vertebrates:2	pfam01138, RNase_PH, 3' exoribonuclease family, domain 1.  This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a ...
CDD:250393	419	EUKprk	Bacteria:114,Environmental:3,Invertebrates:4,Mammals:1,Phages:1,Plants:2	pfam01139, RtcB, tRNA-splicing ligase RtcB.  This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyse the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage.
CDD:250395	336	PRK	Bacteria:57,Environmental:1	pfam01142, TruD, tRNA pseudouridine synthase D (TruD).  TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.
CDD:201623	216	EUKprk	Bacteria:22,Invertebrates:2,Primates:1	pfam01144, CoA_trans, Coenzyme A transferase.  
CDD:250396	176	EUKprk	Bacteria:85,Environmental:1,Invertebrates:5,Phages:4,Plants:2,Primates:1,Vertebrates:2	pfam01145, Band_7, SPFH domain / Band 7 family.  This family has been called SPFH, Band 7 or PHB domain. Recent phylogenetic analysis has shown this domain to be a slipin or Stomatin-like integral membrane domain conserved from protozoa to mammals.
CDD:250397	148	EUK	Invertebrates:2,Mammals:3,Rodents:2,Vertebrates:5	pfam01146, Caveolin, Caveolin.  All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localized and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular ...
CDD:250398	73	EUK	Invertebrates:28	pfam01147, Crust_neurohorm, Crustacean CHH/MIH/GIH neurohormone family.  
CDD:250399	259	EUKprk	Bacteria:24,Invertebrates:3,Plants:4,Primates:1	pfam01148, CTP_transf_1, Cytidylyltransferase family.  The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast. Sec59 is a dolichol kinase EC:2.7.1.108.
CDD:250400	116	EUKprk	Bacteria:69,Environmental:1,Invertebrates:1,Mammals:1,Plants:5,Rodents:1,Viruses:1	pfam01149, Fapy_DNA_glyco, Formamidopyrimidine-DNA glycosylase N-terminal domain.  Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.
CDD:250401	424	EUK	Invertebrates:2,Plants:3,Primates:1,Rodents:1	pfam01150, GDA1_CD39, GDA1/CD39 (nucleoside phosphatase) family.  
CDD:250402	243	EUKprk	Invertebrates:20,Plants:40,Primates:2,Rodents:2,Vertebrates:4,Viruses:3	pfam01151, ELO, GNS1/SUR4 family.  Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway ...
CDD:250403	120	EUKprk	Bacteria:6,Invertebrates:1,Plants:3	pfam01152, Bac_globin, Bacterial-like globin.  This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well.
CDD:250404	558	EUK	Invertebrates:1,Primates:2,Rodents:1,Vertebrates:4	pfam01153, Glypican, Glypican.  
CDD:250405	113	PRK	Bacteria:148	pfam01155, HypA, Hydrogenase expression/synthesis hypA family.  Four conserved cysteines lie either side of the least conserved region.
CDD:250406	305	EUKprk	Bacteria:73,Invertebrates:11,Plants:10,Vertebrates:1	pfam01156, IU_nuc_hydro, Inosine-uridine preferring nucleoside hydrolase.  
CDD:250407	99	EUK	Invertebrates:24,Plants:10,Primates:1,Rodents:1	pfam01158, Ribosomal_L36e, Ribosomal protein L36e.  
CDD:250408	108	EUK	Invertebrates:22,Plants:17,Primates:1,Vertebrates:1	pfam01159, Ribosomal_L6e, Ribosomal protein L6e.  
CDD:189865	49	EUK	Mammals:2,Primates:1,Rodents:2,Vertebrates:16	pfam01160, Opiods_neuropep, Vertebrate endogenous opioids neuropeptide.  
CDD:250409	149	EUKprk	Bacteria:51,Environmental:1,Invertebrates:9,Mammals:1,Plants:24,Vertebrates:2	pfam01161, PBP, Phosphatidylethanolamine-binding protein.  
CDD:250410	186	EUKprk	Bacteria:8,Invertebrates:2,Plants:2,Primates:1	pfam01163, RIO1, RIO1 family.  This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes.   Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined.
CDD:250411	53	EUKprk	Bacteria:93,Environmental:3,Invertebrates:4,Plants:25,Rodents:1,Vertebrates:2	pfam01165, Ribosomal_S21, Ribosomal protein S21.  
CDD:250413	217	EUKprk	Bacteria:279,Environmental:1,Invertebrates:6,Plants:15,nodiv:1	pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.  
CDD:250414	78	EUKprk	Bacteria:80,Invertebrates:5,Plants:11	pfam01169, UPF0016, Uncharacterized protein family UPF0016.  This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions.
CDD:250415	172	EUKprk	Bacteria:5,Rodents:1	pfam01170, UPF0020, Putative RNA methylase family UPF0020.  This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.
CDD:250416	182	EUKprk	Bacteria:18,Plants:1	pfam01171, ATP_bind_3, PP-loop family.  This family of proteins belongs to the PP-loop superfamily.
CDD:250417	91	EUKprk	Bacteria:18,Environmental:3,Invertebrates:22,Mammals:1,Plants:32,Primates:1	pfam01172, SBDS, Shwachman-Bodian-Diamond syndrome (SBDS) protein.  This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, ...
CDD:250418	545	EUKprk	Bacteria:36,Environmental:1,Invertebrates:1,Rodents:1,Vertebrates:1	pfam01175, Urocanase, Urocanase.  
CDD:250419	65	EUKprk	Bacteria:20,Invertebrates:6,Mammals:1,Plants:12,Primates:1,nodiv:1	pfam01176, eIF-1a, Translation initiation factor 1A / IF-1.  This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
CDD:250420	207	EUKprk	Bacteria:128,Environmental:1,Plants:11,nodiv:1	pfam01177, Asp_Glu_race, Asp/Glu/Hydantoin racemase.  This family contains aspartate racemase, maleate isomerases EC:5.2.1.1, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase EC:4.1.1.76.
CDD:250421	410	EUKprk	Bacteria:16,Invertebrates:2,Mammals:1,Plants:25,Primates:2,Rodents:2,Vertebrates:2	pfam01179, Cu_amine_oxid, Copper amine oxidase, enzyme domain.  Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion ...
CDD:250422	291	EUKprk	Bacteria:4,Invertebrates:1,Rodents:1	pfam01180, DHO_dh, Dihydroorotate dehydrogenase.  
CDD:250423	194	EUKprk	Bacteria:236,Environmental:1,Invertebrates:21,Plants:23,Primates:1,Rodents:2,Vertebrates:4,nodiv:1	pfam01182, Glucosamine_iso, Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase.  
CDD:250424	177	PRK	Bacteria:13,Phages:5,nodiv:1	pfam01183, Glyco_hydro_25, Glycosyl hydrolases family 25.  
CDD:250425	210	EUKprk	Bacteria:14,Plants:24	pfam01184, Grp1_Fun34_YaaH, GPR1/FUN34/yaaH family.  The Ady2 protein in is required for acetate in Saccharomyces cerevisiae, and is probably an acetate transporter. A homologue in Yarrowia lipolytica (GPR1) has a role in acetic acid sensitivity.
CDD:250426	82	EUK	Plants:35	pfam01185, Hydrophobin, Fungal hydrophobin.  
CDD:250428	69	EUKprk	Bacteria:617,Environmental:9,Invertebrates:1,Phages:1,Plants:25,nodiv:3	pfam01188, MR_MLE, Mandelate racemase / muconate lactonizing enzyme, C-terminal domain.  C-terminal domain is TIM barrel fold, dehydratase-like domain. Manganese is associated with this domain.
CDD:250429	277	EUKprk	Bacteria:2,Primates:1	pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.  
CDD:250430	95	EUK	Plants:26	pfam01190, Pollen_Ole_e_I, Pollen proteins Ole e I like.  
CDD:250431	74	EUKprk	Bacteria:23,Invertebrates:12,Plants:10,Vertebrates:1,Viruses:3	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-terminal domain.  The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.
CDD:201652	57	EUKprk	Bacteria:23,Invertebrates:6,Plants:8,Viruses:2	pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6.  Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly.
CDD:250432	194	EUKprk	Bacteria:51,Environmental:2,Invertebrates:26,Plants:37,Primates:1,Viruses:1	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerization domain.  The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some ...
CDD:189881	60	EUKprk	Bacteria:16,Environmental:1,Invertebrates:11,Plants:11,Viruses:2	pfam01194, RNA_pol_N, RNA polymerases N / 8 kDa subunit.  
CDD:250433	183	EUKprk	Bacteria:94,Invertebrates:2,Plants:8,Primates:1	pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.  
CDD:250434	97	EUKprk	Bacteria:109,Invertebrates:9,Plants:18,Vertebrates:1,nodiv:1	pfam01196, Ribosomal_L17, Ribosomal protein L17.  
CDD:250435	69	EUKprk	Bacteria:131,Environmental:2,Plants:7	pfam01197, Ribosomal_L31, Ribosomal protein L31.  
CDD:250436	83	EUKprk	Bacteria:11,Environmental:1,Invertebrates:17,Plants:15,Primates:1,Rodents:1	pfam01198, Ribosomal_L31e, Ribosomal protein L31e.  
CDD:201657	94	EUKprk	Bacteria:13,Invertebrates:18,Mammals:1,Plants:12,Rodents:1	pfam01199, Ribosomal_L34e, Ribosomal protein L34e.  
CDD:250437	69	EUKprk	Bacteria:14,Environmental:1,Invertebrates:10,Plants:9	pfam01200, Ribosomal_S28e, Ribosomal protein S28e.  
CDD:250438	129	EUKprk	Bacteria:16,Invertebrates:16,Plants:6	pfam01201, Ribosomal_S8e, Ribosomal protein S8e.  
CDD:250439	158	EUKprk	Bacteria:61,Invertebrates:1,Plants:6,Rodents:1	pfam01202, SKI, Shikimate kinase.  
CDD:250440	220	PRK	Bacteria:42	pfam01203, T2SN, Type II secretion system (T2SS), protein N.  Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown.
CDD:250441	510	EUKprk	Bacteria:5,Invertebrates:4,Plants:8,Primates:1	pfam01204, Trehalase, Trehalase.  Trehalase (EC:3.2.1.28) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with pfam07492 in fungi.
CDD:250442	110	EUKprk	Bacteria:146,Invertebrates:10,Mammals:1,Plants:20	pfam01205, UPF0029, Uncharacterized protein family UPF0029.  
CDD:250443	70	PRK	Bacteria:149	pfam01206, TusA, Sulfurtransferase TusA.  This family includes the TusA sulfurtransferases.
CDD:250444	309	PRK	Bacteria:4	pfam01207, Dus, Dihydrouridine synthase (Dus).  Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members ...
CDD:250445	337	EUKprk	Bacteria:115,Invertebrates:7,Plants:10,Primates:1,Rodents:1,Vertebrates:1	pfam01208, URO-D, Uroporphyrinogen decarboxylase (URO-D).  
CDD:250446	157	EUKprk	Bacteria:24,Invertebrates:2	pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus.  NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
CDD:250447	288	EUKprk	Bacteria:36,Invertebrates:3,Plants:3	pfam01212, Beta_elim_lyase, Beta-eliminating lyase.  
CDD:250449	183	EUK	Invertebrates:16,Plants:15,Primates:1	pfam01214, CK_II_beta, Casein kinase II regulatory subunit.  
CDD:250452	296	EUKprk	Bacteria:57,Invertebrates:7,Plants:10,Primates:1,Rodents:1,Vertebrates:1	pfam01218, Coprogen_oxidas, Coproporphyrinogen III oxidase.  
CDD:250453	104	PRK	Bacteria:64,Environmental:2	pfam01219, DAGK_prokar, Prokaryotic diacylglycerol kinase.  
CDD:250454	140	EUKprk	Bacteria:138,Environmental:6,Plants:7,Synthetic:1,nodiv:1	pfam01220, DHquinase_II, Dehydroquinase class II.  
CDD:250455	86	EUK	Invertebrates:23,Plants:15,Primates:1,Rodents:1,Vertebrates:1	pfam01221, Dynein_light, Dynein light chain type 1.  
CDD:250457	196	EUKprk	Bacteria:23,Invertebrates:7,Plants:3,Primates:1,Rodents:1,Vertebrates:1	pfam01223, Endonuclease_NS, DNA/RNA non-specific endonuclease.  
CDD:250458	80	EUKprk	Bacteria:142,Environmental:2,Plants:2,nodiv:1	pfam01225, Mur_ligase, Mur ligase family, catalytic domain.  This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The ...
CDD:250459	250	EUKprk	Bacteria:138,Environmental:1,Invertebrates:5,Plants:19	pfam01226, Form_Nir_trans, Formate/nitrite transporter.  
CDD:250460	179	EUKprk	Bacteria:85,Environmental:3,Invertebrates:3,Phages:1,Plants:2	pfam01227, GTP_cyclohydroI, GTP cyclohydrolase I.  This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins.
CDD:250461	106	EUKprk	Bacteria:93,Phages:12,Plants:3	pfam01228, Gly_radical, Glycine radical.  
CDD:250462	98	EUKprk	Bacteria:9,Plants:2,Primates:1,Rodents:1	pfam01230, HIT, HIT domain.  
CDD:250463	407	EUKprk	Bacteria:2,Invertebrates:3,Mammals:1,Plants:20,Primates:1,Rodents:2,Vertebrates:2	pfam01231, IDO, Indoleamine 2,3-dioxygenase.  
CDD:144722	151	EUKprk	Bacteria:9,Plants:1	pfam01232, Mannitol_dh, Mannitol dehydrogenase Rossmann domain.  
CDD:250466	353	EUK	Invertebrates:16,Plants:38,Primates:1,Rodents:2,Vertebrates:3	pfam01237, Oxysterol_BP, Oxysterol-binding protein.  
CDD:250468	31	EUK	Invertebrates:12,Mammals:1,Plants:9,Primates:1,Rodents:1	pfam01239, PPTA, Protein prenyltransferase alpha subunit repeat.  Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognize a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognizes a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small ...
CDD:250470	121	EUKprk	Bacteria:121,Environmental:4,Invertebrates:4,Primates:2	pfam01242, PTPS, 6-pyruvoyl tetrahydropterin synthase.  6-Pyruvoyl tetrahydrobiopterin synthase catalyses the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits.
CDD:250471	88	EUKprk	Bacteria:61,Invertebrates:1,Plants:4,Rodents:1,nodiv:1	pfam01243, Pyridox_oxidase, Pyridoxamine 5'-phosphate oxidase.  
CDD:250472	315	EUKprk	Bacteria:30,Invertebrates:2,Plants:2,Primates:1,Rodents:1,nodiv:1	pfam01244, Peptidase_M19, Membrane dipeptidase (Peptidase family M19).  
CDD:201683	113	EUKprk	Bacteria:92,Invertebrates:2,Plants:21	pfam01245, Ribosomal_L19, Ribosomal protein L19.  
CDD:250473	95	EUKprk	Bacteria:3,Invertebrates:22,Plants:15,Primates:1,nodiv:1	pfam01247, Ribosomal_L35Ae, Ribosomal protein L35Ae.  
CDD:250474	95	EUKprk	Bacteria:13,Invertebrates:6,Plants:10,Primates:1,Rodents:1,Vertebrates:1	pfam01248, Ribosomal_L7Ae, Ribosomal protein L7Ae/L30e/S12e/Gadd45 family.  This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.
CDD:189907	81	EUK	Invertebrates:21,Plants:13,Primates:1,Vertebrates:1	pfam01249, Ribosomal_S21e, Ribosomal protein S21e.  
CDD:250475	92	EUKprk	Bacteria:149,Invertebrates:2,Plants:11,Vertebrates:1	pfam01250, Ribosomal_S6, Ribosomal protein S6.  
CDD:250476	184	EUK	Invertebrates:13,Plants:12,Vertebrates:1	pfam01251, Ribosomal_S7e, Ribosomal protein S7e.  
CDD:250477	146	PRK	Bacteria:156,Environmental:2	pfam01252, Peptidase_A8, Signal peptidase (SPase) II.  
CDD:250478	74	EUKprk	Bacteria:64,Environmental:2,Invertebrates:23,Mammals:1,Plants:25,Primates:1,Vertebrates:2,Viruses:1	pfam01253, SUI1, Translation initiation factor SUI1.  
CDD:250479	222	EUKprk	Bacteria:54,Environmental:2,Invertebrates:8,Plants:13,Vertebrates:1	pfam01255, Prenyltransf, Putative undecaprenyl diphosphate synthase.  Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
CDD:250480	242	PRK	Bacteria:1	pfam01256, Carb_kinase, Carbohydrate kinase.  This family is related to pfam02110 and pfam00294 implying that it also is a carbohydrate kinase. (personal obs Yeats C).
CDD:250481	145	EUKprk	Bacteria:126,Environmental:1,Invertebrates:9,Plants:9,Primates:1	pfam01257, 2Fe-2S_thioredx, Thioredoxin-like [2Fe-2S] ferredoxin.  
CDD:250482	36	PRK	Bacteria:173,Environmental:4,Phages:5	pfam01258, zf-dskA_traR, Prokaryotic dksA/traR C4-type zinc finger.  
CDD:250483	243	EUKprk	Bacteria:1,Plants:3	pfam01259, SAICAR_synt, SAICAR synthetase.  Also known as Phosphoribosylaminoimidazole-succinocarboxamide synthase.
CDD:250484	202	EUKprk	Bacteria:110,Invertebrates:5,Plants:5,Vertebrates:1,Viruses:3,nodiv:1	pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel.  This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae.
CDD:250485	150	EUKprk	Bacteria:56,Environmental:1,Invertebrates:6,Plants:9,Rodents:1,Vertebrates:1,nodiv:1	pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal domain.  This family now also contains the lysine 2-oxoglutarate reductases.
CDD:250486	300	EUKprk	Bacteria:21,Invertebrates:1,Mammals:1,Plants:8	pfam01263, Aldose_epim, Aldose 1-epimerase.  
CDD:250487	345	EUKprk	Bacteria:104,Environmental:2,Invertebrates:1,Plants:4	pfam01264, Chorismate_synt, Chorismate synthase.  
CDD:250488	239	EUK	Invertebrates:9,Plants:24,Rodents:1,Vertebrates:3	pfam01265, Cyto_heme_lyase, Cytochrome c/c1 heme lyase.  
CDD:250489	320	EUKprk	Bacteria:136,Environmental:1,Invertebrates:6,Mammals:3,Plants:15,Primates:1,Rodents:2,nodiv:1	pfam01266, DAO, FAD dependent oxidoreductase.  This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
CDD:250490	268	EUK	Invertebrates:12,Plants:23,Primates:1,Rodents:2,Vertebrates:1	pfam01267, F-actin_cap_A, F-actin capping protein alpha subunit.  
CDD:250491	557	EUKprk	Bacteria:110,Environmental:2,Invertebrates:6,Plants:12,Vertebrates:2	pfam01268, FTHFS, Formate--tetrahydrofolate ligase.  
CDD:250492	229	EUKprk	Bacteria:13,Invertebrates:13,Plants:7	pfam01269, Fibrillarin, Fibrillarin.  
CDD:250494	77	PRK	Bacteria:118,Environmental:2,Synthetic:1	pfam01272, GreA_GreB, Transcription elongation factor, GreA/GreB, C-term.  This domain has an FKBP-like fold.
CDD:250495	164	EUK	Invertebrates:2,Mammals:3,Plants:1,Primates:1,Rodents:2,Vertebrates:1	pfam01273, LBP_BPI_CETP, LBP / BPI / CETP family, N-terminal domain.  The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.
CDD:250496	524	EUKprk	Bacteria:6,Plants:5,nodiv:1	pfam01274, Malate_synthase, Malate synthase.  
CDD:110290	118	EUK	Plants:10	pfam01277, Oleosin, Oleosin.  
CDD:250500	101	EUK	Mammals:2,Rodents:1,Vertebrates:4	pfam01279, Parathyroid, Parathyroid hormone family.  
CDD:250501	148	EUKprk	Bacteria:17,Environmental:4,Invertebrates:12,Mammals:1,Plants:9,Rodents:1	pfam01280, Ribosomal_L19e, Ribosomal protein L19e.  
CDD:250502	48	EUKprk	Bacteria:122,Environmental:1,Invertebrates:9,Plants:14,Primates:1,Vertebrates:1	pfam01281, Ribosomal_L9_N, Ribosomal protein L9, N-terminal domain.  
CDD:250503	83	EUKprk	Bacteria:22,Invertebrates:23,Plants:15,Rodents:1	pfam01282, Ribosomal_S24e, Ribosomal protein S24e.  
CDD:250504	113	EUKprk	Bacteria:3,Environmental:1,Invertebrates:16,Plants:12,Primates:1	pfam01283, Ribosomal_S26e, Ribosomal protein S26e.  
CDD:250505	135	EUK	Invertebrates:2,Mammals:2,Plants:26,Primates:1,Rodents:2,Vertebrates:2	pfam01284, MARVEL, Membrane-associating domain.  MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
CDD:250506	424	EUK	Invertebrates:3,Plants:8,Primates:1,Rodents:2,Vertebrates:1	pfam01285, TEA, TEA/ATTS domain family.  
CDD:189926	34	EUK	Invertebrates:4,Plants:1,Primates:1,Rodents:1,Vertebrates:3	pfam01286, XPA_N, XPA protein N-terminal.  
CDD:250507	69	EUKprk	Bacteria:21,Invertebrates:23,Mammals:1,Plants:28,Primates:1	pfam01287, eIF-5a, Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold.  eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast.
CDD:250508	127	EUKprk	Bacteria:100,Environmental:1,Invertebrates:1,Plants:6	pfam01288, HPPK, 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK).  
CDD:250509	41	EUK	Invertebrates:12,Primates:1,Rodents:2,Vertebrates:5,nodiv:1	pfam01290, Thymosin, Thymosin beta-4 family.  
CDD:250511	139	miss	miss	pfam01292, Ni_hydr_CYTB, Prokaryotic cytochrome b561.  This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a prokaryotic family. Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188.
CDD:250512	451	EUKprk	Bacteria:92,Invertebrates:7,Plants:6	pfam01293, PEPCK_ATP, Phosphoenolpyruvate carboxykinase.  
CDD:250514	599	PRK	Bacteria:13	pfam01295, Adenylate_cycl, Adenylate cyclase, class-I.  
CDD:250515	263	PRK	Bacteria:123	pfam01297, TroA, Periplasmic solute binding protein family.  This family includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum.
CDD:250516	523	PRK	Bacteria:11	pfam01298, Lipoprotein_5, Transferrin binding protein-like solute binding protein.  This family of proteins are distantly related to other families of solute binding proteins.
CDD:250517	306	EUK	Invertebrates:3,Mammals:3,Primates:2,Rodents:4,Vertebrates:3	pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).  
CDD:250518	176	EUKprk	Bacteria:130,Invertebrates:7,Plants:5,Vertebrates:1	pfam01300, Sua5_yciO_yrdC, Telomere recombination.  This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.
CDD:250519	317	EUKprk	Bacteria:13,Invertebrates:2,Mammals:1,Plants:9,Rodents:1	pfam01301, Glyco_hydro_35, Glycosyl hydrolases family 35.  
CDD:250520	67	EUK	Invertebrates:19,Mammals:1,Plants:35,Primates:2,Rodents:2,Vertebrates:2	pfam01302, CAP_GLY, CAP-Gly domain.  Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The ...
CDD:250521	121	EUKprk	Bacteria:2,Invertebrates:18	pfam01303, Egg_lysin, Egg lysin (Sperm-lysin).  Egg lysin creates a hole in the envelope of the egg thereby allowing the sperm to pass through the envelope and fuse with the egg.
