Ribosomal protein L11, RNA binding domain	PF00298
Domain of unknown function (DUF392). A eukaryotic specific domain of undetermined function.`	PF04128
Mammalian defensin	PF00323
TAP C-terminal domain. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nucl	PF03943
Uncharacterized LmbE-like protein, COG2120	PF02585
Prp18 domain. The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the seque	PF02840
Delta 1-pyrroline-5-carboxylate reductase	PF01089
Exportin-t. Exportin-t is a specific mediator of tRNA export. RanGTP-binding, importin beta-related factor with predominantly nuclear localization. It shuttles rapidly between nucleus and between nucleus and cytoplasm and interacts with nuclear pore compl	PF04150
TFIIE alpha subunit	PF02002
Adenosine/AMP deaminase	PF00962
Fibronectin type II domain	PF00040
UvrD/REP helicase. 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 t	PF00580
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	PF01255
pfam02937, COX6C, Cytochrome c oxidase subunit VIc. 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 cytochrome c oxidase subunit VIc	PF02937
Cytochrome b(N-terminal)/b6/petB	PF00033
Putative diphthamide synthesis protein. One member is a candidate tumour 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 s	PF01866
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 modi	PF01472
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: T	PF01833
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	PF00570
Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site i	PF02404
Sodium / potassium ATPase beta chain	PF00287
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 homophili	PF01049
tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits	PF03484
DNA / pantothenate metabolism flavoprotein. The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism	PF04127
Metalloenzyme of unknown function DUF136. This family of archaeal proteins has no known function. However they appear to be related to a large superfamily of metalloenzymes	PF02004
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	PF02257
Protein-arginine deiminase (PAD). Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes EC:3.5.3.15 catalyse the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-a	PF03068
Eukaryotic DNA topoisomerase I, DNA binding fragment. 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 rec	PF02919
Peptidase family M28D	PF03570
EPTP domain. Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. This presumed domain has no known function,	PF03736
G10 protein	PF01125
Respiratory-chain NADH dehydrogenase 51 Kd subunit	PF01512
Osteopontin	PF00865
Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn	PF02902
TASK K+ channel	PF02034
Domain of unknown function (DUF339). This family of small proteins are uncharacterised	PF03937
KH domain. KH motifs can bind RNA in vitro . Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia	PF00013
Gamma interferon inducible lysosomal thiol reductase (GILT). This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similari	PF03227
Serotonin (5-HT) neurotransmitter transporter, N-terminus	PF03491
Inner centromere protein, ARK binding region. This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregati	PF03941
Adrenomedullin	PF02039
Glycosyl hydrolase family 85. Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates	PF03644
Beta-ketoacyl synthase, C-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone sythase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains	PF02801
1	PF02364
Domain of unknown function. This putative domain is found in members of the Dicer protein family. This protein is a dsRNA nuclease that is involved in RNAi and related processes. This domain of about 100 amino acids has no known function, but does contain	PF03368
FGGY family of carbohydrate kinases, C-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain	PF02782
Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases	PF02852
Transposase family tnp2	PF02992
UvrD/REP helicase. 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	PF00580
CAP protein	PF01213
Glycosyl transferase. 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	PF00535
Cytochrome C oxidase subunit II, transmembrane domain. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices	PF02790
Ribosomal RNA adenine dimethylase	PF00398
Plant PEC family metallothionein	PF02068
NAC domain	PF01849
Suppressor Mra1. The suppressor Mra1 is found in high-copy-number when Ras1 is mutated, that recovers the mating deficiency caused by the decrease of Ras1 activity. Mutational analysis in yeast suggests that the suppressor Mra1 is essential for cell growt	PF03587
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	PF02374
Paramyxovirus P phosphoprotein. This family consists of paramyxovirus P phosphoprotein from sendai virus and human and bovine parainfluenza viruses. The P protein is an essential part of the viral RNA polymerase complex formed form the P and L proteins.	PF01806
ATP P2X receptor	PF00864
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 su	PF02391
Nucleoplasmin. Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays	PF03066
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	PF00794
SH2 domain	PF00017
Uncharacterized ACR	PF02591
Myosin tail	PF01576
Aconitase C-terminal domain. Members of this family usually also match to pfam00330. This domain undergoes conformational change in the enzyme mechanism	PF00694
Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1)	PF03142
Glycosyl transferase family, a/b domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate	PF00591
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 acid	PF01063
MBOAT family. The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue	PF03062
Ribosomal L18ae protein family	PF01775
Malic enzyme, NAD binding domain	PF03949
Uncharacterized ACR, COG1490	PF02580
Apolipoprotein A1/A4/E family. These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I, Apolipoprotein A-IV, Apolipoprotein E	PF01442
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 catal	PF02022
Caldesmon	PF02029
Chlorohydrolase. This family consist of chlorohydrolase from the ATZ/TRZ family	PF01685
A20-like zinc finger. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation	PF01754
Nup133 nucleoporin. RNA undergoing nuclear export first encounters the basket of the nuclear pore. Nup133 is a nucleoporin accessible on the basket side of the pore	PF04044
