Pfam_families(apr_2023)

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U
1	AC	ID	summary name	pfam summary	#seed	#full	#structures	#species	#architectures	ave. domain length	ave. id% in full alignment	av.coverage% of a seq. by domain	#Uniprot	#RP15	#RP35	#RP55	#RP75	creation date	version number	other DB	category in the DB
2	PF00001	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 function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	63	127566	650	628	1078	254.9	19	66.53	266147	24915	50446	101798	130592	######	24	Prosite	Family
3	PF00002	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 recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 (Swiss:P48960); calcium-independent receptors for latrotoxin (such as Swiss:O94910), and brain-specific angiogenesis inhibitors (such as Swiss:O14514) amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins (e.g. Swiss:P83119). Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling [1].	27	30397	84	854	1112	228.8	23	24.82	47972	4159	9638	22524	30797	######	27	Prosite	Family
4	PF00003	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 Pfam:PF07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor Pfam:PF01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness [1].	616	20570	75	581	286	244.1	26	30.61	31871	3447	7257	16183	20861	######	25	Prosite	Domain
5	PF00004	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 [2].	207	182497	2362	9439	2269	129.9	25	21.37	544521	30931	85687	160221	243904	######	32	Prosite	Domain
6	PF00005	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 Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	55	838816	1197	9150	3055	148.5	26	36.68	3489531	103125	389049	832238	1428870	######	30	Prosite	Domain
7	PF00006	ATP-synt_ab	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	409	42395	2016	8987	290	213	35	43.02	224269	6706	21174	41584	68037	######	28	Prosite	Domain
8	PF00007	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 dimerisation.	24	4182	35	375	44	95.9	26	33.49	8790	346	1218	3117	4224	######	25	Published_alignment enriched with PDOC00234 members.	Domain
9	PF00008	EGF	EGF-like domain	There is no clear separation between noise and signal. Pfam:PF00053 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 but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.	67	154925	409	616	10508	31.8	40	8.46	242496	33444	57674	120681	157842	######	30	Swissprot_feature_table	Domain
10	PF00009	GTP_EFTU	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	142	95606	694	9117	821	224.7	27	35.43	452895	15527	46012	90201	145733	######	30	Prosite	Domain
11	PF00010	HLH	Helix-loop-helix DNA-binding domain	NULL	141	81103	145	1465	692	53.4	29	12.95	134842	11476	32538	63163	84806	######	29	Unknown	Domain
12	PF00011	HSP20	Hsp20/alpha crystallin family	Not only do small heat-shock-proteins occur in eukaryotes and prokaryotes but they have also now been shown to occur in cyanobacterial phages as well as their bacterial hosts [2].	25	31174	400	7414	230	97.4	22	53.6	97369	5773	16056	29180	43776	######	24	Prosite	Domain
13	PF00012	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.	27	54379	446	8954	645	407.8	29	80.76	179547	10726	27103	48810	73912	######	23	Prosite	Family
14	PF00013	KH_1	KH domain	KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.	783	109086	179	8830	849	65.1	23	22.52	216351	15839	41146	84850	120318	######	32	Published_alignment	Domain
15	PF00014	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, Swiss:P17726). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways [1]. TAP molecules are highly dipolar [2], and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix [1].	99	23880	321	540	1416	53.1	36	14.35	44690	7097	11311	19734	24673	######	26	Prosite	Domain
16	PF00015	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.	9	55646	38	3748	873	168.7	31	29.68	297891	7045	27323	57728	108096	######	24	Blast MCP1_ECOLI/361-421	Family
17	PF00016	RuBisCO_large	Ribulose bisphosphate carboxylase large chain, catalytic domain	The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.	16	2894	659	1593	50	248.4	37	63.67	181204	426	1457	2857	4596	######	23	Prosite	Domain