CDD:250522	33	PRK	Bacteria:12	pfam01304, Gas_vesicle_C, Gas vesicles protein GVPc repeated domain.  
CDD:250523	104	PRK	Viruses:74	pfam01307, Plant_vir_prot, Plant viral movement protein.  This family includes several known plant viral movement proteins from a number of different ssRNA plant virus families including potexviruses, hordeiviruses and carlaviruses.
CDD:189937	215	PRK	Viruses:17	pfam01310, Adeno_PVIII, Adenovirus hexon associated protein, protein VIII.  See pfam01065. This family represents Hexon.
CDD:250525	249	PRK	Bacteria:10	pfam01311, Bac_export_1, Bacterial export proteins, family 1.  This family includes the following members;  FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways.
CDD:110325	343	PRK	Bacteria:8	pfam01312, Bac_export_2, FlhB HrpN YscU SpaS Family.  This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse.
CDD:250526	76	EUKprk	Bacteria:154,Environmental:1,Plants:1	pfam01313, Bac_export_3, Bacterial export proteins, family 3.  This family includes the following members;  FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways.
CDD:250527	375	PRK	Bacteria:60,Environmental:2	pfam01314, AFOR_C, Aldehyde ferredoxin oxidoreductase, domains 2 & 3.  Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This family is composed of two structural domains that bind the tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, ...
CDD:250528	111	EUKprk	Bacteria:10,Invertebrates:1,Mammals:1	pfam01315, Ald_Xan_dh_C, Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  
CDD:250529	70	PRK	Bacteria:8	pfam01316, Arg_repressor, Arginine repressor, DNA binding domain.  
CDD:250530	85	PRK	Bacteria:15	pfam01320, Colicin_Pyocin, Colicin immunity protein / pyocin immunity protein.  
CDD:250531	128	EUKprk	Bacteria:87,Invertebrates:2,Plants:3,Vertebrates:1	pfam01321, Creatinase_N, Creatinase/Prolidase N-terminal domain.  This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
CDD:250532	121	PRK	Bacteria:81	pfam01322, Cytochrom_C_2, Cytochrome C'.  
CDD:250533	191	EUKprk	Bacteria:22,Plants:1,Primates:1	pfam01323, DSBA, DSBA-like thioredoxin domain.  This family contains a diverse set of proteins with a thioredoxin-like structure pfam00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways. This family also contains members with functions other than HCCA isomerization, such as Kappa family GSTs, whose similarity to HCCA ...
CDD:110335	58	PRK	Bacteria:7	pfam01325, Fe_dep_repress, Iron dependent repressor, N-terminal DNA binding domain.  This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
CDD:250534	322	EUKprk	Bacteria:61,Environmental:2,Invertebrates:1,Plants:2	pfam01326, PPDK_N, Pyruvate phosphate dikinase, PEP/pyruvate binding domain.  This enzyme catalyses the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP).
CDD:250535	156	EUKprk	Bacteria:103,Environmental:3,Invertebrates:7,Plants:3	pfam01327, Pep_deformylase, Polypeptide deformylase.  
CDD:250537	96	EUKprk	Bacteria:93,Environmental:1,Invertebrates:9,Plants:15,Vertebrates:2	pfam01329, Pterin_4a, Pterin 4 alpha carbinolamine dehydratase.  Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerization cofactor of hepatocyte nuclear factor 1-alpha).
CDD:250538	61	PRK	Bacteria:9	pfam01330, RuvA_N, RuvA N terminal domain.  The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.
CDD:250539	192	EUKprk	Invertebrates:1,Plants:4,Primates:1,Viruses:2	pfam01331, mRNA_cap_enzyme, mRNA capping enzyme, catalytic domain.  This family represents the ATP binding catalytic domain of the mRNA capping enzyme.
CDD:250540	118	EUKprk	Bacteria:14,Invertebrates:1,Plants:34	pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal.  This is a sub-family of cytochrome C. See pfam00034.
CDD:250541	84	EUKprk	Primates:1,Rodents:2,Vertebrates:1,Viruses:6	pfam01335, DED, Death effector domain.  
CDD:250542	75	EUKprk	Bacteria:150,Invertebrates:10,Phages:1,Plants:9,Primates:1,Rodents:2,nodiv:1	pfam01336, tRNA_anti-codon, OB-fold nucleic acid binding domain.  This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG ...
CDD:250543	83	PRK	Bacteria:42	pfam01337, Barstar, Barstar (barnase inhibitor).  
CDD:250544	182	PRK	Bacteria:136	pfam01339, CheB_methylest, CheB methylesterase.  
CDD:250545	297	EUKprk	Bacteria:32,Plants:22	pfam01341, Glyco_hydro_6, Glycosyl hydrolases family 6.  
CDD:250546	81	EUK	Invertebrates:5,Plants:3,Primates:2,Rodents:3,Vertebrates:2	pfam01342, SAND, SAND domain.  The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.
CDD:250547	154	PRK	Bacteria:9,Phages:2	pfam01343, Peptidase_S49, Peptidase family S49.  
CDD:250548	46	EUKprk	Bacteria:1,Invertebrates:3,Plants:3,Primates:1,Rodents:1,Viruses:9	pfam01344, Kelch_1, Kelch motif.  The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that the Drosophila ring canal kelch protein is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415.
CDD:250549	76	PRK	Bacteria:9	pfam01345, DUF11, Domain of unknown function DUF11.  A domain of unknown function found in multiple copies in several archaebacterial proteins.
CDD:250550	124	PRK	Bacteria:101	pfam01346, FKBP_N, Domain amino terminal to FKBP-type peptidyl-prolyl isomerase.  This family is only found at the amino terminus of pfam00254. This domain is of unknown function.
CDD:250551	579	EUK	Invertebrates:16,Mammals:1,Primates:1,Vertebrates:5	pfam01347, Vitellogenin_N, Lipoprotein amino terminal region.  This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.
CDD:250552	142	EUK	Plants:10	pfam01348, Intron_maturas2, Type II intron maturase.  Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.
CDD:250553	254	PRK	Viruses:8	pfam01349, Flavi_NS4B, Flavivirus non-structural protein NS4B.  Flaviviruses encode a single polyprotein.  This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localisation of NS3 and pfam00972.
CDD:201742	145	PRK	Viruses:8	pfam01350, Flavi_NS4A, Flavivirus non-structural protein NS4A.  Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus.
CDD:250554	197	PRK	Bacteria:1	pfam01351, RNase_HII, Ribonuclease HII.  
CDD:201743	41	EUK	Mammals:1,Primates:1,Rodents:2	pfam01352, KRAB, KRAB box.  The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to ...
CDD:250555	218	EUK	Invertebrates:22	pfam01353, GFP, Green fluorescent protein.  
CDD:250556	67	PRK	Bacteria:35	pfam01355, HIPIP, High potential iron-sulfur protein.  
CDD:250557	82	EUK	Plants:36	pfam01357, Pollen_allerg_1, Pollen allergen.  This family contains allergens lol PI, PII and PIII from Lolium perenne.
CDD:250558	80	EUK	Invertebrates:44,Mammals:1,Primates:2,nodiv:1	pfam01359, Transposase_1, Transposase (partial DDE domain).  This family includes the mariner transposase.
CDD:201747	60	PRK	Bacteria:21	pfam01361, Tautomerase, Tautomerase enzyme.  This family includes the enzyme 4-oxalocrotonate tautomerase that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate.
CDD:250559	68	EUKprk	Invertebrates:23,Mammals:2,Plants:34,Primates:1,Rodents:1,Vertebrates:3,Viruses:1	pfam01363, FYVE, FYVE zinc finger.  The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and ...
CDD:250560	340	EUKprk	Bacteria:42,Environmental:3,Plants:1	pfam01364, Peptidase_C25, Peptidase family C25.  
CDD:250561	203	EUK	Mammals:1,Primates:1	pfam01365, RYDR_ITPR, RIH domain.  The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3.
CDD:250562	635	PRK	Viruses:31	pfam01366, PRTP, Herpesvirus processing and transport protein.  The members of this family are associate with capsid intermediates during packaging of the virus.
CDD:250563	100	EUKprk	Bacteria:7,Invertebrates:1	pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.  
CDD:250564	156	EUKprk	Bacteria:76,Invertebrates:1,Phages:1,Plants:2,Primates:1	pfam01368, DHH, DHH family.  It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ.
CDD:250565	188	EUKprk	Bacteria:3,Invertebrates:24,Plants:30,Primates:1,Rodents:2,Vertebrates:1	pfam01369, Sec7, Sec7 domain.  The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the pfam00025 family.
CDD:250566	233	EUKprk	Bacteria:58,Invertebrates:2,Plants:2,Primates:1,Rodents:1,Viruses:1	pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.  This family of proteins utilize NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.
CDD:189960	88	PRK	Bacteria:21	pfam01371, Trp_repressor, Trp repressor protein.  This protein binds to tryptophan and represses transcription of the Trp operon.
CDD:250571	213	EUKprk	Bacteria:3,Plants:1	pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane cofactor binding domain.  
CDD:250572	131	EUKprk	Bacteria:12,Plants:1,Primates:1,nodiv:1	pfam01380, SIS, SIS domain.  SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway.
CDD:250573	55	EUKprk	Bacteria:50,Invertebrates:2,Phages:14,Plants:4,Primates:1	pfam01381, HTH_3, Helix-turn-helix.  This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the Neisseria gonorrhoeae phage associated protein NGO0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family.
CDD:250574	114	EUKprk	Bacteria:6,Invertebrates:2,Vertebrates:2	pfam01382, Avidin, Avidin family.  
CDD:250575	55	EUKprk	Bacteria:30,Plants:2	pfam01383, CpcD, CpcD/allophycocyanin linker domain.  
CDD:250576	304	EUKprk	Bacteria:114,Environmental:2,Invertebrates:14,Plants:18,Primates:1,Synthetic:1,Vertebrates:2,Viruses:1	pfam01384, PHO4, Phosphate transporter family.  This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukaemia virus receptor.
CDD:250577	226	PRK	Bacteria:31,Environmental:1,Phages:1	pfam01385, OrfB_IS605, Probable transposase.  This family includes IS891, IS1136 and IS1341. DUF1225, pfam06774, has now been merged into this family.
CDD:250578	87	PRK	Bacteria:139,Environmental:1	pfam01386, Ribosomal_L25p, Ribosomal L25p family.  Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress.
CDD:250580	92	EUK	Invertebrates:7,Plants:16,Primates:1,Rodents:1,Vertebrates:3	pfam01388, ARID, ARID/BRIGHT DNA binding domain.  This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
CDD:250581	177	PRK	Bacteria:7	pfam01389, OmpA_membrane, OmpA-like transmembrane domain.  The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel. This family includes some other distantly related outer membrane proteins with low scores.
CDD:250582	107	EUK	Invertebrates:6,Mammals:3,Primates:2,Rodents:3,Vertebrates:3	pfam01390, SEA, SEA domain.  Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain.
CDD:189968	60	EUK	Invertebrates:2,Primates:1	pfam01391, Collagen, Collagen triple helix repeat (20 copies).  Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and ...
CDD:250583	114	EUK	Invertebrates:1,Primates:1,Rodents:2,Vertebrates:2	pfam01392, Fz, Fz domain.  Also known as the CRD (cysteine rich domain), the C6 box in MuSK receptor. This domain of unknown function has been independently identified by several groups. The domain contains 10 conserved cysteines.
CDD:250585	37	EUK	Invertebrates:2,Plants:1,Rodents:1,Vertebrates:1	pfam01394, Clathrin_propel, Clathrin propeller repeat.  Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles. The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure. Each leg contains one heavy and one light chain. The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which ...
CDD:250586	113	EUK	Invertebrates:37	pfam01395, PBP_GOBP, PBP/GOBP family.  The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors. This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with ...
CDD:110400	39	PRK	Bacteria:4	pfam01396, zf-C4_Topoisom, Topoisomerase DNA binding C4 zinc finger.  
CDD:250587	177	EUKprk	Plants:67,Synthetic:1	pfam01397, Terpene_synth, Terpene synthase, N-terminal domain.  It has been suggested that this gene family be designated tps (for terpene synthase). It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase, 5-epi- aristolochene synthase, and (+)-delta-cadinene synthase. tpsb includes (-)-limonene synthase. tpsc includes kaurene synthase A. tpsd includes taxadiene synthase, pinene synthase, ...
CDD:250588	118	EUKprk	Bacteria:2,Invertebrates:3,Plants:3,Primates:1,Rodents:1	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease.  Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain, JABP1 domain or JAMM domain. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based ...
CDD:250589	105	EUK	Invertebrates:4,Plants:9,Primates:1,Rodents:1	pfam01399, PCI, PCI domain.  This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
CDD:250590	192	EUK	Invertebrates:3,Primates:1,nodiv:1	pfam01400, Astacin, Astacin (Peptidase family M12A).  The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This ...
CDD:250592	35	PRK	Bacteria:36,Phages:1	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family.  The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected.
CDD:250593	434	EUKprk	Primates:1,Rodents:1,Vertebrates:2,Viruses:1	pfam01403, Sema, Sema domain.  The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and human plexin A-3.
CDD:250594	178	EUK	Invertebrates:3,Primates:1,Rodents:1,Vertebrates:4	pfam01404, Ephrin_lbd, Ephrin receptor ligand binding domain.  The Eph receptors, which bind to ephrins pfam00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand.
CDD:250595	301	PRK	Bacteria:2	pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic domain.  This family includes only cysteinyl tRNA synthetases.
CDD:144848	120	PRK	Viruses:91	pfam01407, Gemini_AL3, Geminivirus AL3 protein.  Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL3 protein comprises approximately 0.05% of the cellular proteins and is present in the soluble and organelle fractions. AL3 may form oligomers. Immunoprecipitation of AL3 in a baculovirus expression system extracts expressing both ...
CDD:250596	120	EUKprk	Bacteria:26,Plants:7,Rodents:1	pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding Rossmann fold.  This family of enzymes utilize NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot.
CDD:250597	243	EUKprk	Bacteria:20,Invertebrates:1,Plants:1	pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).  Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.
CDD:250598	208	EUK	Invertebrates:11,Mammals:2,Primates:1,Rodents:1,Vertebrates:5	pfam01410, COLFI, Fibrillar collagen C-terminal domain.  Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
CDD:250599	551	EUKprk	Bacteria:4,Invertebrates:2,Plants:1,Primates:1	pfam01411, tRNA-synt_2c, tRNA synthetases class II (A).  Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.
CDD:250600	117	EUK	Invertebrates:23,Plants:22,Primates:1,Rodents:2,Vertebrates:2	pfam01412, ArfGap, Putative GTPase activating protein for Arf.  Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
CDD:144854	110	EUK	Invertebrates:4,Primates:1	pfam01413, C4, C-terminal tandem repeated domain in type 4 procollagen.  Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
CDD:144855	63	EUK	Invertebrates:2,Primates:1,Rodents:2,Vertebrates:2	pfam01414, DSL, Delta serrate ligand.  
CDD:250602	103	EUKprk	Bacteria:43,Environmental:2,Invertebrates:17,Plants:10,Rodents:1,Vertebrates:1	pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase.  Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely ...
CDD:250603	124	EUK	Invertebrates:17,Plants:25,Primates:1,Rodents:2,Vertebrates:1	pfam01417, ENTH, ENTH domain.  The ENTH (Epsin N-terminal homology) domain is found in proteins involved in endocytosis and cytoskeletal machinery. The function of the ENTH domain is unknown.
CDD:201784	77	PRK	Bacteria:2	pfam01418, HTH_6, Helix-turn-helix domain, rpiR family.  This domain contains a helix-turn-helix motif. The best characterized member of this family is Escherichia coli rpiR, a regulator of the expression of rpiB gene.
CDD:250604	132	EUK	Plants:5	pfam01419, Jacalin, Jacalin-like lectin domain.  Proteins containing this domain are lectins. It is found in 1 to 6 copies in these proteins. The domain is also found in the animal prostatic spermine-binding protein.
CDD:250605	167	PRK	Bacteria:22,Phages:1	pfam01420, Methylase_S, Type I restriction modification DNA specificity domain.  This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction ...
CDD:250606	197	EUK	Primates:2,Rodents:2,Vertebrates:8	pfam01421, Reprolysin, Reprolysin (M12B) family zinc metalloprotease.  The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins such as human ADAM8 and fertilin. Fertilin and closely related proteins appear to not have some active site ...
CDD:250607	20	EUK	Primates:1	pfam01422, zf-NF-X1, NF-X1 type zinc finger.  This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. The zinc fingers in human NFX1 bind to DNA.
CDD:250608	66	EUKprk	Bacteria:19,Invertebrates:7,Plants:9,Primates:1,Rodents:1,Vertebrates:1	pfam01423, LSM, LSM domain.  The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to ...
CDD:250609	58	EUKprk	Bacteria:161,Invertebrates:37,Plants:52,Primates:1,Rodents:2,Vertebrates:3,Viruses:1	pfam01424, R3H, R3H domain.  The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.
CDD:250610	436	EUKprk	Bacteria:16,Invertebrates:2,Plants:4,Primates:1	pfam01425, Amidase, Amidase.  
CDD:250611	120	EUK	Invertebrates:2,Plants:9,Primates:1,Rodents:1,Vertebrates:1	pfam01426, BAH, BAH domain.  This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
CDD:250613	43	EUKprk	Bacteria:9,Environmental:1,Invertebrates:26,Mammals:2,Plants:36,Primates:2,Rodents:2,Vertebrates:3,Viruses:2	pfam01428, zf-AN1, AN1-like Zinc finger.  Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.
CDD:250614	75	EUK	Invertebrates:1,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam01429, MBD, Methyl-CpG binding domain.  The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl ...
CDD:250615	274	EUKprk	Bacteria:158,Environmental:1,Invertebrates:1,Plants:2,nodiv:1	pfam01430, HSP33, Hsp33 protein.  Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. oxidizing conditions like H2O2 cause disulfide bonds to form in Hsp33, a process that leads to the ...
CDD:250616	206	EUKprk	Bacteria:2,Invertebrates:2	pfam01431, Peptidase_M13, Peptidase family M13.  Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage.
CDD:250617	446	EUKprk	Bacteria:5,Invertebrates:3,Mammals:1,Rodents:1	pfam01432, Peptidase_M3, Peptidase family M3.  This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence.
CDD:250618	389	EUKprk	Bacteria:4,Invertebrates:4,Plants:2,Primates:1,Rodents:2,Vertebrates:2	pfam01433, Peptidase_M1, Peptidase family M1.  Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase, this enzyme also has an aminopeptidase activity.
CDD:250619	192	EUKprk	Bacteria:5,Plants:3,Primates:1	pfam01434, Peptidase_M41, Peptidase family M41.  
CDD:250620	223	EUKprk	Bacteria:12,Plants:2,Primates:1	pfam01435, Peptidase_M48, Peptidase family M48.  
CDD:250621	28	EUKprk	Bacteria:4,Invertebrates:2,Plants:1,Primates:1,Rodents:2	pfam01436, NHL, NHL repeat.  The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Human E3 ...
CDD:250622	48	EUKprk	Invertebrates:5,Mammals:1,Primates:1,Rodents:1,Vertebrates:2,Viruses:1	pfam01437, PSI, Plexin repeat.  A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved ...
CDD:110442	74	EUK	Invertebrates:1,Plants:19	pfam01439, Metallothio_2, Metallothionein.  Members of this family are metallothioneins. These proteins are cysteine rich proteins that bind to heavy metals. Members of this family appear to be closest to Class II metallothioneins, seed pfam00131.
CDD:250623	134	PRK	Viruses:108	pfam01440, Gemini_AL2, Geminivirus AL2 protein.  Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene, and BR1 movement protein.
CDD:250624	160	PRK	Bacteria:8	pfam01441, Lipoprotein_6, Lipoprotein.  Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens.
CDD:250625	167	EUK	Environmental:1,Invertebrates:1,Mammals:7,Primates:2,Rodents:4,Vertebrates:12	pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain.  These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I. Apolipoprotein A-IV, and Apolipoprotein E.
CDD:250626	227	PRK	Viruses:60	pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.  Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.
CDD:250627	232	PRK	Bacteria:23	pfam01446, Rep_1, Replication protein.  Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one ...
CDD:250628	150	PRK	Bacteria:11	pfam01447, Peptidase_M4, Thermolysin metallopeptidase, catalytic domain.  
CDD:250629	55	EUK	Invertebrates:12,Plants:3,Primates:2,Rodents:1,Vertebrates:2	pfam01448, ELM2, ELM2 domain.  The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a member from Arabidopsis thaliana. This suggests that ELM2 may also be ...
CDD:250630	146	EUKprk	Bacteria:7,Plants:3	pfam01450, IlvC, Acetohydroxy acid isomeroreductase, catalytic domain.  Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.
CDD:250631	138	EUKprk	Bacteria:13,Invertebrates:1,Plants:1,Primates:1	pfam01451, LMWPc, Low molecular weight phosphotyrosine protein phosphatase.  
CDD:250632	108	EUKprk	Bacteria:12,Invertebrates:1,Plants:31	pfam01453, B_lectin, D-mannose binding lectin.  These proteins include mannose-specific lectins from plants as well as bacteriocins from bacteria.
CDD:201804	171	EUK	Invertebrates:3,Mammals:3,Plants:11,Primates:2,Rodents:2,Vertebrates:1	pfam01454, MAGE, MAGE family.  The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumors but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been ...
CDD:250633	66	PRK	Bacteria:143,Environmental:1	pfam01455, HupF_HypC, HupF/HypC family.  
CDD:250635	230	EUKprk	Bacteria:111,Invertebrates:1,Plants:2	pfam01458, UPF0051, Uncharacterized protein family (UPF0051).  
CDD:250636	273	EUK	Invertebrates:11,Plants:30,Primates:1,Rodents:2,Vertebrates:3	pfam01459, Porin_3, Eukaryotic porin.  
CDD:201808	28	EUK	Mammals:1,Primates:1,Rodents:1,Vertebrates:1	pfam01462, LRRNT, Leucine rich repeat N-terminal domain.  Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
CDD:250637	25	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:2,Vertebrates:1,nodiv:1	pfam01463, LRRCT, Leucine rich repeat C-terminal domain.  Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the C-terminus of tandem leucine rich repeats.
CDD:189996	117	EUKprk	Bacteria:14,Phages:5,Vertebrates:1	pfam01464, SLT, Transglycosylase SLT domain.  This family is distantly related to pfam00062. Members are found in phages, type II, type III and type IV secretion systems.
CDD:250638	45	EUK	Invertebrates:13,Mammals:1,Plants:14,Primates:1,Rodents:1,Vertebrates:1	pfam01465, GRIP, GRIP domain.  The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in.
CDD:250639	78	EUKprk	Invertebrates:17,Plants:13,Unassigned:1,Viruses:3	pfam01466, Skp1, Skp1 family, dimerization domain.  
CDD:250640	148	EUKprk	Bacteria:20,Invertebrates:1,Plants:2,Primates:1,Rodents:1	pfam01467, CTP_transf_2, Cytidylyltransferase.  This family includes: Cholinephosphate cytidylyltransferase and Glycerol-3-phosphate cytidylyltransferase.
CDD:201812	53	PRK	Bacteria:21	pfam01468, GA, GA module.  The GA (protein G-related Albumin-binding) module is composed of three alpha helices. This module is found in a range of bacterial cell surface proteins. The GA module from Peptostreptococcus magnus pab shows a strong affinity for albumin.