Arp2/3 complex, 34kD subunit p34-Arc. Arp2/3 protein complex has been implicated in the control of actin polymerization in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p4	PF04045
ATP synthase B/B' CF(0)	PF00430
Sm protein. 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 splic	PF01423
Uncharacterized BCR, YceG family COG1559	PF02618
Uncharacterised protein family (Hly-III / UPF0073). Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It is not clear if all the members of this family are hemolysins. It h	PF03006
Exportin-t. Exportin-t is a specific mediator of tRNA export. RanGTP-binding, importin beta-related factor with predominantly nuclear localization. It shuttles rapidly between nucleus and between nucleus and cytoplasm and interacts with nuclear pore comp	PF04150
Acetyltransferase (GNAT) family	PF00583
Origin recognition complex subunit 2. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in	PF04084
Homocysteine S-methyltransferase. This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases also known EC:2.1.1.13,	PF02574
Carboxylesterase	PF00135
Ferrous iron transport protein B	PF02421
ZIP Zinc transporter. The ZIP family consists of zinc transport proteins and many putative metal transporters. The main contribution to this family is from the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the p	PF02535
Surfactant protein B	PF03489
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	PF00628
Putative tyrosine phosphatase family. This family consists of putative tyrosine phosphatase proteins, this function is inferred from several sequences at the top of the noise, EC:3.1.3.48	PF03162
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	PF00430
Uncharacterized protein family UPF0004. This family is the N terminal half of the family. The C-terminal half has been shown to be related to MiaB proteins	PF00919
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 an	PF00086
Uncharacterised protein (DUF314)	PF03757
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 gro	PF01648
Sof1-like domain. Sof1 is essential for cell growth and is a component of the nucleolar rRNA processing machinery	PF04158
Transcription initiation factor IIF	PF02270
GNT-I family. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) EC:2.4.1.101 transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis of	PF03071
Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis	PF00413
NAD-dependent glycerol-3-phosphate dehydrogenase	PF01210
Serine carboxypeptidase	PF00450
Glycosyl hydrolase family 65 central catalytic domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phos	PF03632
Retinoblastoma-associated protein A domain. This domain has the cyclin fold as predicted	PF01858
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 hydroge	PF01179
DnaJ C terminal region. This family consists of the C terminal region form the DnaJ protein. Although the function of this region is unknown, it is always found associated with pfam00226 and pfam00684. DnaJ is a chaperone associated with the Hsp70 heat-sh	PF01556
Dienelactone hydrolase family	PF01738
Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNa	PF03372
Dopey, N-terminal domain. DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organization of multicellular structures in the filamentous fungus Aspergillus nidulans. DopA homologues are found in	PF04118
Indoleamine 2,3-dioxygenase	PF01231
CBS domain. CBS domains are small intracellular modules of unknown function. They are mostly found in 2 or four copies within a protein. Pairs of CBS domains dimerise to form a stable globular domain. Two CBS domains are found in inosine-monophosphate de	PF00571
Treacher Collins syndrome protein Treacle	PF03546
Carbamoyl-phosphate synthase L chain, ATP binding 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 biosy	PF02786
Otx1 transcription factor	PF03529
TT viral orf 1. TT virus (TTV)	PF02956
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-fo	PF01821
HNH endonuclease	PF01844
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 typ	PF00036
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 -	PF00239
60s Acidic ribosomal protein. This family includes archaebacterial L12, eukaryotic P0, P1 and P2	PF00428
Domain of Unknown Function (DUF408)	PF04181
Lipoxygenase	PF00305
SpoVR like protein. Bacillus subtilis stage V sporulation protein R is involved in spore cortex formation. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR	PF04293
Uncharacterised protein family (UPF0170). This family contains uncharacterised eukaryotic proteins of around 250 amino acids	PF03679
Interferon gamma	PF00714
Orexin receptor type 2	PF03827
IMP4 family. This family includes IMP4, which is involved ribosomal RNA processing	PF01945
7 transmembrane receptor (rhodopsin family)	PF00001
tRNA synthetases class I (R). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only arginyl tRNA synthetase	PF00750
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 enzyme	PF00062
Laminin N-terminal (Domain VI)	PF00055
Biotin-requiring enzyme. This family covers two subfamilies, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the model may not currently recognise the Glycine cleavage system H proteins	PF00364
pfam02872, 5_nucleotidaseC, 5'-nucleotidase, C-terminal domain	PF02872
Glycosyl hydrolases family 2, sugar binding domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold	PF02837
Ribosomal L38e protein family	PF01781
ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function	PF00791
Prion/Doppel alpha-helical domain. The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the n	PF00377
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. These proteins contain three strongly conserved histidines in the putative trans	PF01694
eRF1 domain 1. The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 is known.	PF03463
Vps52 / Sac2 family. Vps52 complexes with Vps53 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events	PF04129
Phenazine biosynthesis-like protein. PhzC/PhzF is involved in dimerization of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family appears to be distantly related to pfam01678, including containing a weak internal	PF02567
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	PF01041
Ribosomal protein L32. This family includes ribosomal protein L32 from eukaryotes and archaebacteria	PF01655