18	PF00017	SH2	SH2 domain	NULL	52	59304	847	549	1043	78.5	28	13.73	98685	7704	17810	44201	60346	######	27	Swissprot_feature_table	Domain
19	PF00018	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 Swiss:P12931. The structure is a partly opened beta barrel.	55	92969	767	1443	2425	47.6	29	6.69	146123	11658	28186	66817	93857	######	31	Prosite	Domain
20	PF00019	TGF_beta	Transforming growth factor beta like domain	NULL	263	12309	251	490	102	98.8	35	25.7	26057	1483	4092	9457	12628	######	23	Prosite	Domain
21	PF00020	TNFR_c6	TNFR/NGFR cysteine-rich region	NULL	489	12940	311	435	165	39.8	28	18.95	23405	1328	3528	9135	12915	######	21	Swissprot_feature_table	Domain
22	PF00021	UPAR_LY6	u-PAR/Ly-6 domain	This extracellular disulphide bond rich domain is related to Pfam:PF00087.	27	5051	93	303	52	74.6	21	49.56	8176	391	1307	3505	5064	######	24	Prosite	Domain
23	PF00022	Actin	Actin	NULL	24	31597	1401	1607	413	323.5	29	83.21	75772	6283	14066	24515	32517	######	22	Prosite	Family
24	PF00023	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, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity [2][3].	1062	28509	479	2344	4484	33.5	31	4.18	52743	6448	12640	22523	30270	######	33	Swissprot_feature_table	Repeat
25	PF00024	PAN_1	PAN domain	The PAN domain [1] 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.	86	11531	134	1221	725	80.1	16	18.03	20270	4169	6066	9853	12388	######	29	Patthy L	Domain
26	PF00025	Arf	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	20	28693	263	1781	443	157.3	35	74.08	50915	5528	12763	22556	29822	######	24	Swissprot	Domain
27	PF00026	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 (Pfam:PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.	24	24251	1924	1566	398	284.2	23	68.31	40652	5235	12120	19051	24960	######	26	Overington enriched	Family
28	PF00027	cNMP_binding	Cyclic nucleotide-binding domain	This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	210	87173	731	8105	1219	88.2	20	19.4	273176	15080	38948	79702	128031	######	32	Prosite	Domain
29	PF00028	Cadherin	Cadherin domain	NULL	55	278836	786	929	2360	93.1	25	45.26	455561	34606	87224	209664	284697	######	20	Swissprot_feature_table	Domain
30	PF00029	Connexin	Connexin	Connexin proteins form gap-junctions between cells. They carry four transmembrane regions, hence why this family now includes Connexin_CCC, which represented the second pair of TMs.	176	7511	194	258	43	203.5	40	67.46	15435	514	2225	5783	7717	######	22	Prosite	Domain
31	PF00030	Crystall	Beta/Gamma crystallin	The alignment comprises two Greek key motifs since the similarity between them is very low.	86	19766	170	456	104	81.3	31	45.62	34555	1508	5889	14772	20372	######	22	Swissprot_feature_table	Domain
32	PF00031	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. All members except Swiss:Q03196 and Swiss:Q10993 are found. Pfam:PF00666 are related to this family but have not been included.	34	6502	134	658	82	90.2	18	45.19	11960	925	2225	4915	6730	######	24	Prosite	Domain
33	PF00032	Cytochrom_B_C	Cytochrome b(C-terminal)/b6/petD	NULL	156	4475	208	3501	55	105.1	35	28.48	201107	662	2179	4492	7382	######	20	Prosite	Domain
34	PF00033	Cytochrome_B	Cytochrome b/b6/petB	NULL	8	4593	204	3528	72	181.4	45	48.75	257634	722	2290	4619	7482	######	22	Prosite	Domain
35	PF00034	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, Pfam:PF06181, has now been merged into this family.	53	29176	573	5906	380	98.6	18	32.57	140299	3899	13545	29630	53607	######	24	Prosite	Domain
36	PF00035	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 protein kinase in humans, which is part of the cellular response to dsRNA.	76	35979	137	8357	446	64.9	26	18.42	85393	4905	14116	29403	43094	######	29	Published_alignment	Domain
37	PF00036	EF-hand_1	EF hand	The EF-hands can be divided into two classes: signalling 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 latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.	564	12785	432	1561	535	28.7	30	8.74	26421	2381	5451	10197	13354	######	35	Prosite	Domain
38	PF00037	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.	528	31425	261	7257	1023	23.4	39	8.04	152506	6012	17591	30736	48694	######	30	Prosite	Domain
39	PF00038	Filament	Intermediate filament protein	NULL	26	21973	84	505	176	275.5	32	58	39126	1921	6237	15872	22111	######	24	Prosite	Coiled-coil