CDD:250641	40	EUKprk	Bacteria:26,Invertebrates:2	pfam01469, Pentapeptide_2, Pentapeptide repeats (8 copies).  These repeats are found in many mycobacterial proteins. These repeats are most common in the pfam00823 family of proteins, where they are found in the MPTR subfamily of PPE proteins. The function of these repeats is unknown. The repeat can be approximately described as XNXGX, where X can be any amino acid. These repeats are similar to pfam00805, however it is not clear if these two ...
CDD:250643	57	EUKprk	Bacteria:68,Invertebrates:3,Mammals:2,Phages:6,Plants:3,Primates:1,Rodents:2,Vertebrates:7,nodiv:1	pfam01471, PG_binding_1, Putative peptidoglycan binding domain.  This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found ...
CDD:250644	74	EUKprk	Bacteria:44,Invertebrates:1,Plants:3,Rodents:1	pfam01472, PUA, PUA domain.  The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also ...
CDD:250645	19	PRK	Bacteria:20,Phages:2	pfam01473, CW_binding_1, Putative cell wall binding repeat.  These repeats are characterized by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins. The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in Streptococcus phage Cp-1 lysozyme might be responsible for the specific recognition of choline-containing cell walls. Similar ...
CDD:250646	437	EUKprk	Bacteria:90,Invertebrates:3,Plants:11	pfam01474, DAHP_synth_2, Class-II DAHP synthetase family.  Members of this family are aldolase enzymes that catalyse the first step of the shikimate pathway.
CDD:201817	120	PRK	Bacteria:15	pfam01475, FUR, Ferric uptake regulator family.  This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
CDD:250647	43	EUKprk	Bacteria:29,Invertebrates:2,Phages:4,Plants:3,Rodents:1	pfam01476, LysM, LysM domain.  The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.
CDD:250648	114	EUKprk	Bacteria:5,Invertebrates:11,Mammals:2,Plants:14,Primates:1,Rodents:4,Synthetic:1,Vertebrates:1	pfam01477, PLAT, PLAT/LH2 domain.  This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase pfam01114, which mediates membrane association. So it appears possible that this ...
CDD:250649	103	PRK	Bacteria:73	pfam01478, Peptidase_A24, Type IV leader peptidase family.  Peptidase A24, or the prepilin peptidase as it is also known, processes the N-terminus of the prepilins. The processing is essential for the correct formation of the pseudopili of type IV bacterial protein secretion. The enzyme is found across eubacteria and archaea.
CDD:250650	48	EUKprk	Bacteria:28,Invertebrates:7,Plants:12	pfam01479, S4, S4 domain.  The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be ...
CDD:250651	75	EUK	Invertebrates:13,Mammals:1,Plants:14,Primates:1,Vertebrates:2	pfam01480, PWI, PWI domain.  
CDD:250652	87	EUKprk	Bacteria:15,Invertebrates:11,Plants:10,Primates:1,Rodents:3,Vertebrates:1,Viruses:1	pfam01483, P_proprotein, Proprotein convertase P-domain.  A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
CDD:250653	53	EUK	Invertebrates:9	pfam01484, Col_cuticle_N, Nematode cuticle collagen N-terminal domain.  The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens, see pfam01391. Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins.
CDD:250654	63	EUK	Invertebrates:18,Plants:28,Rodents:2,Vertebrates:3	pfam01485, IBR, IBR domain.  The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in ...
CDD:250655	100	EUK	Plants:21	pfam01486, K-box, K-box region.  The K-box region is commonly found associated with SRF-type transcription factors see pfam00319. The K-box is a possible coiled-coil structure. Possible role in multimer formation.
CDD:250656	222	EUKprk	Bacteria:86,Plants:34	pfam01487, DHquinase_I, Type I 3-dehydroquinase.  Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see pfam01220.
CDD:250657	133	EUKprk	Bacteria:9,Plants:7	pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase.  This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where ...
CDD:250658	405	EUK	Invertebrates:1,Plants:4,Primates:1,Rodents:1	pfam01490, Aa_trans, Transmembrane amino acid transporter protein.  This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline ...
CDD:250659	108	EUKprk	Bacteria:61,Environmental:1,Invertebrates:10,Plants:16,Rodents:1,Vertebrates:1	pfam01491, Frataxin_Cyay, Frataxin-like domain.  This family contains proteins that have a domain related to the globular C-terminus of Frataxin the protein that is mutated in Friedreich's ataxia. This domain is found in a family of bacterial proteins.  The function of this domain is currently unknown. It has been suggested that this family is involved in iron transport.
CDD:110491	85	PRK	Viruses:72	pfam01492, Gemini_C4, Geminivirus C4 protein.  This family consists of the N terminal region of geminivirus C4 or AC4 proteins. In Tomato yellow leaf curl geminivirus (TYLCV) the C4 protein is necessary for efficient spreading of the virus in tomato plants.
CDD:201826	198	EUKprk	Bacteria:7,Plants:1	pfam01493, GXGXG, GXGXG motif.  This domain is found in glutamate synthase, tungsten formylmethanofuran dehydrogenase subunit c (FwdC) and molybdenum formylmethanofuran dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G motif is seen in the alignment.
CDD:250660	349	EUKprk	Bacteria:19,Plants:1	pfam01494, FAD_binding_3, FAD binding domain.  This domain is involved in FAD binding in a number of enzymes.
CDD:250661	694	EUKprk	Bacteria:2,Invertebrates:2,Mammals:1,Plants:2,Primates:1,Rodents:1	pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family.  This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane ...
CDD:250662	238	PRK	Bacteria:31,Environmental:1	pfam01497, Peripla_BP_2, Periplasmic binding protein.  This family includes bacterial periplasmic binding proteins. Several of which are involved in iron transport.
CDD:250663	72	EUK	Invertebrates:10,Plants:5,Vertebrates:3	pfam01498, HTH_Tnp_Tc3_2, Transposase.  Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements.
CDD:250664	538	PRK	Viruses:15	pfam01499, Herpes_UL25, Herpesvirus UL25 family.  The herpesvirus UL25 gene product is a virion component involved in virus penetration and capsid assembly. The product of the UL25 gene is required for packaging but not cleavage of replicated viral DNA. This family includes a number of herpesvirus proteins: EHV-1 36, EBV BVRF1, HCMV UL77, ILTV ORF2, and VZV gene 34.
CDD:250666	247	EUKprk	Bacteria:12,Invertebrates:2,Plants:4,Primates:1,Rodents:1,Viruses:5	pfam01501, Glyco_transf_8, Glycosyl transferase family 8.  This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.
CDD:250667	75	EUKprk	Bacteria:126,Environmental:3,Plants:10	pfam01502, PRA-CH, Phosphoribosyl-AMP cyclohydrolase.  This enzyme catalyses the third step in the histidine biosynthetic pathway. It requires Zn ions for activity.
CDD:250668	83	EUKprk	Bacteria:17,Phages:6,Plants:1,Viruses:1	pfam01503, PRA-PH, Phosphoribosyl-ATP pyrophosphohydrolase.  This enzyme catalyses the second step in the histidine biosynthetic pathway.
CDD:250669	254	EUK	Invertebrates:22,Mammals:1,Plants:26,Primates:1,Rodents:1,Vertebrates:3	pfam01504, PIP5K, Phosphatidylinositol-4-phosphate 5-Kinase.  This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a ...
CDD:201831	43	EUK	Invertebrates:11,Mammals:1,Primates:1,Rodents:2,Vertebrates:5	pfam01505, Vault, Major Vault Protein repeat.  The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
CDD:250670	23	PRK	Viruses:5	pfam01506, HCV_NS5a, Hepatitis C virus non-structural 5a protein membrane anchor.  The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because ...
CDD:201832	173	EUKprk	Bacteria:9,Phages:1,Plants:2	pfam01507, PAPS_reduct, Phosphoadenosine phosphosulfate reductase family.  This domain is found in phosphoadenosine phosphosulfate (PAPS) reductase enzymes or PAPS sulfotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP). It is also found in ...
CDD:250671	62	EUK	Invertebrates:2	pfam01508, Paramecium_SA, Paramecium surface antigen domain.  This domain is a cysteine rich extracellular repeat found in surface antigens of Paramecium. The domain contains 8 cysteine residues.
CDD:250672	149	EUKprk	Bacteria:122,Environmental:2,Invertebrates:2,Plants:5,Rodents:1	pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal domain).  Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
CDD:250673	113	EUKprk	Bacteria:61,Invertebrates:6,Phages:11,Primates:1,Rodents:1,Vertebrates:1	pfam01510, Amidase_2, N-acetylmuramoyl-L-alanine amidase.  This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved ...
CDD:250674	150	EUKprk	Bacteria:94,Environmental:1,Invertebrates:2,Plants:1	pfam01512, Complex1_51K, Respiratory-chain NADH dehydrogenase 51 Kd subunit.  
CDD:250675	243	PRK	Bacteria:18	pfam01513, NAD_kinase, ATP-NAD kinase.  Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86.
CDD:250676	206	PRK	Bacteria:12	pfam01514, YscJ_FliF, Secretory protein of YscJ/FliF family.  This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins.   The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins.
CDD:250677	319	PRK	Bacteria:12	pfam01515, PTA_PTB, Phosphate acetyl/butaryl transferase.  This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate.
CDD:250680	87	PRK	Bacteria:2	pfam01519, DUF16, Protein of unknown function DUF16.  The function of this protein is unknown. It appears to only occur in Mycoplasma pneumoniae. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils.
CDD:250681	172	PRK	Bacteria:67,Environmental:2,Phages:2	pfam01520, Amidase_3, N-acetylmuramoyl-L-alanine amidase.  This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.
CDD:250682	106	EUKprk	Bacteria:60,Plants:1,nodiv:1	pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis.  This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.
CDD:250683	122	EUKprk	Bacteria:37,Plants:1	pfam01522, Polysacc_deac_1, Polysaccharide deacetylase.  This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.
CDD:250684	289	PRK	Bacteria:105,Environmental:3	pfam01523, PmbA_TldD, Putative modulator of DNA gyrase.  tldD and pmbA were found to suppress mutations in letD and inhibitor of DNA gyrase. Therefore it has been hypothesised that the TldD and PmbA proteins modulate the activity of DNA gyrase. It has also been suggested that PmbA may be involved in secretion.
CDD:144934	78	PRK	Viruses:44	pfam01524, Gemini_V1, Geminivirus V1 protein.  Disruption of the V1 gene in Tomato yellow leaf curl virus (TYLCV) stopped its ability to systemically infect tomato plants, suggesting that the V1 gene product is required for successful infection of the host.
CDD:250685	388	PRK	Bacteria:43,Environmental:1	pfam01526, DDE_Tnp_Tn3, Tn3 transposase DDE domain.  This family includes transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from E-coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalysis of numerous transposases.
CDD:250686	75	PRK	Bacteria:33	pfam01527, HTH_Tnp_1, Transposase.  Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
CDD:250687	374	PRK	Viruses:30	pfam01528, Herpes_glycop, Herpesvirus glycoprotein M.  The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments. Glycoprotein M is not essential for viral replication.
CDD:250688	167	EUK	Invertebrates:25,Plants:13,Primates:2,Rodents:2	pfam01529, zf-DHHC, DHHC palmitoyltransferase.  This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
CDD:201844	31	EUK	Invertebrates:6,Mammals:1,Primates:1,Rodents:2,Vertebrates:2	pfam01530, zf-C2HC, Zinc finger, C2HC type.  This is a DNA binding zinc finger domain.
CDD:250690	445	EUKprk	Bacteria:2,Invertebrates:12,Plants:41,Primates:1,Vertebrates:3	pfam01532, Glyco_hydro_47, Glycosyl hydrolase family 47.  Members of this family are alpha-mannosidases that catalyse the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).
CDD:250691	328	EUK	Primates:1,Rodents:2,Vertebrates:1	pfam01534, Frizzled, Frizzled/Smoothened family membrane region.  This family contains the membrane spanning region of frizzled and smoothened receptors. This membrane region is predicted to contain seven transmembrane alpha helices. Proteins related to Drosophila frizzled are receptors for Wnt (mediating the beta-catenin signalling pathway), but also the planar cell polarity (PCP) pathway and the Wnt/calcium pathway. The predominantly ...
CDD:250692	31	EUK	Plants:6,Primates:1	pfam01535, PPR, PPR repeat.  This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The ...
CDD:250693	328	EUK	Invertebrates:5,Mammals:1,Plants:9,Primates:1	pfam01536, SAM_decarbox, Adenosylmethionine decarboxylase.  This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes. In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine. The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme.
CDD:190025	119	PRK	Viruses:18	pfam01537, Herpes_glycop_D, Herpesvirus glycoprotein D/GG/GX domain.  This domain is found in several Herpes viruses glycoproteins. This is a family includes glycoprotein-D (gD or gIV) which is common to herpes simplex virus types 1 and 2, as well as equine herpes, bovine herpes and Marek's disease virus. Glycoprotein-D has been found on the viral envelope and the plasma membrane of infected cells. and gD immunisation can produce an immune response to bovine herpes ...
CDD:201846	195	PRK	Viruses:14	pfam01538, HCV_NS2, Hepatitis C virus non-structural protein NS2.  The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.
CDD:250694	77	EUKprk	Bacteria:45,Environmental:2,Phages:4,Plants:15,Viruses:8,nodiv:1	pfam01541, GIY-YIG, GIY-YIG catalytic domain.  This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded ...
CDD:250695	293	EUKprk	Bacteria:68,Environmental:1,Invertebrates:1,nodiv:1	pfam01544, CorA, CorA-like Mg2+ transporter protein.  The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. The family includes the MRS2 protein from yeast that is thought to be an RNA splicing protein. However its membership of this family suggests that its ...
CDD:250696	273	EUKprk	Bacteria:64,Invertebrates:6,Plants:9,Primates:1,Rodents:1,Vertebrates:2	pfam01545, Cation_efflux, Cation efflux family.  Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells.
CDD:250697	309	EUKprk	Bacteria:123,Environmental:2,Invertebrates:4,Plants:7,Rodents:1,Vertebrates:2,nodiv:1	pfam01546, Peptidase_M20, Peptidase family M20/M25/M40.  This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.
CDD:250698	297	PRK	Bacteria:62	pfam01547, SBP_bac_1, Bacterial extracellular solute-binding protein.  This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.
CDD:250699	143	PRK	Bacteria:109	pfam01548, DEDD_Tnp_IS110, Transposase.  Transposase proteins are necessary for efficient DNA transposition. This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases.
CDD:250700	37	EUK	Invertebrates:4	pfam01549, ShK, ShK domain-like.  This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
CDD:250701	96	EUKprk	Bacteria:86,Environmental:1,Invertebrates:1,Phages:5,Primates:1,Vertebrates:3,nodiv:1	pfam01551, Peptidase_M23, Peptidase family M23.  Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Escherichia coli murein hydrolase activator NlpD, for which no ...
CDD:201855	99	PRK	Viruses:16	pfam01552, Pico_P2B, Picornavirus 2B protein.  Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability.
CDD:250702	131	EUKprk	Bacteria:9,Invertebrates:2,Plants:5,Primates:1,Rodents:1	pfam01553, Acyltransferase, Acyltransferase.  This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene.
CDD:190033	161	EUKprk	Bacteria:8,Plants:1	pfam01554, MatE, MatE.  The MatE domain.
CDD:250703	219	PRK	Bacteria:26,Phages:3	pfam01555, N6_N4_Mtase, DNA methylase.  Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.
CDD:250704	81	EUKprk	Bacteria:38,Invertebrates:18,Plants:11	pfam01556, CTDII, DnaJ C terminal domain.  This family consists of the C terminal region form the DnaJ protein. It is always found associated with pfam00226 and pfam00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and this, CTDII, are necessary for maintaining the J-domains in their specific relative positions.
CDD:250705	205	EUKprk	Bacteria:74,Environmental:1,Invertebrates:3,Plants:7	pfam01557, FAA_hydrolase, Fumarylacetoacetate (FAA) hydrolase family.  This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from Escherichia coli strain W.  FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. ...
CDD:250706	166	EUKprk	Bacteria:84,Environmental:1,Plants:1	pfam01558, POR, Pyruvate ferredoxin/flavodoxin oxidoreductase.  This family includes a region of the large protein pyruvate-flavodoxin oxidoreductase and the whole pyruvate ferredoxin oxidoreductase gamma subunit protein. It is not known whether the gamma subunit has a catalytic or regulatory role. Pyruvate oxidoreductase (POR) catalyses the final step in the fermentation of carbohydrates in anaerobic microorganisms. This involves the ...
CDD:250707	124	EUKprk	Bacteria:1,Invertebrates:3,Mammals:2,Primates:5,Rodents:2,Vertebrates:7	pfam01562, Pep_M12B_propep, Reprolysin family propeptide.  This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
CDD:190039	55	PRK	Viruses:11	pfam01563, Alpha_E3_glycop, Alphavirus E3 glycoprotein.  This protein is found in some alphaviruses as a virion associated spike protein.
CDD:250708	240	EUKprk	Bacteria:6,Invertebrates:1,Plants:2,Primates:1	pfam01564, Spermine_synth, Spermine/spermidine synthase.  Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyses the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase.
CDD:250709	139	EUKprk	Bacteria:83,Invertebrates:3,Plants:11,Rodents:1	pfam01565, FAD_binding_4, FAD binding domain.  This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links ...
CDD:250710	364	EUKprk	Bacteria:89,Environmental:1,Invertebrates:4,Plants:7	pfam01566, Nramp, Natural resistance-associated macrophage protein.  The natural resistance-associated macrophage protein (NRAMP) family consists of Nramp1, Nramp2, and yeast proteins Smf1 and Smf2. The NRAMP family is a novel family of functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains. This family of membrane proteins are divalent cation transporters. Nramp1 is an integral ...
CDD:250711	110	PRK	Bacteria:55,Environmental:1,nodiv:1	pfam01568, Molydop_binding, Molydopterin dinucleotide binding domain.  This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea ...
CDD:250712	123	EUKprk	Bacteria:102,Environmental:1,Invertebrates:15,Plants:11,Rodents:1,Vertebrates:1	pfam01569, PAP2, PAP2 superfamily.  This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidizing halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.
CDD:250713	212	EUKprk	Bacteria:78,Invertebrates:6,Plants:5,Vertebrates:2	pfam01571, GCV_T, Aminomethyltransferase folate-binding domain.  This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.
CDD:250714	276	PRK	Viruses:16	pfam01573, Bromo_MP, Bromovirus movement protein.  
CDD:250715	123	EUKprk	Bacteria:10,Invertebrates:1,Plants:4,Primates:1	pfam01575, MaoC_dehydratas, MaoC like domain.  The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase. The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific ...
CDD:144972	859	EUK	Invertebrates:9	pfam01576, Myosin_tail_1, Myosin tail.  The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural ...
CDD:250716	245	PRK	Viruses:5	pfam01577, Peptidase_S30, Potyvirus P1 protease.  The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for autocatalytic ...
CDD:250717	211	EUKprk	Bacteria:18,Invertebrates:1,Plants:11	pfam01578, Cytochrom_C_asm, Cytochrome C assembly protein.  This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium, CcmC from Escherichia coli and Paracoccus denitrificans and orf240 from wheat mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family ...
CDD:250718	161	EUK	Invertebrates:2	pfam01579, DUF19, Domain of unknown function (DUF19).  This presumed domain has no known function. It is found in one or two copies in several Caenorhabditis elegans proteins. It is roughly 130 amino acids long. The domain contains 12 conserved cysteines which suggests that the domain is an extracellular domain and that these cysteines form six intradomain disulphide bridges. The GO annotation for this protein indicates that it has a function in nematode larval ...
CDD:250719	201	PRK	Bacteria:16	pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family.  FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from Escherichia coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a ...
CDD:110576	11	EUK	Invertebrates:15	pfam01581, FARP, FMRFamide related peptide family.  The neuroactive peptide Phe-Met-Arg-Phe-NH2 (FMRF-amide) has a variety of effects on both mammalian and invertebrate tissues.
CDD:250720	137	EUK	Invertebrates:2,Plants:2,Primates:1,Rodents:2	pfam01582, TIR, TIR domain.  The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to ...
CDD:250721	157	EUKprk	Bacteria:3,Invertebrates:3,Plants:3,Primates:1	pfam01583, APS_kinase, Adenylylsulphate kinase.  Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
CDD:250722	136	PRK	Bacteria:57,nodiv:1	pfam01584, CheW, CheW-like domain.  CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in CheA binds to CheW, suggesting that these domains can interact with each other.
CDD:250723	45	EUKprk	Invertebrates:2,Plants:5,Primates:1,Rodents:1,Viruses:1	pfam01585, G-patch, G-patch domain.  This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.
CDD:250725	94	EUKprk	Bacteria:10,Invertebrates:3,Plants:1,Primates:1	pfam01588, tRNA_bind, Putative tRNA binding domain.  This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may ...
CDD:201874	502	PRK	Viruses:8	pfam01589, Alpha_E1_glycop, Alphavirus E1 glycoprotein.  E1 forms a heterodimer with E2 pfam00943. The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus).
CDD:250726	146	EUKprk	Bacteria:66,Invertebrates:5,Mammals:1,Plants:39,Primates:1,Rodents:2,Vertebrates:2,nodiv:1	pfam01590, GAF, GAF domain.  This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is ...
CDD:250727	223	EUK	Mammals:1,Plants:2,Primates:1,Rodents:1	pfam01591, 6PF2K, 6-phosphofructo-2-kinase.  This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif.
CDD:250728	126	EUKprk	Bacteria:5,Invertebrates:1,Plants:1	pfam01592, NifU_N, NifU-like N terminal domain.  This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.
CDD:250729	444	EUKprk	Bacteria:28,Invertebrates:4,Plants:12,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase.  This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role ...
CDD:250730	327	PRK	Bacteria:10	pfam01594, UPF0118, Domain of unknown function DUF20.  This transmembrane region is found in putative permeases and predicted transmembrane proteins it has no known function. It is not clear what source suggested that these proteins may be permeases and this information should be treated with caution.
CDD:250731	182	EUKprk	Bacteria:92,Environmental:1,Invertebrates:8,Plants:1,Primates:1	pfam01595, DUF21, Domain of unknown function DUF21.  This transmembrane region has no known function. Many of the sequences in this family are annotated as hemolysins, however this is due to a similarity to Treponema hyodysenteriae hemolysin C that does not contain this domain. This domain is found in the N-terminus of the proteins adjacent to two intracellular CBS domains pfam00571.
CDD:250733	122	EUKprk	Bacteria:2,Invertebrates:1,Mammals:1,Plants:2	pfam01597, GCV_H, Glycine cleavage H-protein.  This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.
CDD:250736	609	PRK	Viruses:20	pfam01601, Corona_S2, Coronavirus S2 glycoprotein.  The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2.
CDD:250737	522	EUK	Invertebrates:2,Mammals:1,Plants:4,Primates:1,Rodents:2	pfam01602, Adaptin_N, Adaptin N terminal region.  This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within ...
CDD:250738	405	EUK	Invertebrates:8,Mammals:1,Plants:7,Primates:1,Vertebrates:1	pfam01603, B56, Protein phosphatase 2A regulatory B subunit (B56 family).  Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolizm. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits ...
CDD:250740	52	EUKprk	Invertebrates:12,Plants:1,Viruses:4	pfam01607, CBM_14, Chitin binding Peritrophin-A domain.  This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three ...
CDD:250741	152	EUK	Invertebrates:6,Plants:12,Rodents:1	pfam01608, I_LWEQ, I/LWEQ domain.  I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin and yeast Sla2p interact with F-actin. I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB and SLA110; (3) metazoan Hip1p; and (4) yeast Sla2p. The domain has four conserved blocks, the name of the domain is derived from the initial conserved ...