40	PF00039	fn1	Fibronectin type I domain	NULL	57	12253	70	252	156	38.5	42	15.69	18561	385	1785	7964	12263	######	21	Swissprot_feature_table	Domain
41	PF00040	fn2	Fibronectin type II domain	NULL	256	9529	81	310	394	41.6	48	4.9	15739	720	2117	6842	9610	######	22	Prosite	Domain
42	PF00041	fn3	Fibronectin type III domain	NULL	98	422883	652	3407	10587	84.8	20	24.08	666212	38649	113655	305543	435202	######	24	Swissprot_feature_table	Domain
43	PF00042	Globin	Globin	NULL	73	11967	3105	3665	140	109.1	22	40.31	38232	2111	5002	10455	16204	######	25	Structure_superposition	Domain
44	PF00043	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 E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain [1]. In plants, GSTs are encoded by a large gene family (48 GST genes in Arabidopsis) and can be divided into the phi, tau, theta, zeta, and lambda classes [2].	33	32925	758	4130	455	96.5	17	34.63	109982	4405	14388	28519	48363	######	28	Overington	Domain
45	PF00044	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.	74	18775	767	8657	99	101.8	42	29.03	82487	2505	8618	18195	30276	######	27	Overington	Domain
46	PF00045	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).	76	28053	192	623	278	44.9	27	25.19	48274	2654	7805	20754	28921	######	22	SMART	Repeat
47	PF00046	Homeodomain	Homeodomain	NULL	146	105144	285	1487	898	56.3	33	14.19	189058	16456	41518	82539	108758	######	32	Unknown	Domain
48	PF00047	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.	34	22324	345	513	2041	83.4	16	10.51	38375	2245	5857	14873	21692	######	28	Bateman A	Domain
49	PF00048	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.	310	9244	460	280	52	58.8	25	50.68	17271	525	2284	6328	9314	######	23	Overington enriched	Domain
50	PF00049	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.	28	3578	1799	415	25	69.9	31	53.64	6926	411	1021	2502	3554	######	21	Overington enriched	Domain
51	PF00050	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 Swiss:P46721.	25	8033	95	708	430	52.7	28	16.66	17508	1565	3009	6347	8466	######	24	Prosite	Domain
52	PF00051	Kringle	Kringle domain	Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.	23	13699	244	525	570	78	40	21.5	23071	1818	3977	10003	13724	######	21	Swissprot_feature_table	Domain
53	PF00052	Laminin_B	Laminin B (Domain IV)	NULL	212	7404	3	544	1533	132.9	28	8.65	11705	1123	2581	5675	7631	######	21	Swissprot_feature_table	Domain
54	PF00053	Laminin_EGF	Laminin EGF domain	This family is like Pfam:PF00008 but has 8 conserved cysteines instead of six.	72	114972	65	540	4041	49.5	30	18.54	183606	16230	36232	88373	117318	######	27	Swissprot_feature_table	Domain
55	PF00054	Laminin_G_1	Laminin G domain	NULL	21	14185	54	487	2356	131.1	24	13.02	22419	1815	4401	10692	14478	######	26	Swissprot_feature_table	Domain
56	PF00055	Laminin_N	Laminin N-terminal (Domain VI)	NULL	119	8854	22	483	763	222	32	15.56	14023	1136	2757	6776	8984	######	20	Swissprot_feature_table	Domain
57	PF00056	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 dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.	24	18809	991	7889	145	138.8	30	42.11	69814	2796	8507	16712	26422	######	26	Overington enriched	Domain
58	PF00057	Ldl_recept_a	Low-density lipoprotein receptor domain class A	NULL	33	138677	222	498	5081	38	41	15.83	216911	21955	45836	104088	141124	######	21	Swissprot_feature_table	Repeat
59	PF00058	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 [2].	19	61764	159	483	3074	41.7	31	14.33	98729	6823	16754	45048	62087	######	20	Swiss-Prot	Repeat
60	PF00059	Lectin_C	Lectin C-type domain	This family includes both long and short form C-type	53	65241	1158	944	2238	107.3	21	29.76	104650	11628	23060	50933	66933	######	24	Swissprot_feature_table	Domain
61	PF00060	Lig_chan	Ligand-gated ion channel	This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.	43	21543	1387	959	330	256.9	23	30.91	35057	3969	8883	17337	22711	######	29	Blastp NMZ1_HUMAN	Family
62	PF00061	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 functional grounds. The structure is an eight-stranded beta barrel.	155	9209	1143	500	98	129	18	70.27	16556	1021	2786	6778	9282	######	26	Prosite and HMM_iterative_training	Domain
63	PF00062	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.	12	2181	1437	337	38	115.9	36	66.1	4353	256	709	1503	2232	######	23	Overington and HMM_iterative_training	Domain
64	PF00063	Myosin_head	Myosin head (motor domain)	NULL	16	47835	306	1560	1422	505.6	31	40.8	82872	7221	17293	36672	48855	######	24	Blastp MYSA_HUMAN/1-840	Domain
65	PF00064	Neur	Neuraminidase	Neuraminidases cleave sialic acid residues from glycoproteins. Belong to the sialidase family - but this alignment does not generalise to the other sialidases. Structure is a 6-sheet beta propeller.	3	37	501	32	1	318.7	48	72.06	100112	43	47	48	51	######	21	Overington and HMM_iterative_training	Repeat
66	PF00066	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 [1] and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase [2].	104	7697	55	541	1655	35.6	41	4.83	13012	1226	2533	5847	7789	######	20	Swissprot_feature_table	Domain
67	PF00067	p450	Cytochrome P450	Cytochrome P450s are haem-thiolate proteins [6] 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 relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6].	50	213489	2175	5038	2142	340.7	17	78.98	429127	31772	98434	178969	256957	######	25	Overington and HMM_iterative_training	Domain
68	PF00068	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 venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognised. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognises both families.	111	2982	525	462	31	105.6	35	58.05	6921	503	1017	2296	3063	######	22	Overington and HMM_iterative_training	Domain
69	PF00069	Pkinase	Protein kinase domain	NULL	38	636438	6176	7459	13393	241.4	21	36.71	1154676	112033	280166	517261	703019	######	28	Unknown	Domain
70	PF00070	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.	90	382	175	269	51	66.6	23	16.59	991	138	237	373	497	######	30	Prosite	Domain
71	PF00071	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 Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. 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 [1].	60	116397	1819	1946	1584	150.8	29	56.08	203376	22410	50134	91449	120446	######	25	Swissprot	Domain
72	PF00072	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.	52	391374	790	8295	9932	112.3	25	29.26	1766993	47801	188590	406863	715567	######	27	Prodom	Domain
73	PF00073	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 recognised. 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 8-stranded beta sandwich. Variations (one or two extra strands) occur.	49	295	1690	195	61	139	15	10.26	110539	282	282	294	294	######	23	Overington and HMM_iterative_training	Domain
74	PF00074	RnaseA	Pancreatic ribonuclease	Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices.	140	1876	694	194	16	114.1	27	69.8	3082	129	458	1262	1863	######	23	Overington and HMM_iterative_training	Domain
75	PF00075	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.	23	18650	574	7358	888	135.5	24	30.45	93946	10793	15477	21736	29183	######	27	Swissprot; SCOP and HMM_iterative_training	Domain
76	PF00076	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 consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	68	370166	1349	3091	3801	67.4	23	22.58	607422	60121	151111	282223	384008	######	25	Published_alignment	Domain
77	PF00077	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 (Pfam:PF00026).	8	2204	1782	390	416	97.2	21	12.42	352950	1464	1952	2277	2574	######	23	Eddy SR	Domain
78	PF00078	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.	69	100689	938	4608	5615	170.6	15	25.35	632510	44771	78101	104293	123620	######	30	Published_alignment and HMM_iterative_training	Domain
79	PF00079	Serpin	Serpin (serine protease inhibitor)	Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.	113	20221	498	1889	177	302.3	24	83.75	43699	3608	8576	16502	21884	######	23	Overington and HMM_iterative_training	Domain
80	PF00080	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 disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold.	398	8329	869	3710	116	130.7	31	58.57	25320	1621	4033	7424	11304	######	23	Overington and HMM_iterative_training	Domain
81	PF00081	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 hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?	20	11790	521	7325	77	83.5	41	37.9	49862	1770	5659	11308	19175	######	25	Overington and HMM_iterative_training	Domain