CDD:250742	193	EUKprk	Bacteria:64,Plants:1	pfam01609, DDE_Tnp_1, Transposase DDE domain.  Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. This family contains transposases for IS4, ...
CDD:250743	238	EUKprk	Bacteria:109,Environmental:4,Invertebrates:1,Phages:1,nodiv:2	pfam01610, DDE_Tnp_ISL3, Transposase.  Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165.
CDD:250744	174	EUKprk	Bacteria:3,Invertebrates:2,Phages:2,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease.  This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in Escherichia coli polI it is also found in the Werner syndrome helicase ...
CDD:250745	150	EUKprk	Bacteria:114,Environmental:1,Plants:12	pfam01613, Flavin_Reduct, Flavin reductase like domain.  This is a flavin reductase family consisting of enzymes known to be flavin reductases as well as various oxidoreductase and monooxygenase components. VlmR is a flavin reductase that functions in a two-component enzyme system to provide isobutylamine N-hydroxylase with reduced flavin and may be involved in the synthesis of valanimycin. SnaC is a flavin reductase that provides ...
CDD:250746	129	PRK	Bacteria:11,nodiv:2	pfam01614, IclR, Bacterial transcriptional regulator.  This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this family covers the C-terminal region that may bind to the regulatory substrate (unpublished observation, Bateman A.).
CDD:250747	194	PRK	Viruses:11	pfam01616, Orbi_NS3, Orbivirus NS3.  The function of this Orbivirus non structural protein is uncertain. However it may play a role on release of the virus from infected cells.
CDD:250748	247	PRK	Bacteria:5	pfam01617, Surface_Ag_2, Surface antigen.  This family includes a number of bacterial surface antigens expressed on the surface of pathogens.
CDD:250749	139	PRK	Bacteria:16	pfam01618, MotA_ExbB, MotA/TolQ/ExbB proton channel family.  This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across ...
CDD:250750	309	EUKprk	Bacteria:6,Invertebrates:2,Plants:1,Primates:1	pfam01619, Pro_dh, Proline dehydrogenase.  
CDD:250752	337	PRK	Viruses:10	pfam01621, Fusion_gly_K, Cell fusion glycoprotein K.  This protein is probably an integral membrane bound glycoprotein that is involved in viral fusion with the host cell.
CDD:250753	91	PRK	Viruses:10	pfam01623, Carla_C4, Carlavirus putative nucleic acid binding protein.  This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF. These proteins may function as viral transcriptional regulators. The carlavirus family includes garlic latent virus and potato virus S and M, these viruses are positive strand, ...
CDD:250754	113	EUKprk	Bacteria:20,Invertebrates:3,Plants:5,Primates:1,Rodents:1,nodiv:1	pfam01624, MutS_I, MutS domain I.  This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various ...
CDD:250755	147	EUKprk	Bacteria:50,Invertebrates:4,Plants:4	pfam01625, PMSR, Peptide methionine sulfoxide reductase.  This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.
CDD:250756	88	EUKprk	Bacteria:48,Invertebrates:1,Plants:5,Viruses:1,nodiv:1	pfam01627, Hpt, Hpt domain.  The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined. The ...
CDD:250757	222	PRK	Bacteria:146	pfam01628, HrcA, HrcA protein C terminal domain.  HrcA is found to negatively regulate the transcription of heat shock genes. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain.
CDD:145002	112	PRK	Bacteria:7,Environmental:1	pfam01629, DUF22, Domain of unknown function DUF22.  This domain is found in 1 to 3 copies in archaebacterial proteins. The function of the domain is unknown. This family appears to be expanded in Archaeoglobus fulgidus.
CDD:250758	336	EUK	Invertebrates:2,Mammals:2,Primates:1,Rodents:2	pfam01630, Glyco_hydro_56, Hyaluronidase.  
CDD:145004	61	EUKprk	Bacteria:9,Invertebrates:3,Primates:1,Vertebrates:1	pfam01632, Ribosomal_L35p, Ribosomal protein L35.  
CDD:250759	208	EUKprk	Bacteria:6,Invertebrates:6,Plants:5,Rodents:2	pfam01633, Choline_kinase, Choline/ethanolamine kinase.  Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only.
CDD:110621	161	EUKprk	Bacteria:4,Plants:2	pfam01634, HisG, ATP phosphoribosyltransferase.  
CDD:145006	221	PRK	Viruses:13	pfam01635, Corona_M, Coronavirus M matrix/glycoprotein.  This family consists of various coronavirus matrix proteins which are transmembrane glycoproteins. The M protein or E1 glycoprotein is The coronavirus M protein is implicated in virus assembly. The E1 viral membrane protein is required for formation of the viral envelope and is transported via the Golgi complex.
CDD:250760	237	EUKprk	Bacteria:90,Environmental:2,Invertebrates:1,Plants:2,Rodents:1,nodiv:2	pfam01636, APH, Phosphotransferase enzyme family.  This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate ...
CDD:250761	223	PRK	Bacteria:11	pfam01637, Arch_ATPase, Archaeal ATPase.  This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family.
CDD:250762	91	PRK	Bacteria:6	pfam01638, HxlR, HxlR-like helix-turn-helix.  HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.
CDD:250763	110	PRK	Viruses:2	pfam01639, v110, Viral family 110.  This family of viral proteins is known as the 110 family. The function of members of this family is unknown. The family contains a central cysteine rich region with eight conserved cysteines. Some members of the family contains two copies of the cysteine rich region.
CDD:250764	192	PRK	Bacteria:25	pfam01640, Peptidase_C10, Peptidase C10 family.  This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate. The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide.
CDD:201899	124	EUKprk	Bacteria:8,Invertebrates:1,Plants:1	pfam01641, SelR, SelR domain.  Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for ...
CDD:201900	517	EUKprk	Bacteria:6,Primates:1	pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase.  The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA.
CDD:250765	249	EUKprk	Bacteria:8,Plants:15	pfam01643, Acyl-ACP_TE, Acyl-ACP thioesterase.  This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid.
CDD:110632	367	EUKprk	Bacteria:3,Plants:1	pfam01645, Glu_synthase, Conserved region in glutamate synthase.  This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.
CDD:250767	178	PRK	Viruses:16	pfam01646, Herpes_UL24, Herpes virus protein UL24.  This family consists of various herpes virus proteins; the gene 20 product, U49 protein, UL24 protein and BXRF1. The UL24 gene (product of the 24th ORF) is not essential for virus replication, mutants with lesions in UL24 show a reduced ability to replicate in tissue culture and have reduced thymidine kinase activity as the UL24 gene overlaps with thymidine kinase.
CDD:250768	107	EUKprk	Bacteria:114,Environmental:3,Invertebrates:7,Plants:13,Vertebrates:1	pfam01648, ACPS, 4'-phosphopantetheinyl transferase superfamily.  Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of pfam00550. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP. This superfamily consists of two subtypes: The ACPS type and the ...
CDD:250769	83	EUKprk	Bacteria:4,Plants:3	pfam01649, Ribosomal_S20p, Ribosomal protein S20.  Bacterial ribosomal protein S20 interacts with 16S rRNA.
CDD:250770	257	EUKprk	Bacteria:5,Invertebrates:9,Plants:11,Primates:1,Vertebrates:1	pfam01650, Peptidase_C13, Peptidase C13 family.  Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl ...
CDD:250771	162	EUK	Invertebrates:30,Mammals:1,Plants:40,Primates:1,Rodents:1,Vertebrates:2	pfam01652, IF4E, Eukaryotic initiation factor 4E.  
CDD:250772	314	EUKprk	Bacteria:1,Primates:1	pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation domain.  DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of ...
CDD:250773	433	PRK	Bacteria:158	pfam01654, Bac_Ubq_Cox, Bacterial Cytochrome Ubiquinol Oxidase.  This family are the alternative oxidases found in many bacteria which oxidize ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase Escherichia coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in ...
CDD:250774	110	EUKprk	Bacteria:16,Environmental:3,Invertebrates:16,Mammals:1,Plants:15,Rodents:1,Vertebrates:1	pfam01655, Ribosomal_L32e, Ribosomal protein L32.  This family includes ribosomal protein L32 from eukaryotes and archaebacteria.
CDD:250775	211	PRK	Bacteria:33,nodiv:1	pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.  This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient ...
CDD:250776	106	EUK	Plants:8	pfam01657, Stress-antifung, Salt stress response/antifungal.  This domain is often found in association with the kinase domains pfam00069 or pfam07714. In many proteins it is duplicated. It contains six conserved cysteines which are involved in disulphide bridges. It has a role in salt stress response and has antifungal activity.
CDD:250777	108	EUKprk	Bacteria:41,Environmental:1,Invertebrates:10,Plants:5,Primates:1	pfam01658, Inos-1-P_synth, Myo-inositol-1-phosphate synthase.  This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol. Inositol phosphates play an important role in signal transduction.
CDD:250778	305	PRK	Viruses:97	pfam01660, Vmethyltransf, Viral methyltransferase.  This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in ...
CDD:250779	114	EUKprk	Bacteria:51,Invertebrates:7,Phages:1,Plants:10,Primates:1,Rodents:2,Vertebrates:3,Viruses:20	pfam01661, Macro, Macro domain.  This domain is an ADP-ribose binding module. It is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein. This domain is found in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alphaviruses. This domain is also found on its own in a family of proteins from ...
CDD:250780	342	EUKprk	Bacteria:32,Invertebrates:1,Plants:11,Primates:1,Rodents:2,Vertebrates:2,Viruses:2	pfam01663, Phosphodiest, Type I phosphodiesterase / nucleotide pyrophosphatase.  This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars. Also in this ...
CDD:250783	68	PRK	Bacteria:46	pfam01668, SmpB, SmpB protein.  
CDD:250785	155	EUKprk	Bacteria:7,Plants:4	pfam01670, Glyco_hydro_12, Glycosyl hydrolase family 12.  
CDD:250786	215	PRK	Viruses:4	pfam01671, ASFV_360, African swine fever virus multigene family 360 protein.  The multigene family 360 protein are found within the African swine fever virus (ASF) genome which consist of dsDNA and has similar structural features to the poxyviruses. The biological function of this family is not known. Although a member from African swine fever virus is a major structural protein.
CDD:250787	85	PRK	Bacteria:7	pfam01672, Plasmid_parti, Putative plasmid partition protein.  This family consists of conserved hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete, some of which are putative plasmid partition proteins.
CDD:250788	483	PRK	Viruses:31	pfam01673, Herpes_env, Herpesvirus putative major envelope glycoprotein.  This family consists of probable major envelope glycoproteins from members of the herpesviridae including herpes simplex virus, human cytomegalovirus and varicella-zoster virus. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication.
CDD:250789	218	EUKprk	Bacteria:1,Invertebrates:1	pfam01674, Lipase_2, Lipase (class 2).  This family consists of hypothetical C. elegans proteins and lipases. Lipases or triacylglycerol acylhydrolases hydrolyse ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol and free fatty acids. One member is a extracellular lipase from B. subtilis 168.
CDD:250790	428	EUKprk	Bacteria:6,Plants:6	pfam01676, Metalloenzyme, Metalloenzyme superfamily.  This family includes phosphopentomutase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This family is also related to pfam00245. The alignment contains the most conserved residues that are probably involved in metal binding and catalysis.
CDD:250791	223	PRK	Viruses:32	pfam01677, Herpes_UL7, Herpesvirus UL7 like.  This family consists of various functionally undefined proteins from the herpesviridae and UL7 from bovine herpes virus. UL7 is not essential for virus replication in cell culture, and is found localized in the cytoplasm of infected cells accumulated around the nucleus but could not be detected in purified virions. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication.
CDD:250792	121	PRK	Bacteria:3	pfam01678, DAP_epimerase, Diaminopimelate epimerase.  Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.
CDD:250793	51	EUKprk	Bacteria:40,Environmental:1,Invertebrates:4,Plants:32,nodiv:1	pfam01679, Pmp3, Proteolipid membrane potential modulator.  Pmp3 is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated ...
CDD:250795	92	EUK	Invertebrates:2	pfam01681, C6, C6 domain.  This domain of unknown function is found in a C. elegans protein. It is presumed to be an extracellular domain. The C6 domain contains six conserved cysteine residues in most copies of the domain. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge.
CDD:250796	96	EUK	Invertebrates:6	pfam01682, DB, DB module.  This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657.
CDD:250797	52	EUK	Invertebrates:8	pfam01683, EB, EB module.  This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains pfam00014.
CDD:110668	82	EUK	Invertebrates:1	pfam01684, ET, ET module.  This domain has no known function. It is found in several C. elegans proteins. The domain contains 8-10 conserved cysteines that probably form 4-5 disulphide bridges. By inspection of the conservation of cysteines it looks like cysteines 1,2,3,4,9 and 10 are always present and that sometimes the pair 5 and 8 or the pair 6 and 7 are missing. This suggests that cysteines 5/8 and 6/7 make disulphide bridges.
CDD:145042	454	PRK	Viruses:19	pfam01686, Adeno_Penton_B, Adenovirus penton base protein.  This family consists of various adenovirus penton base proteins, from both the Mastadenoviradae having mammalian hosts and the Aviadenoviradae having avian hosts. The penton base is a major structural protein forming part of the penton which consists of a base and a fibre, the pentons hold a morphologically prominent position at the vertex capsomer in the adenovirus particle. In mammalian adenovirus there ...
CDD:250798	125	EUKprk	Bacteria:119,Environmental:1,Invertebrates:7,Plants:4	pfam01687, Flavokinase, Riboflavin kinase.  This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolizm. This domain is thought to have kinase activity.
CDD:145044	161	PRK	Viruses:12	pfam01688, Herpes_gI, Alphaherpesvirus glycoprotein I.  This family consists of glycoprotein I form various members of the alphaherpesvirinae these include herpesvirus, varicella-zoster virus and pseudorabies virus. Glycoprotein I (gI) is important during natural infection, mutants lacking gI produce smaller lesions at the site of infection and show reduced neuronal spread. gI forms a heterodimeric complex with gE; this complex displays Fc receptor activity (binds ...
CDD:250799	460	PRK	Viruses:11	pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.  This family consists mainly of the potato leaf roll virus readthrough protein. This is generated via a readthrough of open reading frame 3 a coat protein allowing transcription of open reading frame 5 to give an extended coat protein with a large c-terminal addition or read through domain. The readthrough protein is thought to play a role in the circulative aphid transmission of potato leaf roll ...
CDD:145046	135	PRK	Viruses:17	pfam01691, Adeno_E1B_19K, Adenovirus E1B 19K protein / small t-antigen.  This family consists of adenovirus E1B 19K protein or small t-antigen. The E1B 19K protein inhibits E1A induced apoptosis and hence prolongs the viability of the host cell. It can also inhibit apoptosis mediated by tumor necrosis factor alpha and Fas antigen. E1B 19K blocks apoptosis by interacting with and inhibiting the p53-inducible and death- promoting Bax protein. The E1B region of ...
CDD:250800	43	EUKprk	Bacteria:78,Environmental:1,Invertebrates:9,Phages:1,Plants:42,Vertebrates:3,Viruses:15,nodiv:1	pfam01693, Cauli_VI, Caulimovirus viroplasmin.  This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and ...
CDD:250801	146	EUKprk	Bacteria:27,Invertebrates:2,Plants:6,Primates:1	pfam01694, Rhomboid, Rhomboid family.  This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes.   Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease.4] ...
CDD:110677	178	PRK	Bacteria:8	pfam01695, IstB_IS21, IstB-like ATP binding protein.  This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
CDD:250802	387	PRK	Viruses:15	pfam01696, Adeno_E1B_55K, Adenovirus EB1 55K protein / large t-antigen.  This family consists of adenovirus E1B 55K protein or large t-antigen. E1B 55K binds p53 the tumor suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site. This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the adenovirus E1A protein. The ...
CDD:250803	263	EUKprk	Bacteria:2,Invertebrates:3,Plants:1	pfam01697, Glyco_transf_92, Glycosyltransferase family 92.  Members of this family act as galactosyltransferases, belonging to glycosyltransferase family 92. The aligned region contains several conserved cysteine residues and several charged residues that may be catalytic residues. This is supported by the inclusion of this family in the GT-A glycosyl transferase superfamily.
CDD:250804	382	EUK	Plants:35	pfam01698, FLO_LFY, Floricaula / Leafy protein.  This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.
CDD:250805	135	EUKprk	Bacteria:24,Invertebrates:3,Mammals:1,Plants:8,Primates:1,Rodents:1,Vertebrates:1	pfam01699, Na_Ca_ex, Sodium/calcium exchanger protein.  This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or ...
CDD:145055	37	EUKprk	Bacteria:10,Invertebrates:1,Plants:21	pfam01701, PSI_PsaJ, Photosystem I reaction centre subunit IX / PsaJ.  This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood. PsaJ can be cross-linked ...
CDD:250806	237	EUKprk	Bacteria:80,Environmental:4,Invertebrates:21,Plants:7,Rodents:1,Vertebrates:2	pfam01702, TGT, Queuine tRNA-ribosyltransferase.  This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyses the exchange of guanine-34 at the wobble position with ...
CDD:250808	61	EUK	Invertebrates:2	pfam01705, CX, CX module.  This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges.
CDD:190075	110	PRK	Bacteria:132,Environmental:1	pfam01706, FliG_C, FliG C-terminal domain.  FliG is a component of the flageller rotor, present in about 25 copies per flagellum. This domain functions specifically in motor rotation.
CDD:250809	92	PRK	Viruses:9	pfam01708, Gemini_mov, Geminivirus putative movement protein.  This family consists of putative movement proteins from Maize streak and wheat dwarf virus.
CDD:250810	234	EUKprk	Bacteria:201,Invertebrates:5,Plants:13,Rodents:1	pfam01709, Transcrip_reg, Transcriptional regulator.  This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region.
CDD:250811	146	EUKprk	Bacteria:3,Invertebrates:1,Primates:1,Viruses:2	pfam01712, dNK, Deoxynucleoside kinase.  This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process.
CDD:250812	80	EUKprk	Bacteria:80,Invertebrates:6,Plants:14,Primates:1	pfam01713, Smr, Smr domain.  This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no ...
CDD:250813	253	EUKprk	Bacteria:6,Plants:1	pfam01715, IPPT, IPP transferase.  This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37).
CDD:250814	324	EUKprk	Bacteria:3,Plants:2	pfam01717, Meth_synt_2, Cobalamin-independent synthase, Catalytic domain.  This is a family of vitamin-B12 independent methionine synthases or 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferases, EC:2.1.1.14 from bacteria and plants. Plants are the only higher eukaryotes that have the required enzymes for methionine synthesis. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from ...
CDD:145067	546	PRK	Viruses:7	pfam01718, Orbi_NS1, Orbivirus non-structural protein NS1, or hydrophobic tubular protein.  This family consists of orbivirus non-structural protein NS1, or hydrophobic tubular protein. NS1 has no specific function in virus replication, it is however thought to play a role in transport of mature virus particles from virus inclusion bodies to the cell membrane. Orbivirus are part of the larger reoviridae which have a dsRNA genome of at least 10 segments encoding at ...
CDD:250815	192	PRK	Bacteria:18	pfam01719, Rep_2, Plasmid replication protein.  This family consists of various bacterial plasmid replication (Rep) proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence.
CDD:110699	36	PRK	Bacteria:13	pfam01721, Bacteriocin_II, Class II bacteriocin.  The bacteriocins are small peptides that inhibit the growth of various bacteria. Bacteriocins of lactic acid bacteria may inhibit their target cells by permeabilizing the cell membrane.
CDD:250816	72	EUKprk	Bacteria:131,Environmental:2,Invertebrates:14,Plants:18,Rodents:2,Vertebrates:2,nodiv:1	pfam01722, BolA, BolA-like protein.  This family consist of the morphoprotein BolA from Escherichia coli and its various homologues. In Escherichia coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the ...
CDD:250817	176	EUK	Invertebrates:3	pfam01723, Chorion_1, Chorion protein.  This family consists of the chorion superfamily proteins classes A, B, CA, CB and high-cysteine HCB from silk, gypsy and polyphemus moths. The chorion proteins make up the moths egg shell a complex extracellular structure.
CDD:250818	139	PRK	Bacteria:25	pfam01724, DUF29, Domain of unknown function DUF29.  This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family. The structure 3FCN is a small protein that has a novel all-alpha fold. The N-terminal helical hairpin is likely to function as a dimerization module. This protein is ...
CDD:250819	181	EUKprk	Bacteria:76,Environmental:3,Invertebrates:9,Plants:6,Rodents:1,Viruses:1	pfam01725, Ham1p_like, Ham1 family.  This family consists of the HAM1 protein and hypothetical archaeal bacterial and C. elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in S. cerevisiae. The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions.
CDD:250820	177	EUKprk	Bacteria:127,Environmental:2,Invertebrates:24,Plants:22,Primates:1,Viruses:12	pfam01728, FtsJ, FtsJ-like methyltransferase.  This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N ...
CDD:250821	169	EUKprk	Bacteria:7,Plants:2,Primates:1	pfam01729, QRPTase_C, Quinolinate phosphoribosyl transferase, C-terminal domain.  Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate ...
CDD:250822	150	EUKprk	Bacteria:161,Environmental:1,Invertebrates:1,Plants:1,nodiv:1	pfam01730, UreF, UreF.  This family consists of the Urease accessory protein UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid. UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to noncarbamylated protein.
CDD:250823	307	PRK	Bacteria:19	pfam01732, DUF31, Putative peptidase (DUF31).  This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas. It appears to be related to the superfamily of trypsin peptidases and so may have a peptidase function.
CDD:250825	190	EUKprk	Bacteria:68,Invertebrates:8,Plants:8,Viruses:4	pfam01734, Patatin, Patatin-like phospholipase.  This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
CDD:201944	490	EUK	Plants:4	pfam01735, PLA2_B, Lysophospholipase catalytic domain.  This family consists of Lysophospholipase / phospholipase B EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which also has a C2 domain pfam00168. Phospholipase B enzymes catalyse the release of fatty acids from lysophsopholipids and are capable in vitro of hydrolysing all phospholipids extractable form yeast cells. Cytosolic phospholipase A2 associates with natural membranes in response to physiological ...
CDD:250826	59	EUKprk	Bacteria:7,Plants:15	pfam01737, Ycf9, YCF9.  This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and cyanobacteria. These proteins have no known function.
CDD:250827	215	EUKprk	Bacteria:8,Invertebrates:1,Plants:1	pfam01738, DLH, Dienelactone hydrolase family.  
CDD:250828	194	PRK	Bacteria:15	pfam01739, CheR, CheR methyltransferase, SAM binding domain.  CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase - the C-terminal domain (this one) binds SAM.
CDD:250829	106	PRK	Bacteria:5	pfam01740, STAS, STAS domain.  The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
CDD:250831	408	PRK	Bacteria:3	pfam01742, Peptidase_M27, Clostridial neurotoxin zinc protease.  These toxins are zinc proteases that block neurotransmitter release by proteolytic cleavage of synaptic proteins such as synaptobrevins, syntaxin and SNAP-25.
CDD:250832	126	EUKprk	Bacteria:9,Invertebrates:1,Plants:2	pfam01743, PolyA_pol, Poly A polymerase head domain.  This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily.
CDD:145086	29	EUKprk	Bacteria:11,Invertebrates:2,Plants:1	pfam01744, GLTT, GLTT repeat (6 copies).  This short repeat of unknown function is found in multiple copies in several C. elegans proteins. The repeat is five residues long and consists of XGLTT where X can be any amino acid.
CDD:250833	185	EUKprk	Bacteria:8,Invertebrates:2,Plants:3,Primates:1,Rodents:1	pfam01746, tRNA_m1G_MT, tRNA (Guanine-1)-methyltransferase.  This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA.