82	PF00082	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 Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.	44	62667	659	7106	2336	303	20	44.22	191774	9445	29900	58444	89086	######	25	Overington	Domain
83	PF00083	Sugar_tr	Sugar (and other) transporter	NULL	33	129815	42	5845	1191	360	17	79.51	302041	17950	52278	100978	161171	######	27	Prosite hmmls-iteration	Family
84	PF00084	Sushi	Sushi repeat (SCR repeat)	NULL	32	132661	716	572	2483	56.7	26	30.82	215470	17081	38814	96551	134575	######	23	Swissprot_feature_table	Domain
85	PF00085	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.	34	80736	676	9088	970	101.2	23	41.25	219851	14392	37473	70868	106116	######	23	Prosite	Domain
86	PF00086	Thyroglobulin_1	Thyroglobulin type-1 repeat	Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation [2]. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.	165	13946	45	472	589	66.4	30	19.44	24890	2526	5186	10805	14328	######	21	Swissprot_feature_table	Domain
87	PF00087	Toxin_TOLIP	Snake toxin and toxin-like protein	This family predominantly includes venomous neurotoxins and cytotoxins from snakes, but also structurally similar (non-snake) toxin-like proteins (TOLIPs) such as Lymphocyte antigen 6D and Ly6/PLAUR domain-containing protein. Snake toxins are short proteins with a compact, disulphide-rich structure. TOLIPs have similar structural features (abundance of spaced cysteine residues, a high frequency of charge residues, a signal peptide for secretion and a compact structure) but, are not associated with a venom gland or poisonous function. They are endogenous animal proteins that are not restricted to poisonous animals [1].	4	623	67	216	8	72.7	31	55.86	1878	89	192	495	647	######	24	Overington	Domain
88	PF00088	Trefoil	Trefoil (P-type) domain	NULL	192	4462	53	504	247	42.9	33	6.34	7265	891	1615	3629	4654	######	21	Swissprot_feature_table	Domain
89	PF00089	Trypsin	Trypsin	NULL	70	76462	3278	2833	2023	204.6	25	53.4	156981	13899	31198	61206	84736	######	29	SCOP and Prosite	Domain
90	PF00090	TSP_1	Thrombospondin type 1 domain	NULL	24	63967	219	583	3437	49.5	34	10.76	104636	14309	24279	51747	66704	######	22	Published_alignment	Domain
91	PF00091	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 envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.	87	31772	2701	8702	367	177.9	36	42.93	120720	6070	14912	27484	40045	######	28	Prosite	Domain
92	PF00092	VWA	von Willebrand factor type A domain	NULL	127	63476	351	6291	3269	171.6	19	29.48	146161	9608	23957	51986	74201	######	31	Prodom	Domain
93	PF00093	VWC	von Willebrand factor type C domain	The high cutoff was used to prevent overlap with Pfam:PF00094.	19	22367	7	464	794	58.6	34	11.93	36084	2608	6226	16070	22580	######	21	Published_alignment	Domain
94	PF00094	VWD	von Willebrand factor type D domain	Swiss:P17554 contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.	40	22690	31	579	2293	144.4	22	18.98	37435	3849	8366	18218	23276	######	28	Dotter	Domain
95	PF00095	WAP	WAP-type (Whey Acidic Protein) 'four-disulfide core'	WAP belongs to the group of Elafin or elastase-specific inhibitors.	419	9552	27	477	519	44.5	35	14.91	16110	1995	3403	7441	9750	######	24	Swissprot_feature_table	Domain
96	PF00096	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 stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].	159	1201914	586	1648	14182	23.1	41	20.45	1783352	155577	362801	822960	1209189	######	29	Boehm S	Domain
97	PF00097	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 [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].	35	34770	37	1614	1326	43.6	32	7.03	50099	4425	10063	18822	25347	######	28	Swissprot_feature_table	Domain
98	PF00098	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.	79	62734	88	1680	2213	17.7	43	5.45	203238	15514	34258	52154	66850	######	26	Overington and HMM_iterative_training	Domain
99	PF00100	Zona_pellucida	Zona pellucida-like domain	NULL	337	12634	31	476	571	230.9	17	38.14	22076	2149	4972	10256	13166	######	26	Swissprot_feature_table	Family
100	PF00101	RuBisCO_small	Ribulose bisphosphate carboxylase, small chain	NULL	82	2175	363	819	27	98.2	36	57.22	7919	334	1207	2078	3327	######	23	Swissprot	Domain