CDD:250834	214	EUKprk	Bacteria:68,Environmental:4,Invertebrates:6,Plants:14,Primates:1	pfam01747, ATP-sulfurylase, ATP-sulfurylase.  This domain is the catalytic domain of ATP-sulfurylase or sulfate adenylyltransferase EC:2.7.7.4 some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase pfam01583. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate. ATP sulfurylase catalyses the synthesis of ...
CDD:201951	97	EUK	Invertebrates:1,Plants:3,Rodents:1	pfam01749, IBB, Importin beta binding domain.  This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain.
CDD:250835	130	PRK	Bacteria:12,nodiv:1	pfam01750, HycI, Hydrogenase maturation protease.  The family consists of hydrogenase maturation proteases. In Escherichia coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.
CDD:250836	85	EUKprk	Bacteria:45,Phages:5,Plants:2,Rodents:1	pfam01751, Toprim, Toprim domain.  This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a ...
CDD:250838	39	EUKprk	Invertebrates:26,Plants:23,Primates:1,Rodents:2,Vertebrates:2,Viruses:2	pfam01753, zf-MYND, MYND finger.  
CDD:250839	25	EUK	Invertebrates:9,Mammals:1,Plants:6,Primates:1,Rodents:1,Vertebrates:1	pfam01754, zf-A20, A20-like zinc finger.  The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
CDD:250840	200	EUKprk	Bacteria:3,Primates:1	pfam01755, Glyco_transf_25, Glycosyltransferase family 25 (LPS biosynthesis protein).  Members of this family belong to Glycosyltransferase family 25 This is a family of glycosyltransferases involved in lipopolysaccharide (LPS) biosynthesis. These enzymes catalyse the transfer of various sugars onto the growing LPS chain during its biosynthesis.
CDD:201956	186	EUK	Invertebrates:3,Mammals:1,Plants:11,Primates:1,Rodents:1,Vertebrates:2	pfam01756, ACOX, Acyl-CoA oxidase.  This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
CDD:250841	321	EUKprk	Bacteria:83,Invertebrates:4,Plants:5,nodiv:1	pfam01757, Acyl_transf_3, Acyltransferase family.  This family includes a range of acyltransferase enzymes. This domain is found in many as yet uncharacterized C. elegans proteins and it is approximately 300 amino acids long.
CDD:250842	188	EUKprk	Bacteria:7,Plants:1	pfam01758, SBF, Sodium Bile acid symporter family.  This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, a putative transmembrane protein involved in resistance to arsenic compounds.
CDD:250843	109	EUK	Invertebrates:11,Mammals:4,Primates:2,Rodents:3,Vertebrates:10	pfam01759, NTR, UNC-6/NTR/C345C module.  Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in. Subsequently, many additional members of the family were identified on the basis of sequence similarity between the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type ...
CDD:250844	260	EUKprk	Bacteria:62,Plants:2	pfam01761, DHQ_synthase, 3-dehydroquinate synthase.  The 3-dehydroquinate synthase EC:4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide. 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate. This reaction is part of the shikimate pathway which is involved ...
CDD:250845	196	EUK	Invertebrates:2,Plants:1,Primates:1,Rodents:2	pfam01762, Galactosyl_T, Galactosyltransferase.  This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.
CDD:250846	556	PRK	Viruses:30	pfam01763, Herpes_UL6, Herpesvirus UL6 like.  This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome.
CDD:250847	139	EUKprk	Bacteria:3,Invertebrates:2,Plants:17,Viruses:2	pfam01764, Lipase_3, Lipase (class 3).  
CDD:250848	165	EUKprk	Bacteria:94,Environmental:2,Invertebrates:8,Plants:17,Primates:1	pfam01765, RRF, Ribosome recycling factor.  The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.
CDD:110745	135	EUKprk	Bacteria:10,Invertebrates:1	pfam01769, MgtE, Divalent cation transporter.  This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the ...
CDD:145103	410	EUK	Invertebrates:8,Mammals:1,Primates:1,Rodents:1,Vertebrates:4	pfam01770, Folate_carrier, Reduced folate carrier.  The reduced folate carrier (a transmembrane glycoprotein) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy, such as methotrexate (MTX). Mammalian cells have an absolute requirement for exogenous folates which are needed ...
CDD:250851	458	PRK	Viruses:14	pfam01771, Herpes_alk_exo, Herpesvirus alkaline exonuclease.  This family includes various alkaline exonucleases from members of the herpesviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus.
CDD:250852	75	EUKprk	Bacteria:129,Environmental:2,Invertebrates:4,Mammals:1,Plants:5,Primates:1,Rodents:1,Vertebrates:2	pfam01773, Nucleos_tra2_N, Na+ dependent nucleoside transporter N-terminus.  This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral ...
CDD:250853	204	EUKprk	Bacteria:145,Environmental:1,Plants:13	pfam01774, UreD, UreD urease accessory protein.  UreD is a urease accessory protein. Urease pfam00449 hydrolyses urea into ammonia and carbamic acid. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex and is required for urease nickel metallocenter assembly. See also UreF pfam01730, UreG pfam01495.
CDD:250854	60	EUKprk	Bacteria:27,Environmental:2,Invertebrates:19,Plants:10,Vertebrates:1	pfam01775, Ribosomal_L18ae, Ribosomal L18ae/LX protein domain.  This family includes eukaryotic L18ae as well as archaebacterial specific LX. Ribosomal protein L18ae forms part of the 60S ribosomal subunit.
CDD:250855	112	EUK	Invertebrates:18,Plants:12,Primates:1	pfam01776, Ribosomal_L22e, Ribosomal L22e protein family.  
CDD:250856	85	EUK	Invertebrates:21,Plants:12	pfam01777, Ribosomal_L27e, Ribosomal L27e protein family.  The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family.
CDD:250857	111	EUK	Invertebrates:38,Plants:22,Vertebrates:1	pfam01778, Ribosomal_L28e, Ribosomal L28e protein family.  
CDD:201968	40	EUK	Invertebrates:22,Plants:8,Primates:1	pfam01779, Ribosomal_L29e, Ribosomal L29e protein family.  
CDD:250858	90	EUKprk	Bacteria:17,Environmental:1,Invertebrates:17,Plants:15,Vertebrates:1	pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family.  This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
CDD:250859	69	EUK	Invertebrates:14,Plants:14	pfam01781, Ribosomal_L38e, Ribosomal L38e protein family.  
CDD:250860	84	EUKprk	Bacteria:151,Environmental:2,Invertebrates:4,Plants:3	pfam01782, RimM, RimM N-terminal domain.  The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.
CDD:250861	56	EUKprk	Bacteria:115,Invertebrates:4,Plants:30,Vertebrates:2	pfam01783, Ribosomal_L32p, Ribosomal L32p protein family.  
CDD:250862	237	EUKprk	Bacteria:95,Environmental:2,Invertebrates:5,Plants:7,Rodents:1,Vertebrates:2	pfam01784, NIF3, NIF3 (NGG1p interacting factor 3).  This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown.
CDD:250863	188	PRK	Viruses:8	pfam01785, Closter_coat, Closterovirus coat protein.  This family consist of coat proteins from closteroviruses a member of the closteroviridae. The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript. Members of the closteroviridae include Sugar beet yellow virus and Grapevine leafroll-associated virus, closteroviruses have a positive strand ssRNA genome with no DNA ...
CDD:250864	206	EUKprk	Bacteria:2,Invertebrates:9,Plants:37	pfam01786, AOX, Alternative oxidase.  The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process. In rice the transcript levels of the alternative oxidase are increased by low temperature.
CDD:250865	204	PRK	Viruses:17	pfam01787, Ilar_coat, Ilarvirus coat protein.  This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants. Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication.
CDD:250866	40	EUKprk	Bacteria:8,Invertebrates:1,Plants:17	pfam01788, PsbJ, PsbJ.  This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. In Synechocystis sp. PCC 6803 PsbJ regulates the number of photosystem II centres in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain.
CDD:250867	163	EUKprk	Bacteria:14,Invertebrates:1,Plants:12	pfam01789, PsbP, PsbP.  This family consists of the 23 kDa subunit of oxygen evolving system of photosystem II or PsbP from various plants (where it is encoded by the nuclear genome) and Cyanobacteria. The 23 KDa PsbP protein is required for PSII to be fully operational in vivo, it increases the affinity of the water oxidation site for Cl- and provides the conditions required for high affinity binding of Ca2+.
CDD:250868	255	PRK	Bacteria:57,nodiv:1	pfam01790, LGT, Prolipoprotein diacylglyceryl transferase.  
CDD:250869	231	PRK	Bacteria:13	pfam01791, DeoC, DeoC/LacD family aldolase.  This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolizm. The family also includes a group of related bacterial proteins of unknown function. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
CDD:250870	286	EUK	Plants:36	pfam01793, Glyco_transf_15, Glycolipid 2-alpha-mannosyltransferase.  This is a family of alpha-1,2 mannosyl-transferases involved in N-linked and O-linked glycosylation of proteins. Some of the enzymes in this family have been shown to be involved in O- and N-linked glycan modifications in the Golgi.
CDD:250871	122	EUKprk	Bacteria:69,Invertebrates:6,Mammals:3,Plants:39,Primates:1,Rodents:2,Vertebrates:1	pfam01794, Ferric_reduct, Ferric reductase like transmembrane component.  This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The ...
CDD:250872	310	PRK	Bacteria:6	pfam01795, Methyltransf_5, MraW methylase family.  Members of this family are probably SAM dependent methyltransferases based on Escherichia coli rsmH. This family appears to be related to pfam01596.
CDD:250873	66	PRK	Bacteria:78,Environmental:2	pfam01796, DUF35, DUF35 OB-fold domain.  This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in a member from Mycobacterium tuberculosis. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. ...
CDD:250874	120	PRK	Bacteria:119,Environmental:3,Phages:3	pfam01797, Y1_Tnp, Transposase IS200 like.  Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from Escherichia coli.
CDD:250875	149	EUKprk	Bacteria:4,Invertebrates:1,Plants:2,Primates:1,Rodents:1	pfam01798, Nop, Putative snoRNA binding domain.  This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) from yeast is the protein component of a ribonucleoprotein protein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p ...
CDD:250876	75	EUKprk	Bacteria:107,Invertebrates:4,Rodents:1	pfam01799, Fer2_2, [2Fe-2S] binding domain.  
CDD:250878	296	PRK	Viruses:32	pfam01802, Herpes_V23, Herpesvirus VP23 like capsid protein.  This family consist of various capsid proteins from members of the herpesviridae. The capsid protein VP23 in herpes simplex virus forms a triplex together with VP19C these fit between and link together adjacent capsomers as formed by VP5 and VP26. VP3 along with the scaffolding proteins helps to form normal capsids by defining the curvature of the shell and size of the particle.
CDD:250879	232	EUK	Invertebrates:6,Plants:33,Vertebrates:1	pfam01803, LIM_bind, LIM-domain binding protein.  The LIM-domain binding protein, binds to the LIM domain pfam00412 of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent ...
CDD:250880	668	PRK	Bacteria:14	pfam01804, Penicil_amidase, Penicillin amidase.  Penicillin amidase or penicillin acylase EC:3.5.1.11 catalyses the hydrolysis of benzylpenicillin to phenylacetic acid and 6-aminopenicillanic acid (6-APA) a key intermediate in the the synthesis of penicillins. Also in the family is cephalosporin acylase and aculeacin A acylase, which are involved in the synthesis of related peptide antibiotics.
CDD:250881	55	EUK	Invertebrates:8,Plants:11,Primates:1,Rodents:1,Vertebrates:1	pfam01805, Surp, Surp module.  This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
CDD:110780	98	PRK	Bacteria:1	pfam01807, zf-CHC2, CHC2 zinc finger.  This domain is principally involved in DNA binding in DNA primases.
CDD:250883	68	EUKprk	Bacteria:202,Phages:1,Plants:2	pfam01809, Haemolytic, Haemolytic domain.  This domain has haemolytic activity. It is found in short (73-103 amino acid) proteins and contains three conserved cysteine residues.
CDD:250884	191	PRK	Bacteria:12	pfam01810, LysE, LysE type translocator.  This family consists of various hypothetical proteins and an l-lysine exporter LysE from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide ...
CDD:250885	182	EUKprk	Bacteria:15,Invertebrates:2,Mammals:1,Plants:1,Primates:1	pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase family.  5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin.
CDD:250886	194	EUKprk	Bacteria:60,Environmental:2,Invertebrates:18,Plants:7,Rodents:1	pfam01813, ATP-synt_D, ATP synthase subunit D.  This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase.
CDD:250887	130	EUKprk	Bacteria:118,Invertebrates:7,Plants:5,Rodents:1	pfam01814, Hemerythrin, Hemerythrin HHE cation binding domain.  Iteration of the HHE family found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor MP II binds Cadmium so as to protect the organism from ...
CDD:250888	26	PRK	Bacteria:6	pfam01816, LRV, Leucine rich repeat variant.  The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix.
CDD:250889	81	EUKprk	Bacteria:69,Plants:6	pfam01817, CM_2, Chorismate mutase type II.  Chorismate mutase EC:5.4.99.5 catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine.
CDD:250892	110	EUKprk	Bacteria:151,Plants:3	pfam01820, Dala_Dala_lig_N, D-ala D-ala ligase N-terminus.  This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), ...
CDD:145142	36	EUK	Invertebrates:1,Mammals:3,Primates:1,Rodents:1,Vertebrates:8	pfam01821, ANATO, Anaphylotoxin-like domain.  C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.
CDD:250893	80	EUK	Invertebrates:5,Mammals:1,Plants:31,Primates:1,Rodents:2,Vertebrates:2	pfam01822, WSC, WSC domain.  This domain may be involved in carbohydrate binding.
CDD:250894	209	EUKprk	Bacteria:5,Invertebrates:14,Mammals:1,Plants:3,Primates:1,Rodents:1,Vertebrates:4	pfam01823, MACPF, MAC/Perforin domain.  The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 ...
CDD:250896	43	EUK	Invertebrates:13,Mammals:4,Primates:3,Rodents:2,Vertebrates:3	pfam01825, GPS, Latrophilin/CL-1-like GPS domain.  Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
CDD:250897	55	EUK	Invertebrates:30,Mammals:5,Plants:1,Primates:4,Rodents:2,Vertebrates:4	pfam01826, TIL, Trypsin Inhibitor like cysteine rich domain.  This family contains trypsin inhibitors as well as a domain found in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9.
CDD:250898	141	EUK	Invertebrates:1	pfam01827, FTH, FTH domain.  This presumed domain is likely to be a protein-protein interaction module. It is found in many proteins from C. elegans. The domain is found associated with the F-box pfam00646. This domain is named FTH after FOG-2 homology domain.
CDD:250899	208	EUK	Plants:10	pfam01828, Peptidase_A4, Peptidase A4 family.  
CDD:250901	137	PRK	Bacteria:124,Environmental:1,Phages:3	pfam01832, Glucosaminidase, Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.  This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96. As well as the flagellar protein J that has been shown to hydrolyse peptidoglycan.
CDD:250902	84	EUKprk	Bacteria:21,Invertebrates:8,Plants:3,Primates:4,Rodents:1,Vertebrates:2	pfam01833, TIG, IPT/TIG domain.  This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognize a significant number of members.
CDD:250904	95	EUKprk	Bacteria:82,Invertebrates:5,Primates:1,Rodents:3,Vertebrates:3,nodiv:1	pfam01835, A2M_N, MG2 domain.  This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
CDD:250905	335	PRK	Bacteria:58,Environmental:3	pfam01837, DUF39, Domain of unknown function DUF39.  This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS pfam00571 domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain. The protein MTH_855 has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains.
CDD:250906	30	EUKprk	Bacteria:38,Invertebrates:11,Mammals:3,Plants:2,Primates:1,Rodents:3,Vertebrates:2	pfam01839, FG-GAP, FG-GAP repeat.  This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to ...
CDD:250908	108	EUKprk	Bacteria:53,Environmental:4,Invertebrates:3,Plants:2,Vertebrates:1	pfam01841, Transglut_core, Transglutaminase-like superfamily.  This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood ...
CDD:250909	66	EUKprk	Bacteria:37,Invertebrates:3,Plants:5,Rodents:1	pfam01842, ACT, ACT domain.  This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95, which is inhibited by serine. Aspartokinase ...
CDD:250910	105	EUK	Invertebrates:7,Plants:16,Primates:1,Rodents:1,Vertebrates:1	pfam01843, DIL, DIL domain.  The DIL domain has no known function.
CDD:250911	47	EUKprk	Bacteria:38,Phages:17,Plants:5	pfam01844, HNH, HNH endonuclease.  
CDD:190136	102	PRK	Bacteria:12	pfam01845, CcdB, CcdB protein.  
CDD:250912	50	EUKprk	Bacteria:1,Invertebrates:10,Plants:27,Primates:1,Rodents:1,Vertebrates:2	pfam01846, FF, FF domain.  This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.
CDD:202008	43	PRK	Bacteria:31	pfam01848, HOK_GEF, Hok/gef family.  
CDD:202009	50	EUKprk	Bacteria:16,Environmental:3,Invertebrates:19,Plants:21,Primates:1,Rodents:1	pfam01849, NAC, NAC domain.  
CDD:250913	120	PRK	Bacteria:39,Environmental:1	pfam01850, PIN, PIN domain.  
CDD:250914	35	EUKprk	Bacteria:1,Invertebrates:9,Plants:16,Primates:1,Rodents:2,Vertebrates:2	pfam01851, PC_rep, Proteasome/cyclosome repeat.  
CDD:250915	205	EUK	Invertebrates:1,Mammals:1,Plants:1,Primates:1,Rodents:1	pfam01852, START, START domain.  
CDD:250916	189	EUK	Invertebrates:2,Plants:2,Primates:1,Rodents:1,nodiv:1	pfam01853, MOZ_SAS, MOZ/SAS family.  This region of these proteins has been suggested to be homologous to acetyltransferases.
CDD:250917	230	PRK	Bacteria:10	pfam01855, POR_N, Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg.  This family includes the N terminal structural domain of the pyruvate ferredoxin oxidoreductase. This domain binds thiamine diphosphate, and along with domains II and IV, is involved in inter subunit contacts. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited.
CDD:250918	154	PRK	Bacteria:2	pfam01856, HP_OMP, Helicobacter outer membrane protein.  This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
CDD:250922	159	PRK	Bacteria:21,Environmental:3	pfam01862, PvlArgDC, Pyruvoyl-dependent arginine decarboxylase (PvlArgDC).  Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase ...
CDD:145171	205	PRK	Bacteria:69,Environmental:2	pfam01863, DUF45, Protein of unknown function DUF45.  This protein has no known function. Members are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines. This motif is similar to that found in Zinc proteases, suggesting that this family may also be proteases.
CDD:250923	214	PRK	Bacteria:1	pfam01865, PhoU_div, Protein of unknown function DUF47.  This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Sinorhizobium meliloti. However, the function of this protein is also unknown (Pit stands for Phosphate transport). It is probably distantly related to pfam01895 (personal obs:Yeats C).
CDD:250924	302	EUKprk	Bacteria:22,Environmental:2,Invertebrates:8,Plants:10,Primates:1,Vertebrates:2	pfam01866, Diphthamide_syn, Putative diphthamide synthesis protein.  Human DPH1 is a candidate tumor suppressor gene. DPH2 from yeast, which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact ...
CDD:250925	284	PRK	Bacteria:6	pfam01867, Cas_Cas1, CRISPR associated protein Cas1.  Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR.
CDD:250926	89	EUKprk	Bacteria:23,Environmental:1,Invertebrates:4,Plants:4,Vertebrates:1	pfam01868, UPF0086, Domain of unknown function UPF0086.  This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins.
CDD:250927	290	EUKprk	Bacteria:12,Plants:1	pfam01869, BcrAD_BadFG, BadF/BadG/BcrA/BcrD ATPase family.  This family includes the BadF and BadG proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase. An uncharacterized protein from Aquifex aeolicus contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be ...
CDD:250928	89	PRK	Bacteria:13,Phages:1	pfam01870, Hjc, Archaeal holliday junction resolvase (hjc).  This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.
CDD:250929	172	EUKprk	Bacteria:50,Environmental:1,Invertebrates:9,Plants:5	pfam01871, AMMECR1, AMMECR1.  This family consists of several AMMECR1 as well as several uncharacterized proteins. The contiguous gene deletion syndrome AMME is characterized by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1. This family contains sequences from several eukaryotic species as well ...
CDD:250930	196	PRK	Bacteria:8	pfam01872, RibD_C, RibD C-terminal domain.  The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG, in combination with pfam00383, as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186.
CDD:250931	125	EUKprk	Bacteria:1,Invertebrates:1,Mammals:1,Plants:1,Rodents:1	pfam01873, eIF-5_eIF-2B, Domain found in IF2B/IF5.  This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger.
CDD:250932	245	PRK	Bacteria:116,Environmental:3	pfam01874, CitG, ATP:dephospho-CoA triphosphoribosyl transferase.  The citG gene is found in a gene cluster with citrate lyase subunits. The function of the CitG protein was elucidated as ATP:dephospho-CoA triphosphoribosyl transferase.
CDD:250933	274	EUKprk	Bacteria:1,Invertebrates:1	pfam01875, Memo, Memo-like protein.  This family contains members from all branches of life. The molecular function of this protein is unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family. It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton.
CDD:250934	152	EUKprk	Bacteria:25,Environmental:1,Invertebrates:10,Plants:20,Rodents:1,Vertebrates:2	pfam01876, RNase_P_p30, RNase P subunit p30.  This protein is part of the RNase P complex that is involved in tRNA maturation.
CDD:250935	118	PRK	Bacteria:27,Environmental:2	pfam01877, RNA_binding, RNA binding.  PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. ...
CDD:250936	143	EUKprk	Bacteria:119,Environmental:2,Invertebrates:2,Plants:6,Primates:1	pfam01878, EVE, EVE domain.  This domain was formerly known as DUF55. Crystal structures have shown that this domain is part of the PUA superfamily. This domain has been named EVE and is thought to be RNA-binding.
CDD:145182	96	PRK	Bacteria:46,Environmental:1	pfam01880, Desulfoferrodox, Desulfoferrodoxin.  Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin.
CDD:250937	152	PRK	Bacteria:33,Phages:1	pfam01881, Cas_Cas6, CRISPR associated protein Cas6.  This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair ...
CDD:250938	85	PRK	Bacteria:125	pfam01882, DUF58, Protein of unknown function DUF58.  This family of prokaryotic proteins have no known function. Caldicellulosiruptor saccharolyticus PepX, a protein of unknown function in the family has been misannotated as alpha-dextrin 6-glucanohydrolase.
CDD:250939	72	EUKprk	Bacteria:65,Environmental:1,Invertebrates:1,Plants:1	pfam01883, DUF59, Domain of unknown function DUF59.  This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF), PaaI (PhaG) and PaaK (PhaI), which ...
CDD:250941	169	EUKprk	Bacteria:44,Environmental:1,Invertebrates:6,Mammals:1,Plants:22,Vertebrates:1,Viruses:2	pfam01885, PTS_2-RNA, RNA 2'-phosphotransferase, Tpt1 / KptA family.  Tpt1 catalyses the last step of tRNA splicing in yeast. It transfers the splice junction 2'-phosphate from ligated tRNA to NAD, to produce ADP-ribose 1"-2"-cyclic phosphate. This is presumed to be followed by a transesterification step to release the RNA.    The first step of this reaction is similar to that catalysed ...
CDD:145187	132	PRK	Bacteria:13	pfam01886, DUF61, Protein of unknown function DUF61.  Protein found in Archaebacteria. These proteins have no known function.
CDD:250942	257	PRK	Bacteria:113,Environmental:2	pfam01887, SAM_adeno_trans, S-adenosyl-l-methionine hydroxide adenosyltransferase.  This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme. S-adenosyl-l-methionine hydroxide adenosyltransferases utilizes a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to ...
CDD:250944	272	PRK	Bacteria:9,Environmental:2	pfam01889, DUF63, Membrane protein of unknown function DUF63.  Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane proteins.
CDD:250945	120	PRK	Bacteria:184,nodiv:1	pfam01890, CbiG_C, Cobalamin synthesis G C-terminus.  Members of this family are involved in cobalamin synthesis. A Synechocystis sp. PCC 6803 precorrin methylase has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction ...
CDD:250946	201	PRK	Bacteria:125,Environmental:3	pfam01891, CbiM, Cobalt uptake substrate-specific transmembrane region.  This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no ...
CDD:145192	88	PRK	Bacteria:16,Environmental:2	pfam01893, UPF0058, Uncharacterized protein family UPF0058.  This archaebacterial protein has no known function.
CDD:250947	118	EUKprk	Bacteria:87,Environmental:2,Invertebrates:4,Plants:6	pfam01894, UPF0047, Uncharacterized protein family UPF0047.  This family has no known function. The alignment contains a conserved aspartate and histidine that may be functionally important.
CDD:250948	87	PRK	Bacteria:219,Environmental:2	pfam01895, PhoU, PhoU domain.  This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif.
CDD:250949	131	EUKprk	Bacteria:20,Environmental:1,Invertebrates:9,Phages:1,Plants:12,Primates:1,Rodents:1,Vertebrates:2,Viruses:14	pfam01896, DNA_primase_S, Eukaryotic and archaeal DNA primase small subunit.  DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. Bacterial ...
CDD:250950	156	PRK	Bacteria:121,nodiv:1	pfam01899, MNHE, Na+/H+ ion antiporter subunit.  Subunit of a Na+/H+ Prokaryotic antiporter complex.
CDD:250951	104	EUKprk	Bacteria:30,Environmental:1,Invertebrates:7,Plants:21,Primates:1,Rodents:1,Vertebrates:2	pfam01900, RNase_P_Rpp14, Rpp14/Pop5 family.  tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. This protein is known as Pop5 in eukaryotes.
CDD:250952	331	PRK	Bacteria:10	pfam01901, DUF70, Protein of unknown function DUF70.  Archaebacterial proteins of unknown function. Members of this family may be transmembrane proteins.
CDD:250954	106	EUKprk	Bacteria:39,Plants:1	pfam01903, CbiX, CbiX.  The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation.
CDD:250955	230	EUKprk	Bacteria:163,Environmental:3,Invertebrates:1,Plants:1,nodiv:1	pfam01904, DUF72, Protein of unknown function DUF72.  The function of this family is unknown.
CDD:250956	265	PRK	Bacteria:23	pfam01905, DevR, CRISPR-associated negative auto-regulator DevR/Csa2.  This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between ...
CDD:250957	102	EUKprk	Bacteria:139,Environmental:3,Plants:4,nodiv:1	pfam01906, YbjQ_1, Putative heavy-metal-binding.  From comparative structural analysis, this family is likely to be a heavy-metal binding domain. The domain oligomerises as a pentamer. The domain is about 100 amino acids long and is found in prokaryotes.
CDD:250958	54	EUKprk	Bacteria:22,Invertebrates:17,Plants:9,Vertebrates:1	pfam01907, Ribosomal_L37e, Ribosomal protein L37e.  This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc.
CDD:250959	92	EUKprk	Bacteria:25,Environmental:1,Invertebrates:3,Mammals:1,Plants:5,Primates:1,Rodents:1	pfam01909, NTP_transf_2, Nucleotidyltransferase domain.  Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalyzing the addition of a nucleotidyl group onto the drug.
CDD:250960	92	EUKprk	Bacteria:89,Plants:10	pfam01910, DUF77, Domain of unknown function DUF77.  Domain of unknown function. The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions ...
CDD:250961	198	EUKprk	Bacteria:25,Environmental:3,Invertebrates:13,Mammals:1,Plants:7	pfam01912, eIF-6, eIF-6 family.  This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues.
CDD:250962	144	PRK	Bacteria:19,Environmental:5	pfam01913, FTR, Formylmethanofuran-tetrahydromethanopterin formyltransferase.  This enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe.
CDD:250963	203	PRK	Bacteria:2	pfam01914, MarC, MarC family integral membrane protein.  Integral membrane protein family that includes the antibiotic resistance protein MarC. These proteins may be transporters.
CDD:250964	221	EUKprk	Bacteria:30,Invertebrates:1,Plants:14	pfam01915, Glyco_hydro_3_C, Glycosyl hydrolase family 3 C-terminal domain.  This domain is involved in catalysis and may be involved in binding beta-glucan. This domain is found associated with pfam00933.
CDD:250965	151	PRK	Bacteria:31,Environmental:1	pfam01917, Arch_flagellin, Archaebacterial flagellin.  Members of this family are the proteins that form the flagella in archaebacteria.
CDD:250966	67	EUKprk	Bacteria:24,Environmental:1,Invertebrates:20,Mammals:1,Plants:28,Rodents:1,Vertebrates:3	pfam01918, Alba, Alba.  Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.
CDD:250967	104	EUKprk	Bacteria:3,Invertebrates:7,Plants:7,Primates:1,Rodents:1,Vertebrates:1	pfam01920, Prefoldin_2, Prefoldin subunit.  This family includes prefoldin subunits that are not detected by pfam02996.
CDD:250968	355	PRK	Bacteria:28,Environmental:2	pfam01921, tRNA-synt_1f, tRNA synthetases class I (K).  This family includes only lysyl tRNA synthetases from prokaryotes.
CDD:250969	91	EUKprk	Bacteria:27,Invertebrates:19,Plants:22,Primates:2,Vertebrates:2	pfam01922, SRP19, SRP19 protein.  The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and ...
CDD:250970	161	EUKprk	Bacteria:164,Environmental:1,Invertebrates:2,Plants:2,Primates:1,Vertebrates:1	pfam01923, Cob_adeno_trans, Cobalamin adenosyltransferase.  Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation.The EutT enzyme appears ...
CDD:250971	355	PRK	Bacteria:71,Environmental:1	pfam01924, HypD, Hydrogenase formation hypA family.  HypD is involved in hydrogenase formation. It contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into hypD resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas.
CDD:250972	236	EUKprk	Bacteria:355,Environmental:10,Phages:1,Plants:1,Synthetic:1,nodiv:1	pfam01925, TauE, Sulfite exporter TauE/SafE.  This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane during taurine metabolizm as an exporter of sulfoacetate. This family used to be known as DUF81.
CDD:250973	114	EUKprk	Bacteria:174,Environmental:1,Invertebrates:9,Plants:15,Primates:1,Rodents:1,Vertebrates:2,nodiv:1	pfam01926, MMR_HSR1, 50S ribosome-binding GTPase.  The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.
CDD:250974	146	EUKprk	Bacteria:47,Environmental:1,Invertebrates:5,Plants:2	pfam01927, Mut7-C, Mut7-C RNAse domain.  RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.
CDD:250975	177	EUKprk	Bacteria:11,Invertebrates:1,Mammals:1,Plants:2	pfam01928, CYTH, CYTH domain.  These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved.
CDD:250976	77	EUK	Invertebrates:27,Mammals:1,Plants:14,Vertebrates:2	pfam01929, Ribosomal_L14e, Ribosomal protein L14.  This family includes the eukaryotic ribosomal protein L14.
CDD:250977	162	PRK	Bacteria:48	pfam01930, Cas_Cas4, Domain of unknown function DUF83.  This domain has no known function. The domain contains three conserved cysteines at its C terminus.
CDD:110891	168	EUKprk	Bacteria:16,Invertebrates:4	pfam01931, NTPase_I-T, Protein of unknown function DUF84.  The function of this prokaryotic protein family is unknown.
CDD:250978	291	PRK	Bacteria:7	pfam01933, UPF0052, Uncharacterized protein family UPF0052.  
CDD:250979	120	PRK	Bacteria:83,Environmental:3,nodiv:1	pfam01934, DUF86, Protein of unknown function DUF86.  The function of members of this family is unknown.
CDD:250980	219	PRK	Bacteria:33,Environmental:1	pfam01935, DUF87, Domain of unknown function DUF87.  The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
CDD:250981	141	EUKprk	Bacteria:96,Environmental:1,Invertebrates:1,Plants:5	pfam01936, NYN, NYN domain.  These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 ...
CDD:250982	315	EUKprk	Bacteria:39,Environmental:2,Invertebrates:8,Plants:19,Primates:1,Rodents:2,Vertebrates:2	pfam01937, DUF89, Protein of unknown function DUF89.  This family has no known function.
CDD:110897	59	EUKprk	Bacteria:11,Invertebrates:2,Plants:3	pfam01938, TRAM, TRAM domain.  This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).
CDD:250983	224	EUKprk	Bacteria:59,Environmental:2,Invertebrates:4,Plants:5,Rodents:1,Vertebrates:2	pfam01940, DUF92, Integral membrane protein DUF92.  Members of this family have several predicted transmembrane helices. The function of these prokaryotic proteins is unknown.
CDD:250984	394	PRK	Bacteria:27,Environmental:1	pfam01941, AdoMet_Synthase, S-adenosylmethionine synthetase (AdoMet synthetase).  This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolizm of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl ...
CDD:250985	272	PRK	Bacteria:11	pfam01943, Polysacc_synt, Polysaccharide biosynthesis protein.  Members of this family are integral membrane proteins. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon. The family includes SpoVB from Bacillus subtilis, which is involved in spore cortex biosynthesis.
CDD:250986	167	PRK	Bacteria:149,Environmental:2	pfam01944, DUF95, Integral membrane protein DUF95.  Members of this family have several predicted transmembrane regions. The function of this family is unknown.
CDD:145232	149	EUKprk	Bacteria:16,Plants:4	pfam01947, DUF98, Protein of unknown function (DUF98).  This is a family of uncharacterized proteins.
CDD:250987	96	PRK	Bacteria:53	pfam01948, PyrI, Aspartate carbamoyltransferase regulatory chain, allosteric domain.  The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the regulatory chain dimerization interface.
CDD:250988	185	PRK	Bacteria:28,Environmental:1	pfam01949, DUF99, Protein of unknown function DUF99.  The function of this archaebacterial protein family is unknown.
CDD:202059	363	PRK	Bacteria:33,Environmental:1	pfam01950, FBPase_3, Fructose-1,6-bisphosphatase.  This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases). FBPase catalyses the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway.
CDD:250989	135	EUKprk	Bacteria:71,Environmental:3,Invertebrates:12,Plants:2,Primates:1,Vertebrates:1	pfam01951, Archease, Archease protein family (MTH1598/TM1083).  This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolizm.
CDD:250990	60	PRK	Bacteria:13,Environmental:2	pfam01954, DUF104, Protein of unknown function DUF104.  This family includes short archaebacterial proteins of unknown function.   Archaeoglobus fulgidus has twelve copies of this protein, with several being clustered together in the genome.
CDD:250991	190	PRK	Bacteria:61,Environmental:1	pfam01955, CbiZ, Adenosylcobinamide amidohydrolase.  This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route.
CDD:250992	168	EUKprk	Bacteria:18,Environmental:1,Invertebrates:17,Mammals:1,Plants:18	pfam01956, DUF106, Integral membrane protein DUF106.  This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.
CDD:250993	144	PRK	Bacteria:26	pfam01957, NfeD, NfeD-like C-terminal, partner-binding.  NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second ...
CDD:250994	92	EUKprk	Bacteria:50,Environmental:1,Invertebrates:1,Primates:1,Rodents:1,Vertebrates:2	pfam01958, DUF108, Domain of unknown function DUF108.  This family has no known function. It is found to compose the complete protein in archaebacteria and a single domain in a large C. elegans protein.
CDD:250995	347	EUKprk	Bacteria:21,Plants:1	pfam01959, DHQS, 3-dehydroquinate synthase (EC 4.6.1.3).  3-Dehydroquinate synthase is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; ...
CDD:250996	386	EUKprk	Bacteria:85,Environmental:4,Invertebrates:1,Plants:4	pfam01960, ArgJ, ArgJ family.  Members of the ArgJ family catalyse the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis.
CDD:250997	261	EUKprk	Bacteria:109,Environmental:1,Invertebrates:4,Plants:2	pfam01963, TraB, TraB family.  pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of ...
CDD:250998	421	PRK	Bacteria:75,Environmental:1	pfam01964, ThiC, ThiC family.  ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis. The precise catalytic function of ThiC is still not known. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis.
CDD:250999	140	EUKprk	Bacteria:14,Invertebrates:2,Plants:3,Rodents:1	pfam01965, DJ-1_PfpI, DJ-1/PfpI family.  The family includes the protease PfpI. This domain is also found in transcriptional regulators such as Streptomyces coelicolor AraC. This N-terminal region of the full-length AdpA proteins is necessary for dimerization of the molecule.
CDD:251000	110	EUKprk	Bacteria:36,Invertebrates:2,Plants:2,Primates:1,Viruses:1	pfam01966, HD, HD domain.  HD domains are metal dependent phosphohydrolases.
CDD:251001	136	EUKprk	Bacteria:3,Plants:1	pfam01967, MoaC, MoaC family.  Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.
CDD:251002	285	EUKprk	Bacteria:28,Invertebrates:2,Plants:2	pfam01968, Hydantoinase_A, Hydantoinase/oxoprolinase.  This family includes the enzymes hydantoinase and oxoprolinase EC:3.5.2.9. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds.
CDD:251003	381	PRK	Bacteria:84,Environmental:1	pfam01969, DUF111, Protein of unknown function DUF111.  This prokaryotic family has no known function.
CDD:251004	418	PRK	Bacteria:112,Environmental:2	pfam01970, TctA, Tripartite tricarboxylate transporter TctA family.  This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. TctA is part of the tripartite TctABC system which, as characterized in S. typhimurium, is a secondary carrier that depends for ...
CDD:251005	170	PRK	Bacteria:107,Environmental:3	pfam01973, MAF_flag10, Protein of unknown function DUF115.  This family of archaebacterial proteins has no known function.
CDD:251006	85	EUKprk	Bacteria:32,Environmental:2,Invertebrates:8,Mammals:1,Plants:11,Vertebrates:1	pfam01974, tRNA_int_endo, tRNA intron endonuclease, catalytic C-terminal domain.  Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.
CDD:251007	188	EUKprk	Bacteria:114,Invertebrates:2,Plants:8	pfam01975, SurE, Survival protein SurE.  Escherichia coli cells with the surE gene disrupted are found to survive poorly in stationary phase. It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family, probable tubulin-tyrosine ligase PBY1. Yarrowia lipolytica PHO2 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.
CDD:251008	158	PRK	Bacteria:41,Environmental:2	pfam01976, DUF116, Protein of unknown function DUF116.  This archaebacterial protein has no known function. The protein contains seven conserved cysteines and may also be an integral membrane protein.
CDD:251009	405	EUKprk	Bacteria:118,Environmental:1,Plants:8	pfam01977, UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase.  This family has been characterized as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+.
CDD:251010	68	PRK	Bacteria:20	pfam01978, TrmB, Sugar-specific transcriptional regulator TrmB.  One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
CDD:251011	307	EUKprk	Bacteria:23,Invertebrates:1,Plants:1,Rodents:1	pfam01979, Amidohydro_1, Amidohydrolase family.  This family of enzymes are a a large metal dependent hydrolase superfamily. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, ...
CDD:251012	118	EUKprk	Bacteria:94,Environmental:1,Invertebrates:6,Plants:4,Vertebrates:1	pfam01980, UPF0066, Uncharacterized protein family UPF0066.  
CDD:251013	116	EUKprk	Bacteria:19,Environmental:1,Invertebrates:16,Plants:14,Viruses:2	pfam01981, PTH2, Peptidyl-tRNA hydrolase PTH2.  Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.
CDD:145259	121	PRK	Bacteria:43,Environmental:1	pfam01982, CTP-dep_RFKase, Domain of unknown function DUF120.  This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and ...
CDD:251015	105	EUKprk	Bacteria:26,Invertebrates:9,Plants:19,Primates:1	pfam01984, dsDNA_bind, Double-stranded DNA-binding domain.  This domain is believed to bind double-stranded DNA of 20 bases length.
CDD:251016	84	EUKprk	Bacteria:112,Environmental:3,Plants:4,Synthetic:1	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain.  Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron ...
CDD:251017	99	PRK	Bacteria:35,Environmental:3	pfam01986, DUF123, Domain of unknown function DUF123.  This archaebacterial domain has no known function. It is attached to an endonuclease domain in the putative endonuclease MJ0613. The domain contains several conserved cysteines and histidines. This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.).
CDD:251018	206	EUKprk	Bacteria:105,Environmental:1,Invertebrates:2,Plants:9	pfam01987, AIM24, Mitochondrial biogenesis AIM24.  In eukaryotes, this domain is involved in mitochondrial biogenesis. Its function in prokaryotes in unknown.
CDD:251019	208	EUKprk	Bacteria:91,Invertebrates:10,Plants:12	pfam01988, VIT1, VIT family.  This family includes the vacuolar Fe2+/Mn2+ uptake transporter, Ccc1 and the vacuolar iron transporter VIT1.
CDD:251020	83	EUKprk	Bacteria:43,Plants:5	pfam01989, DUF126, Protein of unknown function DUF126.  This archaebacterial protein family has no known function.
CDD:251021	95	EUKprk	Bacteria:53,Environmental:1,Invertebrates:16,Plants:13,Rodents:1	pfam01990, ATP-synt_F, ATP synthase (F/14-kDa) subunit.  This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F.
CDD:251022	195	EUKprk	Bacteria:4,Invertebrates:3,Plants:4,Primates:1	pfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit.  This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit.
CDD:251023	335	EUKprk	Bacteria:5,Invertebrates:1,Plants:1	pfam01992, vATP-synt_AC39, ATP synthase (C/AC39) subunit.  This family includes the AC39 subunit from vacuolar ATP synthase, and the C subunit from archaebacterial ATP synthase. The family also includes subunit C from the Sodium transporting ATP synthase from Enterococcus hirae.
CDD:251024	121	PRK	Bacteria:27,Environmental:2	pfam01994, Trm56, tRNA ribose 2'-O-methyltransferase, aTrm56.  This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin.
CDD:251025	236	PRK	Bacteria:22,Environmental:1	pfam01995, DUF128, Domain of unknown function DUF128.  This archaebacterial protein family has no known function. The domain is found duplicated in MTH_1569. Many of these are attached to an N-terminal winged helix domain suggesting these are transcriptional regulators and that this domain has a ligand binding function.
CDD:251026	219	PRK	Bacteria:68,Environmental:3	pfam01996, F420_ligase, F420-0:Gamma-glutamyl ligase.  F420-0:Gamma-glutamyl ligase (EC:6.3.2.-) is an enzyme involved in F420 biosynthesis pathway. It catalyses the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0). This reaction produces polyglutamated F420 derivatives. GTP + F420-0 + n L-glutamate -> GDP + phosphate + F420-n.
CDD:251027	186	EUKprk	Bacteria:4,Invertebrates:2,Plants:13,Primates:2,Rodents:1	pfam01997, Translin, Translin family.  Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes human translin-associated protein X, which was found to interact with translin with yeast two-hybrid screen.
CDD:145272	59	PRK	Bacteria:26,Environmental:1	pfam01998, DUF131, Protein of unknown function DUF131.  This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices.
CDD:251030	375	EUKprk	Bacteria:3,Invertebrates:1	pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.  This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria.
CDD:251031	178	PRK	Bacteria:21,Environmental:2	pfam02006, DUF137, Protein of unknown function DUF137.  This family of archaeal proteins has no known function.
CDD:251032	48	EUK	Invertebrates:5,Mammals:2,Primates:1,Rodents:1,Vertebrates:3	pfam02008, zf-CXXC, CXXC zinc finger domain.  This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is ...
CDD:251033	290	EUK	Invertebrates:1	pfam02009, Rifin_STEVOR, Rifin/stevor family.  Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens.
CDD:251034	435	EUK	Invertebrates:4,Primates:1,Rodents:1	pfam02010, REJ, REJ domain.  The REJ (Receptor for Egg Jelly) domain is found in PKD1, and the sperm receptor for egg jelly. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains.
CDD:202087	12	EUKprk	Bacteria:15,Invertebrates:3,Mammals:1,Phages:1,Plants:5,Rodents:3,Viruses:1	pfam02012, BNR, BNR/Asp-box repeat.  Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function.
CDD:251036	36	EUKprk	Bacteria:5,Environmental:1,Plants:9	pfam02013, CBM_10, Cellulose or protein binding domain.  This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the ...
CDD:251037	127	EUK	Invertebrates:5,Vertebrates:1	pfam02014, Reeler, Reeler domain.  
CDD:251039	277	PRK	Bacteria:97,Environmental:3	pfam02016, Peptidase_S66, LD-carboxypeptidase.  Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid.   The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein. This family corresponds to Merops family S66.
CDD:251041	135	EUKprk	Bacteria:12,Plants:1	pfam02018, CBM_4_9, Carbohydrate binding domain.  This family includes diverse carbohydrate binding domains.
CDD:251042	132	EUK	Invertebrates:5,Primates:1,Vertebrates:2	pfam02019, WIF, WIF domain.  The WIF domain is found in the RYK tyrosine kinase receptors and WIF, the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, ...
CDD:251043	77	EUK	Invertebrates:4,Plants:11,Primates:1,Rodents:1	pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon.  This domain of unknown function is found at the C-terminus of several translation initiation factors.
CDD:110969	94	PRK	Bacteria:3	pfam02021, UPF0102, Uncharacterized protein family UPF0102.  The function of this family is unknown.
CDD:202092	40	EUKprk	Mammals:2,Rodents:1,Viruses:16	pfam02022, Integrase_Zn, Integrase Zinc binding domain.  Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.
CDD:251044	92	EUK	Mammals:1,Primates:8,Rodents:2	pfam02023, SCAN, SCAN domain.  The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.
CDD:251046	95	EUKprk	Bacteria:4,Invertebrates:3,Mammals:2,Rodents:1,Vertebrates:1	pfam02026, RyR, RyR domain.  This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
CDD:251047	189	EUKprk	Bacteria:6,Plants:2,nodiv:1	pfam02027, RolB_RolC, RolB/RolC glucosidase family.  This family of proteins includes RolB and RolC. RolC releases cytokinins from glucoside conjugates. Whereas RolB hydrolyses indole glucosides.
CDD:251048	482	EUKprk	Bacteria:109,Plants:1	pfam02028, BCCT, BCCT family transporter.  
CDD:251051	104	EUKprk	Bacteria:161,Invertebrates:1,Plants:3,Vertebrates:1	pfam02033, RBFA, Ribosome-binding factor A.  
CDD:251053	99	EUKprk	Bacteria:103,Invertebrates:10,Mammals:2,Plants:17,Primates:1,Rodents:1,Vertebrates:3	pfam02036, SCP2, SCP-2 sterol transfer family.  This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145.
CDD:251054	35	EUKprk	Bacteria:4,Environmental:1,Invertebrates:21,Plants:46,Primates:2,Rodents:2,Vertebrates:3,Viruses:2,nodiv:1	pfam02037, SAP, SAP domain.  The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.
CDD:145295	51	EUK	Mammals:2,Primates:2,Rodents:2,Vertebrates:4	pfam02038, ATP1G1_PLM_MAT8, ATP1G1/PLM/MAT8 family.  
CDD:190197	52	EUK	Invertebrates:2,Plants:10	pfam02042, RWP-RK, RWP-RK domain.  This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
CDD:251056	57	EUK	Invertebrates:4,Plants:13,Primates:1	pfam02045, CBFB_NFYA, CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B.  
CDD:145298	116	EUK	Invertebrates:4,Plants:19,Primates:1,Rodents:1,Vertebrates:5	pfam02046, COX6A, Cytochrome c oxidase subunit VIa.  
CDD:251058	97	EUKprk	Bacteria:165,Environmental:1,Invertebrates:1	pfam02049, FliE, Flagellar hook-basal body complex protein FliE.  
CDD:251059	122	PRK	Bacteria:137,Synthetic:1	pfam02050, FliJ, Flagellar FliJ protein.  
CDD:251063	89	EUK	Mammals:3,Primates:1,Rodents:3,Vertebrates:2	pfam02058, Guanylin, Guanylin precursor.  
CDD:251066	121	EUK	Invertebrates:21,Mammals:1,Rodents:1,Vertebrates:1	pfam02064, MAS20, MAS20 protein import receptor.  
CDD:251067	395	EUKprk	Bacteria:8,Plants:3	pfam02065, Melibiase, Melibiase.  Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36A-B and GH36D-K and from GH27.
CDD:111011	52	PRK	Bacteria:12	pfam02069, Metallothio_Pro, Prokaryotic metallothionein.  
CDD:251070	12	EUKprk	Bacteria:1,Invertebrates:3,Mammals:1,Plants:2,Primates:1,Rodents:1,Viruses:1	pfam02071, NSF, Aromatic-di-Alanine (AdAR) repeat.  This repeat is found in NSF attachment proteins. Its structure is similar to that found in TPR repeats pfam00515.
CDD:145308	404	PRK	Bacteria:65	pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29).  
CDD:251074	284	EUK	Plants:35	pfam02076, STE3, Pheromone A receptor.  
CDD:251075	66	EUKprk	Bacteria:143,Environmental:1,Invertebrates:1	pfam02080, TrkA_C, TrkA-C domain.  This domain is often found next to the pfam02254 domain. The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand. The domain is predicted to adopt an all beta structure.
CDD:251077	83	PRK	Bacteria:60,nodiv:1	pfam02082, Rrf2, Transcriptional regulator.  This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
CDD:251079	99	PRK	Bacteria:10	pfam02085, Cytochrom_CIII, Class III cytochrome C family.  
CDD:251080	254	PRK	Bacteria:17,Phages:1,Viruses:1	pfam02086, MethyltransfD12, D12 class N6 adenine-specific DNA methyltransferase.  
CDD:251082	549	EUKprk	Bacteria:137,Environmental:1,Plants:2	pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit.  
CDD:251083	194	EUKprk	Bacteria:104,Invertebrates:5,Plants:15,Primates:2,Vertebrates:1	pfam02096, 60KD_IMP, 60Kd inner membrane protein.  
CDD:251084	150	EUK	Invertebrates:5	pfam02098, His_binding, Tick histamine binding protein.  
CDD:251085	158	EUK	Invertebrates:2,Mammals:1,Plants:5,Primates:1	pfam02099, Josephin, Josephin.  
CDD:251086	97	EUK	Invertebrates:7,Plants:12,Primates:1,Vertebrates:4	pfam02100, ODC_AZ, Ornithine decarboxylase antizyme.  This family consists of ornithine decarboxylase antizyme proteins. The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1).
CDD:251088	206	EUKprk	Bacteria:107,Invertebrates:8,Plants:16,nodiv:1	pfam02104, SURF1, SURF1 family.  
CDD:251089	181	PRK	Bacteria:125,Environmental:1	pfam02107, FlgH, Flagellar L-ring protein.  
CDD:111047	128	PRK	Bacteria:43,Environmental:2	pfam02108, FliH, Flagellar assembly protein FliH.  
CDD:251090	113	EUK	Invertebrates:13,Plants:15,Vertebrates:2	pfam02109, DAD, DAD family.  Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated, these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation.
CDD:251091	246	PRK	Bacteria:1	pfam02110, HK, Hydroxyethylthiazole kinase family.  
CDD:251093	444	PRK	Bacteria:9	pfam02113, Peptidase_S13, D-Ala-D-Ala carboxypeptidase 3 (S13) family.  
CDD:251095	200	EUK	Invertebrates:4,Plants:4,Primates:1,Rodents:1,Vertebrates:2	pfam02115, Rho_GDI, RHO protein GDP dissociation inhibitor.  
CDD:251096	284	EUK	Plants:18	pfam02116, STE2, Fungal pheromone mating factor STE2 GPCR.  
CDD:111054	328	EUK	Invertebrates:1	pfam02117, 7TM_GPCR_Sra, Serpentine type 7TM GPCR chemoreceptor Sra.  Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sra is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
CDD:251097	275	EUK	Invertebrates:2	pfam02118, Srg, Srg family chemoreceptor.  
CDD:251098	342	PRK	Bacteria:117,Environmental:1	pfam02119, FlgI, Flagellar P-ring protein.  
CDD:251099	79	EUKprk	Bacteria:269,Environmental:1,Invertebrates:1	pfam02120, Flg_hook, Flagellar hook-length control protein FliK.  This is the C terminal domain of FliK. FliK controls the length of the flagellar hook by directly measuring the hook length as a molecular ruler. This family also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems.
CDD:111059	203	PRK	Viruses:14	pfam02122, Peptidase_S39, Peptidase S39.  This family contains polyprotein processing endopeptidases from RNA viruses.
CDD:251101	365	PRK	Viruses:28	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.
CDD:251102	211	PRK	Viruses:15	pfam02124, Marek_A, Marek's disease glycoprotein A.  
CDD:251104	425	EUKprk	Bacteria:2,Rodents:1	pfam02127, Peptidase_M18, Aminopeptidase I zinc metalloprotease (M18).  
CDD:251105	368	EUKprk	Bacteria:9,Environmental:1,Plants:12	pfam02128, Peptidase_M36, Fungalysin metallopeptidase (M36).  
CDD:251106	265	EUKprk	Bacteria:39,Invertebrates:1	pfam02129, Peptidase_S15, X-Pro dipeptidyl-peptidase (S15 family).  
CDD:251107	142	EUKprk	Bacteria:147,Invertebrates:5,Plants:1	pfam02130, UPF0054, Uncharacterized protein family UPF0054.  
CDD:251108	41	PRK	Bacteria:176,Environmental:2	pfam02132, RecR, RecR protein.  
CDD:251109	439	EUKprk	Bacteria:1,Plants:2	pfam02133, Transp_cyt_pur, Permease for cytosine/purines, uracil, thiamine, allantoin.  
CDD:251110	67	EUK	Invertebrates:28,Mammals:2,Plants:23,Primates:2,Rodents:2,Vertebrates:1	pfam02134, UBACT, Repeat in ubiquitin-activating (UBA) protein.  
CDD:251111	74	EUK	Invertebrates:8,Mammals:1,Plants:4,Rodents:1	pfam02135, zf-TAZ, TAZ zinc finger.  The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumor suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC.
CDD:251112	116	EUKprk	Bacteria:9,Invertebrates:2,Plants:3,Primates:1,Rodents:2	pfam02136, NTF2, Nuclear transport factor 2 (NTF2) domain.  This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.
CDD:251113	328	EUK	Invertebrates:12,Plants:19,Primates:3,Rodents:1,Vertebrates:4	pfam02137, A_deamin, Adenosine-deaminase (editase) domain.  Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer ...
CDD:251114	274	EUK	Invertebrates:12,Plants:13,Primates:1,Rodents:1	pfam02138, Beach, Beige/BEACH domain.  
CDD:251115	79	EUKprk	Bacteria:1,Invertebrates:10,Plants:16,Primates:2,Rodents:1,Vertebrates:10,nodiv:1	pfam02140, Gal_Lectin, Galactose binding lectin domain.  
CDD:251116	185	EUK	Invertebrates:6,Mammals:1,Plants:5,Primates:2,Rodents:1,Vertebrates:2	pfam02141, DENN, DENN (AEX-3) domain.  DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
CDD:251117	92	EUKprk	Bacteria:73,Environmental:1,Invertebrates:3,Plants:5,Primates:1,Vertebrates:1,nodiv:1	pfam02142, MGS, MGS-like domain.  This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site.
CDD:251118	252	EUK	Invertebrates:6,Plants:18,Primates:2,Vertebrates:1	pfam02144, Rad1, Repair protein Rad1/Rec1/Rad17.  
CDD:251119	187	EUK	Invertebrates:9,Mammals:2,Plants:12,Primates:1,Rodents:1,Vertebrates:2	pfam02145, Rap_GAP, Rap/ran-GAP.  
CDD:251120	177	EUKprk	Bacteria:4,Invertebrates:4,Plants:5	pfam02146, SIR2, Sir2 family.  This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule ...
CDD:251121	63	EUKprk	Bacteria:13,Invertebrates:28,Mammals:1,Plants:27,Primates:3,Rodents:2,Vertebrates:3,Viruses:1	pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein.  
CDD:190228	46	EUK	Invertebrates:2,Plants:14,Primates:1,Vertebrates:1	pfam02149, KA1, Kinase associated domain 1.  
CDD:251122	35	EUKprk	Bacteria:1,Plants:1	pfam02150, RNA_POL_M_15KD, RNA polymerases M/15 Kd subunit.  
CDD:251123	36	EUKprk	Bacteria:53,Invertebrates:5,Mammals:1,Plants:4	pfam02151, UVR, UvrB/uvrC motif.  
CDD:251124	113	EUKprk	Bacteria:109,Plants:8	pfam02152, FolB, Dihydroneopterin aldolase.  This enzyme EC:4.1.2.25 catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate.
CDD:251125	258	PRK	Bacteria:6	pfam02153, PDH, Prephenate dehydrogenase.  Members of this family are prephenate dehydrogenases EC:1.3.1.12 involved in tyrosine biosynthesis.
CDD:251129	206	EUKprk	Bacteria:7,Invertebrates:1,Plants:1,Rodents:1	pfam02163, Peptidase_M50, Peptidase family M50.  
CDD:251131	216	EUKprk	Bacteria:101,Invertebrates:13,Plants:10,Vertebrates:1	pfam02167, Cytochrom_C1, Cytochrome C1 family.  
CDD:251132	90	PRK	Bacteria:65,Environmental:1	pfam02169, LPP20, LPP20 lipoprotein.  This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein.
CDD:251133	115	EUK	Invertebrates:9,Plants:2,Primates:1,Rodents:1,Vertebrates:1	pfam02170, PAZ, PAZ domain.  This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and ...
CDD:251134	296	EUKprk	Bacteria:2,Invertebrates:1,Plants:1,Primates:1	pfam02171, Piwi, Piwi domain.  This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are ...
CDD:145367	41	EUK	Invertebrates:8,Primates:1,Rodents:2,Vertebrates:2	pfam02173, pKID, pKID domain.  CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
CDD:251136	99	EUK	Invertebrates:4,Mammals:1,Primates:2,Rodents:1,Vertebrates:4,nodiv:1	pfam02174, IRS, PTB domain (IRS-1 type).  
CDD:251137	60	EUK	Primates:1	pfam02176, zf-TRAF, TRAF-type zinc finger.  
CDD:251138	102	EUK	Invertebrates:10,Rodents:1,Vertebrates:2	pfam02177, APP_N, Amyloid A4 N-terminal heparin-binding.  This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such ...
CDD:251139	13	EUKprk	Bacteria:4,Invertebrates:3,Plants:8,Primates:1,Rodents:1	pfam02178, AT_hook, AT hook motif.  At hooks are DNA binding motifs with a preference for A/T rich regions.
CDD:251140	76	EUK	Invertebrates:7,Mammals:1,Plants:25,Primates:2,Rodents:2,Vertebrates:4	pfam02179, BAG, BAG domain.  Domain present in Hsp70 regulators.
CDD:145370	27	EUK	Invertebrates:1,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	pfam02180, BH4, Bcl-2 homology region 4.  
CDD:251141	372	EUK	Invertebrates:3,Plants:8,Primates:1,Rodents:1,Vertebrates:2	pfam02181, FH2, Formin Homology 2 Domain.  
CDD:251142	154	EUKprk	Bacteria:2,Invertebrates:2,Plants:9,Rodents:2,Vertebrates:1	pfam02182, SAD_SRA, SAD/SRA domain.  The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the ...
CDD:202143	45	EUK	Plants:25	pfam02183, HALZ, Homeobox associated leucine zipper.  
CDD:251143	63	EUK	Invertebrates:3,Plants:23,Primates:2,Rodents:2,Vertebrates:3	pfam02185, HR1, Hr1 repeat.  
CDD:251144	65	EUK	Invertebrates:2,Mammals:1,Plants:6	pfam02186, TFIIE_beta, TFIIE beta subunit core domain.  General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.
CDD:251145	23	EUK	Invertebrates:8,Mammals:1,Primates:1,Rodents:2,Vertebrates:2	pfam02188, GoLoco, GoLoco motif.  
CDD:111119	21	EUK	Mammals:1,Primates:1,Rodents:3,Vertebrates:1	pfam02189, ITAM, Immunoreceptor tyrosine-based activation motif.  
CDD:251146	192	EUKprk	Bacteria:99,Environmental:1,Invertebrates:10,Mammals:1,Plants:16,Primates:1,Rodents:1	pfam02190, LON, ATP-dependent protease La (LON) domain.  This domain has been shown to be part of the PUA superfamily.
CDD:251147	249	EUK	Invertebrates:3,Mammals:3,Primates:1,Rodents:2,Vertebrates:5	pfam02191, OLF, Olfactomedin-like domain.  
CDD:145379	78	EUK	Invertebrates:2,Mammals:1,Primates:1,Rodents:1,Vertebrates:3	pfam02192, PI3K_p85B, PI3-kinase family, p85-binding domain.  
CDD:251148	182	EUK	Invertebrates:4,Plants:27,Rodents:1,Vertebrates:2	pfam02194, PXA, PXA domain.  This domain is associated with PX domains pfam00787.
CDD:251149	90	EUKprk	Bacteria:27,Phages:2,Plants:1	pfam02195, ParBc, ParB-like nuclease domain.  
CDD:202147	71	EUK	Invertebrates:1,Primates:1,Rodents:1,Vertebrates:1	pfam02196, RBD, Raf-like Ras-binding domain.  
CDD:251150	37	EUK	Primates:1	pfam02197, RIIa, Regulatory subunit of type II PKA R-subunit.  
CDD:251151	84	EUK	Invertebrates:3,Primates:1,Rodents:2,Vertebrates:2	pfam02198, SAM_PNT, Sterile alpha motif (SAM)/Pointed domain.  
CDD:202150	34	EUK	Invertebrates:5,Mammals:4,Primates:2,Rodents:1,Vertebrates:4	pfam02199, SapA, Saposin A-type domain.  
CDD:251152	76	EUKprk	Bacteria:3,Invertebrates:2,Plants:4,Primates:1,Rodents:2,Vertebrates:3,Viruses:1	pfam02201, SWIB, SWIB/MDM2 domain.  This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumor suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.
CDD:251153	146	PRK	Bacteria:49	pfam02203, TarH, Tar ligand binding domain homologue.  
CDD:251154	104	EUK	Invertebrates:12,Plants:10,Primates:1,Rodents:1	pfam02204, VPS9, Vacuolar sorting protein 9 (VPS9) domain.  This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.
CDD:251155	28	EUKprk	Invertebrates:11,Mammals:2,Plants:13,Primates:1,Rodents:2,Vertebrates:2,Viruses:4,nodiv:1	pfam02205, WH2, WH2 motif.  The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP and Scar1 (mammalian homologue) to be the region that interacts with actin.
CDD:251156	69	EUK	Invertebrates:2	pfam02206, WSN, Domain of unknown function.  
CDD:251157	71	EUK	Invertebrates:18,Plants:25,Primates:1,Rodents:1,Vertebrates:2	pfam02207, zf-UBR, Putative zinc finger in N-recognin (UBR box).  This region is found in E3 ubiquitin ligases that recognize N-recognins.
CDD:202157	36	EUK	Invertebrates:1,Plants:1,Primates:1	pfam02209, VHP, Villin headpiece domain.  
CDD:251158	127	EUK	Invertebrates:6,Mammals:4,Primates:1,Rodents:2,Vertebrates:3	pfam02210, Laminin_G_2, Laminin G domain.  This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
CDD:251159	220	PRK	Bacteria:31	pfam02211, NHase_beta, Nitrile hydratase beta subunit.  Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron ...
CDD:251160	90	EUK	Invertebrates:8,Mammals:2,Plants:13,Primates:2,Rodents:1,Vertebrates:2	pfam02212, GED, Dynamin GTPase effector domain.  
CDD:251161	57	EUK	Invertebrates:17,Mammals:1,Plants:28,Primates:1,Vertebrates:3	pfam02213, GYF, GYF domain.  The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.
CDD:251162	93	EUK	Invertebrates:4,Mammals:1,Primates:1,Rodents:2	pfam02214, BTB_2, BTB/POZ domain.  In voltage-gated K+ channels this domain is responsible for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. In KCTD1 this domain functions as a transcriptional repressor. It also mediates homomultimerization of KCTD1 and interaction of KCTD1 with the transcription factor AP-2-alpha.
CDD:111145	94	PRK	Viruses:10	pfam02217, T_Ag_DNA_bind, Origin of replication binding protein.  This domain of large T antigen binds to the SV40 origin of DNA replication.
CDD:251163	286	EUKprk	Bacteria:3,Plants:2,Primates:1	pfam02219, MTHFR, Methylenetetrahydrofolate reductase.  This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from bacteria and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known to be a TIM barrel.
CDD:251164	132	EUK	Invertebrates:27,Mammals:6,Plants:27,Primates:2,Rodents:3,Vertebrates:7	pfam02221, E1_DerP2_DerF2, ML domain.  ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2. It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to ...
CDD:251165	171	EUKprk	Bacteria:7,Plants:2	pfam02222, ATP-grasp, ATP-grasp domain.  This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
CDD:251166	186	EUKprk	Bacteria:5,Invertebrates:1,Plants:1,Primates:1,Viruses:2	pfam02223, Thymidylate_kin, Thymidylate kinase.  
CDD:251167	158	PRK	Bacteria:4	pfam02224, Cytidylate_kin, Cytidylate kinase.  Cytidylate kinase EC:2.7.4.14 catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP.
CDD:251168	92	EUKprk	Bacteria:23,Environmental:1,Invertebrates:4,Plants:13,Primates:1,Rodents:2,Vertebrates:1	pfam02225, PA, PA domain.  The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
CDD:251169	68	PRK	Viruses:29	pfam02226, Pico_P1A, Picornavirus coat protein (VP4).  VP1, VP2, VP3 and VP4 for the basic unit that forms the icosahedral coat of picornaviruses. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis.
CDD:251170	55	EUKprk	Bacteria:81,Environmental:1,Invertebrates:27,Mammals:1,Phages:1,Plants:59,Primates:1,Vertebrates:1	pfam02229, PC4, Transcriptional Coactivator p15 (PC4).  p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
CDD:251171	213	EUKprk	Bacteria:4,Invertebrates:2,Mammals:1,Plants:2,Primates:1	pfam02230, Abhydrolase_2, Phospholipase/Carboxylesterase.  This family consists of both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases pfam00561.
CDD:145407	346	PRK	Viruses:12	pfam02232, Alpha_TIF, Alpha trans-inducing protein (Alpha-TIF).  Alpha-TIF, a virion protein (VP16), is involved in transcriptional activation of viral immediate early (IE) promoters (alpha genes). Specificity of tegument protein VP16 of human herpesvirus 2 for IE genes is conferred by the 400 residue N-terminal, the 80 residue C-terminal is responsible for transcriptional activation.
CDD:251173	51	EUK	Invertebrates:6,Plants:13,Primates:1,Rodents:1,Vertebrates:4	pfam02234, CDI, Cyclin-dependent kinase inhibitor.  Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.
CDD:111160	85	PRK	Viruses:10	pfam02236, Viral_DNA_bi, Viral DNA-binding protein, all alpha domain.  This family represents a domain of the viral DNA- binding protein, a multi functional protein involved in DNA replication and transcription control.
CDD:251174	47	EUKprk	Bacteria:39,Environmental:2,Invertebrates:1,Plants:2,Rodents:1	pfam02237, BPL_C, Biotin protein ligase C terminal domain.  The function of this structural domain is unknown. It is found to the C terminus of the biotin protein ligase catalytic domain pfam01317.
CDD:251177	75	EUK	Invertebrates:20,Mammals:2,Plants:1,Primates:1,Rodents:1,Vertebrates:5	pfam02244, Propep_M14, Carboxypeptidase activation peptide.  Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme.
CDD:251178	185	EUKprk	Bacteria:101,Environmental:1,Invertebrates:6,Plants:1,Primates:1,Vertebrates:2	pfam02245, Pur_DNA_glyco, Methylpurine-DNA glycosylase (MPG).  Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA.
CDD:251181	127	PRK	Bacteria:6,Environmental:5	pfam02249, MCR_alpha, Methyl-coenzyme M reductase alpha subunit, C-terminal domain.  Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (pfam02241), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The C-terminal domain is comprised of an all-alpha multi-helical bundle.
CDD:251182	64	EUK	Invertebrates:3,Rodents:1,Vertebrates:8	pfam02251, PA28_alpha, Proteasome activator pa28 alpha subunit.  PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the alpha subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
CDD:145416	150	EUK	Invertebrates:5,Plants:1,Primates:1,Rodents:1,Vertebrates:1	pfam02252, PA28_beta, Proteasome activator pa28 beta subunit.  PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the beta subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
CDD:251183	259	PRK	Bacteria:77	pfam02253, PLA1, Phospholipase A1.  Phospholipase A1 is a bacterial outer membrane bound acyl hydrolase with a broad substrate specificity EC:3.1.1.32. It has been proposed that Ser164 is the active site for Escherichia coli phospholipase A1.
CDD:251184	116	PRK	Bacteria:98,Environmental:1	pfam02254, TrkA_N, TrkA-N domain.  This domain is found in a wide variety of proteins. These protein include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD.
CDD:251185	96	PRK	Bacteria:72	pfam02255, PTS_IIA, PTS system, Lactose/Cellobiose specific IIA subunit.  The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilized by a centrally ...
CDD:251186	60	EUKprk	Bacteria:52,Invertebrates:7,Plants:6,Rodents:2,Vertebrates:1	pfam02256, Fe_hyd_SSU, Iron hydrogenase small subunit.  This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.
CDD:251187	85	EUK	Invertebrates:6,Plants:14,Primates:1,Rodents:1,Vertebrates:3	pfam02257, RFX_DNA_binding, RFX DNA-binding domain.  RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using ...
CDD:251189	350	EUK	Invertebrates:7,Mammals:2,Plants:26,Primates:1,Rodents:1	pfam02259, FAT, FAT domain.  The FAT domain is named after FRAP, ATM and TRRAP.
CDD:251190	33	EUK	Invertebrates:15,Plants:32,Primates:1,Vertebrates:1	pfam02260, FATC, FATC domain.  The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability.
CDD:251191	116	PRK	Bacteria:141,Environmental:1	pfam02261, Asp_decarbox, Aspartate decarboxylase.  Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of ...
CDD:111185	264	EUK	Invertebrates:2,Primates:1,Rodents:1,Vertebrates:1	pfam02263, GBP, Guanylate-binding protein, N-terminal domain.  Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.
CDD:251193	251	EUKprk	Bacteria:19,Environmental:1,Invertebrates:11,Plants:21	pfam02265, S1-P1_nuclease, S1/P1 Nuclease.  This family contains both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity.
CDD:145427	243	EUK	Invertebrates:3,Mammals:2,Primates:3,Rodents:2,Vertebrates:1	pfam02267, Rib_hydrolayse, ADP-ribosyl cyclase.  ADP-ribosyl cyclase EC:3.2.2.5 (also know as cyclic ADP-ribose hydrolase or CD38) synthesizes cyclic-ADP ribose, a second messenger for glucose-induced insulin secretion.
CDD:251194	47	EUK	Plants:11,Rodents:1	pfam02268, TFIIA_gamma_N, Transcription initiation factor IIA, gamma subunit, helical domain.  Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.
CDD:251195	258	EUK	Invertebrates:4,Mammals:1,Plants:12,Vertebrates:1	pfam02270, TFIIF_beta, Transcription initiation factor IIF, beta subunit.  Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA ...
CDD:202184	105	EUK	Invertebrates:4,Plants:17,Primates:1,Vertebrates:2	pfam02271, UCR_14kD, Ubiquinol-cytochrome C reductase complex 14kD subunit.  The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex.
CDD:251196	70	EUKprk	Bacteria:27,Invertebrates:2,Plants:1	pfam02272, DHHA1, DHHA1 domain.  This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.
CDD:251197	286	EUKprk	Bacteria:46,Invertebrates:1,Plants:1,Primates:1	pfam02274, Amidinotransf, Amidinotransferase.  This family contains glycine (EC:2.1.4.1) and inosamine (EC:2.1.4.2) amidinotransferases, enzymes involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases, EC:3.5.3.6. These enzymes catalyse the reaction: arginine + H2O <=> citrulline + NH3. Also found in this family is the Streptococcus anti tumor glycoprotein.
CDD:145434	315	PRK	Bacteria:18,Environmental:3	pfam02276, CytoC_RC, Photosynthetic reaction centre cytochrome C subunit.  Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidized electron donor.
CDD:251199	339	PRK	Bacteria:15	pfam02277, DBI_PRT, Phosphoribosyltransferase.  This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis ...
CDD:251201	143	PRK	Viruses:6	pfam02282, Herpes_UL42, DNA polymerase processivity factor (UL42).  The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerization and makes little contribution to the catalytic activity of the polymerase.
CDD:251202	166	PRK	Bacteria:181	pfam02283, CobU, Cobinamide kinase / cobinamide phosphate guanyltransferase.  This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.
CDD:145441	136	PRK	Bacteria:14	pfam02287, Dehydratase_SU, Dehydratase small subunit.  This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.
CDD:202190	112	PRK	Bacteria:44	pfam02288, Dehydratase_MU, Dehydratase medium subunit.  This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.
CDD:251204	91	EUK	Invertebrates:8,Plants:12	pfam02290, SRP14, Signal recognition particle 14kD protein.  The signal recognition particle (SRP) is a multimeric protein involved in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP14 and SRP9 form a complex essential for SRP RNA binding.
CDD:251205	166	PRK	Bacteria:11	pfam02293, AmiS_UreI, AmiS/UreI family transporter.  This family includes UreI and proton gated urea channel as well as putative amide transporters.
CDD:251207	112	EUK	Invertebrates:4,Mammals:1,Plants:12,Rodents:1,Vertebrates:1	pfam02296, Alpha_adaptin_C, Alpha adaptin AP2, C-terminal domain.  Alpha adaptin is a hetero tetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site.
CDD:251208	66	EUK	Invertebrates:11,Mammals:1,Plants:26,Primates:2,Rodents:1,Vertebrates:2	pfam02297, COX6B, Cytochrome oxidase c subunit VIb.  Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.
CDD:251209	84	EUK	Plants:9	pfam02298, Cu_bind_like, Plastocyanin-like domain.  This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family may not bind copper due to the lack of key residues.
CDD:111216	128	PRK	Bacteria:18	pfam02300, Fumarate_red_C, Fumarate reductase subunit C.  Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C.
CDD:251210	185	EUK	Invertebrates:20,Mammals:1,Plants:33,Primates:1,Rodents:1,Vertebrates:2	pfam02301, HORMA, HORMA domain.  The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.
CDD:251211	96	EUKprk	Bacteria:140,Plants:1	pfam02302, PTS_IIB, PTS system, Lactose/Cellobiose specific IIB subunit.  The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian ...
CDD:111223	130	PRK	Bacteria:7	pfam02308, MgtC, MgtC family.  The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB. The function of MgtC and its homologues is not known.
CDD:251214	188	EUK	Plants:19	pfam02309, AUX_IAA, AUX/IAA family.  Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain.
CDD:251215	120	PRK	Bacteria:99	pfam02310, B12-binding, B12 binding domain.  This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
CDD:145456	134	PRK	Bacteria:22,nodiv:1	pfam02311, AraC_binding, AraC-like ligand binding domain.  This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.
CDD:111228	118	PRK	Bacteria:19	pfam02313, Fumarate_red_D, Fumarate reductase subunit D.  Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D.
CDD:251217	152	EUKprk	Bacteria:28,Invertebrates:9,Plants:2	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain.  This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids.
CDD:251218	118	EUK	Invertebrates:2,Mammals:3,Primates:1,Rodents:2,Vertebrates:6	pfam02318, FYVE_2, FYVE-type zinc finger.  This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.
CDD:251219	67	EUK	Invertebrates:4,Plants:5,Primates:1,Rodents:1	pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding domain.  This family contains the transcription factor E2F and its dimerization partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F ...
CDD:251220	65	EUK	Invertebrates:11,Plants:9,Primates:1,Vertebrates:2	pfam02320, UCR_hinge, Ubiquinol-cytochrome C reductase hinge protein.  The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex.
CDD:251221	186	PRK	Bacteria:89	pfam02321, OEP, Outer membrane efflux protein.  The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria.  Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm.
CDD:251222	327	PRK	Bacteria:125	pfam02322, Cyto_ox_2, Cytochrome oxidase subunit II.  This Family consists of cytochrome bd type terminal oxidases that catalyses Quinol dependent, Na+ independent oxygen uptake. Members of this family are integral membrane proteins andi contain a protohaem IX centre B558. One member of the family is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae.
CDD:251224	75	EUKprk	Bacteria:143,Environmental:1,Plants:10,nodiv:1	pfam02325, YGGT, YGGT family.  This family consists of a repeat found in conserved hypothetical integral membrane proteins. The function of this region and the proteins which possess it is unknown.
CDD:251225	84	EUK	Invertebrates:3,Plants:18	pfam02326, YMF19, Plant ATP synthase F0.  This family corresponds to subunit 8 (YMF19) of the F0 complex of plant and algae mitochondrial F-ATPases (EC:3.6.1.34).
CDD:251230	233	PRK	Bacteria:16	pfam02332, Phenol_Hydrox, Methane/Phenol/Toluene Hydroxylase.  Bacterial phenol hydroxylase is a multicomponent enzyme that catabolises phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A.
CDD:251231	383	PRK	Bacteria:33,nodiv:1	pfam02335, Cytochrom_C552, Cytochrome c552.  Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme in the nitrogen cycle catalyzing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups.
CDD:251233	113	EUKprk	Invertebrates:3,Plants:5,Primates:1,Rodents:1,Viruses:12	pfam02338, OTU, OTU-like cysteine protease.  This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian tumor (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.
CDD:251234	181	EUKprk	Bacteria:64,Invertebrates:8,Plants:3	pfam02342, TerD, TerD domain.  The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins. It is found in a stress response operon with TerB and TerC. TerD has a maximum of two calcium binding sites {2] depending on the conservation of aspartates {2]. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter ...
CDD:251235	131	EUK	Invertebrates:1	pfam02343, TRA-1_regulated, TRA-1 regulated protein R03H10.4.  This family of proteins represents the protein product of the gene R03H10.4 which is located near a sequence that matches the TRA-1 binding consensus. TRA-1 is a transcription factor which controls sexual differentiation in C.elegans. R03H10.4 shows male-enriched reporter gene expression and acts as a direct target of TRA-1 regulation.
CDD:111257	57	PRK	Viruses:11	pfam02346, Vac_Fusion, Chordopoxvirus fusion protein.  This is a family of viral fusion proteins from the chordopoxviruses. A 14-kDa Vaccinia Virus protein has been demonstrated to function as a viral fusion protein mediating cell fusion at endosmomal (low) pH.
CDD:251236	429	EUKprk	Bacteria:4,Invertebrates:1,Plants:3,Primates:1,Vertebrates:1	pfam02347, GDC-P, Glycine cleavage system P-protein.  This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalysed by this protein is:- Glycine ...
CDD:251237	213	PRK	Bacteria:11	pfam02348, CTP_transf_3, Cytidylyltransferase.  This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalyzing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43, catalyzing the reaction:- CTP + N-acylneuraminate <=> diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of ...
CDD:251238	81	EUK	Plants:2	pfam02349, MSG, Major surface glycoprotein.  This is a novel repeat in Pneumocystis carinii Major surface glycoprotein (MSG) some members of the alignment have up to nine repeats of this family, the repeats containing several conserved cysteines. The MSG of P. carinii is an important protein in host-pathogen interactions. Surface glycoprotein A from Pneumocystis carinii is a main target for the host immune system, this protein is implicated in the attachment of ...
CDD:251239	341	EUKprk	Bacteria:126,Vertebrates:1	pfam02350, Epimerase_2, UDP-N-acetylglucosamine 2-epimerase.  This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyses the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional; in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is ...
CDD:251240	84	EUK	Invertebrates:5,Mammals:2,Primates:2,Rodents:2,Vertebrates:3	pfam02351, GDNF, GDNF/GAS1 domain.  This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked ...
CDD:251242	273	PRK	Bacteria:6	pfam02353, CMAS, Mycolic acid cyclopropane synthetase.  This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase EC:2.1.1.79 this enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid <=> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.
CDD:216990	189	PRK	Bacteria:7	pfam02355, SecD_SecF, Protein export membrane protein.  This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force.
CDD:251244	90	PRK	Bacteria:90,Environmental:3,nodiv:1	pfam02357, NusG, Transcription termination factor nusG.  
CDD:251245	235	EUKprk	Bacteria:5,Plants:3	pfam02358, Trehalose_PPase, Trehalose-phosphatase.  This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. The aligned region is present in trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - ...
CDD:251246	87	EUKprk	Bacteria:46,Environmental:1,Invertebrates:19,Plants:16,Primates:1,Rodents:2,Vertebrates:2	pfam02359, CDC48_N, Cell division protein 48 (CDC48), N-terminal domain.  This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a ...
CDD:251247	217	PRK	Bacteria:10	pfam02361, CbiQ, Cobalt transport protein.  This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system.
CDD:251248	101	EUK	Plants:7	pfam02362, B3, B3 DNA binding domain.  This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by.
CDD:251249	17	EUK	Invertebrates:5	pfam02363, C_tripleX, Cysteine rich repeat.  This Cysteine repeat C-X3-C-X3-C is repeated in sequences of this family, 34 times in one member. The function of these repeats is unknown as is the function of the proteins in which they occur. Most of the sequences in this family are from C. elegans.
CDD:251251	130	EUK	Plants:18	pfam02365, NAM, No apical meristem (NAM) protein.  This is a family of no apical meristem (NAM) proteins these are plant development proteins. Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos. NAM is indicated as having a role in determining positions of meristems and primordial. One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and ...
CDD:251252	244	EUKprk	Bacteria:4,Invertebrates:1,Plants:3,Primates:1	pfam02366, PMT, Dolichyl-phosphate-mannose-protein mannosyltransferase.  This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein. Also in this family is the Drosophila rotated abdomen protein which is a ...
CDD:251253	123	PRK	Bacteria:6	pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.  This uncharacterized family contains a P-loop.
CDD:251254	79	EUKprk	Bacteria:14,Invertebrates:1,Phages:7,Primates:1	pfam02368, Big_2, Bacterial Ig-like domain (group 2).  This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins.
CDD:251255	93	PRK	Bacteria:4	pfam02369, Big_1, Bacterial Ig-like domain (group 1).  This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity.
CDD:111279	21	PRK	Bacteria:4	pfam02370, M, M protein repeat.  This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis.
CDD:251256	87	PRK	Bacteria:100,Environmental:1	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family.  Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.
CDD:251257	135	EUK	Mammals:3,Primates:1,Rodents:3,Vertebrates:7	pfam02372, IL15, Interleukin 15.  Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses.
CDD:202224	114	EUK	Invertebrates:3,Plants:5,Primates:1,Rodents:2	pfam02373, JmjC, JmjC domain, hydroxylase.  The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.
CDD:251258	304	EUKprk	Bacteria:4,Plants:1	pfam02374, ArsA_ATPase, Anion-transporting ATPase.  This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
CDD:190295	34	EUK	Invertebrates:6,Plants:19,Primates:1,Rodents:2,Vertebrates:1	pfam02375, JmjN, jmjN domain.  
CDD:202226	87	EUK	Invertebrates:5,Mammals:1,Primates:1,Rodents:1,Vertebrates:1	pfam02376, CUT, CUT domain.  The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein.
CDD:251259	314	PRK	Bacteria:18	pfam02378, PTS_EIIC, Phosphotransferase system, EIIC.  The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate.
CDD:145497	93	EUKprk	Rodents:1,Viruses:9	pfam02380, Papo_T_antigen, T-antigen specific domain.  This domain represents a conserved region in papovavirus small and middle T-antigens. It is found as the N-terminal domain in the small T-antigen, and is centrally located in the middle T-antigen.
CDD:111290	72	PRK	Bacteria:6	pfam02381, MraZ, MraZ protein.  This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin).
CDD:251261	299	EUK	Invertebrates:26,Plants:37,Primates:1,Rodents:2,Vertebrates:2	pfam02383, Syja_N, SacI homology domain.  This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
CDD:251262	312	PRK	Bacteria:9	pfam02384, N6_Mtase, N-6 DNA Methylase.  Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence ...
CDD:251263	335	EUKprk	Bacteria:12,Plants:4	pfam02386, TrkH, Cation transport protein.  This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilizing ATP in the process. TrkH a member of the family from Escherichia coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in Escherichia coli.
CDD:251264	279	PRK	Bacteria:12	pfam02387, IncFII_repA, IncFII RepA protein family.  This protein is plasmid encoded and found to be essential for plasmid replication.
CDD:251265	408	PRK	Bacteria:37	pfam02388, FemAB, FemAB family.  The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance.
CDD:251266	199	EUKprk	Bacteria:6,Invertebrates:2,Plants:1,Rodents:1	pfam02390, Methyltransf_4, Putative methyltransferase.  This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
CDD:111299	117	EUKprk	Bacteria:6,Invertebrates:1,Plants:1	pfam02391, MoaE, MoaE protein.  This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.
CDD:145503	180	EUKprk	Bacteria:16,Invertebrates:1,Plants:41	pfam02392, Ycf4, Ycf4.  This family consists of hypothetical Ycf4 proteins from various chloroplast genomes. It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts.
CDD:251267	121	EUKprk	Invertebrates:1,Vertebrates:2,Viruses:10	pfam02393, US22, US22 like.  US22 proteins have been found across many animal DNA viruses and some vertebrates. The name sake of this family, US22, is an early nuclear protein that is secreted from cells. The US22 family may have a role in virus replication and pathogenesis. Domain analysis showed that US22 proteins #=GF CC   usually contain two copies of conserved modules which is homologous to several other families like SMI1 and ...
CDD:251268	103	EUK	Mammals:6,Primates:2,Rodents:3,Vertebrates:1	pfam02394, IL1_propep, Interleukin-1 propeptide.  The Interleukin-1 cytokines are translated as precursor proteins. The N terminal approx. 115 amino acids form a propeptide that is cleaved off to release the active interleukin-1.
CDD:251270	186	PRK	Bacteria:285,nodiv:1	pfam02397, Bac_transf, Bacterial sugar transferase.  This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways.
CDD:251271	829	PRK	Viruses:10	pfam02399, Herpes_ori_bp, Origin of replication binding protein.  This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.
CDD:251272	280	PRK	Bacteria:1	pfam02401, LYTB, LytB protein.  The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway.
CDD:251274	108	EUKprk	Bacteria:42,Invertebrates:2,Plants:4,Rodents:1,nodiv:1	pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.  This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
CDD:145511	215	EUKprk	Bacteria:165,Environmental:2,Plants:5	pfam02405, Permease, Permease.  This domain functions as a permease. In a hypothetical protein from Neisseria it is involved in L-glutamate import into the cell. In Arabidopsis ABC transporter I family member 14 it is involved in lipid transfer within the cell.
CDD:251275	87	PRK	Bacteria:34	pfam02406, MmoB_DmpM, MmoB/DmpM family.  This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilizes intermediates required for the activation of dioxygen. Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors ...
CDD:251276	85	PRK	Viruses:8	pfam02407, Viral_Rep, Putative viral replication protein.  This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function "viral replication associated protein" has not be found.
CDD:251277	120	EUK	Invertebrates:1	pfam02408, CUB_2, CUB-like domain.  This is a family of hypothetical C. elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain.
CDD:251278	99	EUKprk	Bacteria:133,Environmental:1,Invertebrates:7,Plants:5	pfam02410, Oligomerization, Oligomerization domain.  In yeasts, this domain is required for the oligomerization of ATP synthase subunit 9 into a ring structure.
CDD:202235	35	EUKprk	Bacteria:1,Invertebrates:3,Primates:1,Vertebrates:1	pfam02412, TSP_3, Thrombospondin type 3 repeat.  The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
CDD:251279	126	PRK	Bacteria:33,Phages:10	pfam02413, Caudo_TAP, Caudovirales tail fibre assembly protein.  This family contains bacterial and phage tail fibre assembly proteins. E.coli contains several members of this family although the function of these proteins is uncertain.
CDD:251280	287	PRK	Bacteria:6	pfam02414, Borrelia_orfA, Borrelia ORF-A.  This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown.
CDD:145519	19	PRK	Bacteria:10	pfam02415, Chlam_PMP, Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat.  This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterized by conserved tryptophans ...
CDD:145520	53	EUKprk	Bacteria:6,Plants:1	pfam02416, MttA_Hcf106, mttA/Hcf106 family.  Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts. Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif.
CDD:251281	169	EUKprk	Bacteria:75,Environmental:2,Invertebrates:1	pfam02417, Chromate_transp, Chromate transporter.  Members of this family probably act as chromate transporters. Members of this family are found in both bacteria and archaebacteria. The proteins are composed of one or two copies of this region. The alignment contains two conserved motifs, FGG and PGP.
CDD:111326	12	EUK	Invertebrates:1	pfam02420, AFP, Insect antifreeze protein repeat.  This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix. Each repeat contains two cys residues that form a disulphide bridge.
CDD:251282	156	PRK	Bacteria:107,Environmental:2	pfam02421, FeoB_N, Ferrous iron transport protein B.  Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
CDD:251283	312	EUKprk	Bacteria:9,Primates:1,nodiv:1	pfam02423, OCD_Mu_crystall, Ornithine cyclodeaminase/mu-crystallin family.  This family contains the bacterial Ornithine cyclodeaminase enzyme EC:4.3.1.12, which catalyses the deamination of ornithine to proline. This family also contains mu-Crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina.
CDD:251284	254	EUKprk	Bacteria:181,Environmental:2,Invertebrates:3	pfam02424, ApbE, ApbE family.  This prokaryotic family of lipoproteins are related to ApbE from Salmonella typhimurium. ApbE is involved in thiamine synthesis. More specifically is may be involved in the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP).
CDD:145527	61	EUKprk	Bacteria:13,Invertebrates:1,Plants:11	pfam02427, PSI_PsaE, Photosystem I reaction centre subunit IV / PsaE.  PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains.
CDD:251288	199	EUK	Invertebrates:1,Plants:42	pfam02431, Chalcone, Chalcone-flavanone isomerase.  Chalcone-flavanone isomerase is a plant enzyme responsible for the isomerization of chalcone to naringenin, a key step in the biosynthesis of flavonoids.
CDD:251289	238	PRK	Bacteria:3	pfam02432, Fimbrial_K88, Fimbrial, major and minor subunit.  Fimbriae (also know as pili) are polar filaments found on the bacterial surface, allowing colonisation of the host. This family consists of the minor and major fimbrial subunits.
CDD:111339	226	PRK	Bacteria:49	pfam02433, FixO, Cytochrome C oxidase, mono-heme subunit/FixO.  The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex.
CDD:190308	248	EUK	Invertebrates:9,Primates:1,Rodents:2,Vertebrates:5	pfam02434, Fringe, Fringe-like.  The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localized to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions.
CDD:251291	195	EUKprk	Bacteria:81,Environmental:1,Invertebrates:3,Plants:7	pfam02436, PYC_OADA, Conserved carboxylase domain.  This domain represents a conserved region in pyruvate carboxylase (PYC), oxaloacetate decarboxylase alpha chain (OADA), and transcarboxylase 5s subunit. The domain is found adjacent to the HMGL-like domain (pfam00682) and often close to the biotin_lipoyl domain (pfam00364) of biotin requiring enzymes.
CDD:251292	583	PRK	Viruses:19	pfam02438, Adeno_100, Late 100kD protein.  The late 100kD protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus.
CDD:251293	63	PRK	Viruses:14	pfam02440, Adeno_E3_CR1, Adenovirus E3 region protein CR1.  Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. This region called CR1 (conserved region 1) is found three times in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably ...
CDD:251294	130	EUKprk	Bacteria:103,Environmental:4,Invertebrates:6,Plants:8,Primates:1	pfam02441, Flavoprotein, Flavoprotein.  This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN. This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain ...
CDD:251295	185	PRK	Viruses:25	pfam02442, L1R_F9L, Lipid membrane protein of large eukaryotic DNA viruses.  The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with ...
CDD:251296	237	PRK	Viruses:9	pfam02443, Circo_capsid, Circovirus capsid protein.  Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long.
CDD:251297	296	PRK	Bacteria:99,Environmental:2	pfam02445, NadA, Quinolinate synthetase A protein.  Quinolinate synthetase catalyses the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid. This synthesis requires two enzymes, a FAD-containing "B protein" and an "A protein".
CDD:251298	493	EUKprk	Bacteria:7,Plants:1	pfam02446, Glyco_hydro_77, 4-alpha-glucanotransferase.  These enzymes EC:2.4.1.25 transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan.
CDD:251299	441	PRK	Bacteria:3	pfam02447, GntP_permease, GntP family permease.  This is a family of integral membrane permeases that are involved in gluconate uptake. Escherichia coli contains several members of this family including GntU, a low affinity transporter and GntT, a high affinity transporter.
CDD:251300	74	EUK	Invertebrates:1	pfam02448, L71, L71 family.  This family of insect proteins are each about 100 amino acids long and have 6 conserved cysteine residues. They all have a predicted signal peptide and are probably excreted. The function of the proteins is unknown.
CDD:251301	376	PRK	Bacteria:21,Environmental:2	pfam02449, Glyco_hydro_42, Beta-galactosidase.  This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.
CDD:251304	111	PRK	Bacteria:205,Environmental:2,Phages:1,nodiv:1	pfam02452, PemK, PemK-like protein.  PemK is a growth inhibitor in Escherichia coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This Pfam family consists of the PemK protein in addition to ChpA, ChpB and other PemK-like proteins.
CDD:251305	164	EUK	Invertebrates:13,Mammals:1,Plants:26,Rodents:1,Vertebrates:10	pfam02453, Reticulon, Reticulon.  Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of