Myelin proteolipid protein (PLP or lipophilin)	PF01275
Fringe-like. The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs	PF02434
Hus1-like protein. Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast. These proteins are known to form a stable complex in vivo. Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, a	PF04005
XPG N-terminal domain	PF00752
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 endop	PF01421
Domain of unknown function (DUF382). This domain is specific to the human splicing factor 3b subunit 2 and it's orthologs	PF04037
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 bin	PF02252
BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not b	PF00533
metallopeptidase family M24	PF00557
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. The family consists of various type I, II and III PIP5K enzymes. PIP5K catal	PF01504
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 lipovitell	PF01347
SCP-like extracellular protein	PF00188
Tubulin/FtsZ family. This family includes the tubulin alpha	PF00091
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	PF01645
Tubulin/FtsZ family, C-terminal 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 bacte	PF03953
Galactose-1-phosphate uridyl transferase, N-terminal domain. SCOP reports fold duplication with C-terminal domain. Both involved in Zn and Fe binding	PF01087
pfam02920, integrase_DNA, DNA binding domain of tn916 integrase	PF02920
HELP motif. The HELP (Hydrophobic ELP) motif is found in EMAP and EMAP-like proteins (ELPs). The HELP motif contains a predicted transmembrane helix so probably does not form a globular domain. It is also not clear if these proteins localize to membranes	PF03451
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 famil	PF00031
PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain	PF02758
Kinase associated domain 1	PF02149
Spore germination protein	PF03845
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 comple	PF01728
RNA polymerase alpha subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Members of this family	PF00623
Transglutaminase family	PF00868
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	PF01907
Sec34-like family. Sec34 and Sec35 form a sub-complex, in a seven protein complex that includes Dor1 (PFAM:PF04124). This complex is thought to be important for tether vesicles to the Golgi	PF04136
Iron/manganese superoxide dismutases, C-terminal domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. I	PF02777
SCP-like extracellular protein. This domain is also found in prokaryotes	PF00188
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 ha	PF01769
CutA1 divalent ion tolerance protein. Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide var	PF03091
LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar	PF02886
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 euk	PF01248
Helper component proteinase. This protein is found in genome polyproteins of potyviruses	PF00851
Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions	PF00085
Exo70 exocyst complex subunit. The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae , Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst	PF03081
CG-1 domain. CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are asso	PF03859
Tub family	PF01167
pfam02880, PGM_PMM_III, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III	PF02880
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	PF01391
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 the three reticulon isoforms and their homologues	PF02453
Tricarboxylate carrier	PF03820
Sec23/Sec24 family. 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/24	PF04105
Las1-like. Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth	PF04031
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 bu	PF00550
Autophagy protein Apg5. Apg5p is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway	PF04106
eRF1 domain 2. The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 is known.	PF03464
ssDNA binding protein. This protein is found in herpesviruses and is needed for replication	PF00747
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 some members, proteolysis has shown that the Peptidyl-alp	PF01436
TAP C-terminal domain. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nucle	PF03943
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 for one member that the amino terminal 93 amino acids are necessary and sufficient	PF00861
Thymidylate synthase	PF00303
Coproporphyrinogen III oxidase	PF01218
Allantoicase repeat. This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-	PF03561
Formin Homology 2 Domain	PF02181
Dihydroorotase-like. This family are predicted to adopt a TIM barrel fold	PF00744
Phosphatidylinositol 3- and 4-kinase	PF00454
pfam02886, LBP_BPI_CETP_C, LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar	PF02886
Double-stranded RNA binding motif. 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 localization of at least five different mRNAs in the ea	PF00035
Thymidylate kinase	PF02223
MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known	PF01967
Globin	PF00042
UTP--glucose-1-phosphate uridylyltransferase. This family consists of UTP--glucose-1-phosphate uridylyltransferases, EC:2.7.7.9. Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uri	PF01704
UDP-glucoronosyl and UDP-glucosyl transferase	PF00201
Ribosomal protein L23, N-terminal domain. The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a	PF03939
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 barre	PF02219
Serum albumin family	PF00273
dUTPase. dUTPase hydrolyzes dUTP to dUMP and pyrophosphate	PF00692
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	PF01798
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	PF01734
SET domain. 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 dom	PF00856
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	PF00607
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 transporte	PF00005
Histone deacetylase family. 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	PF00850
Sterile alpha motif (SAM)/Pointed domain	PF02198
Uncharacterised protein family UPF0066	PF01980
Arginyl tRNA synthetase N terminal domain. This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA r	PF03485
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 splic	PF01057
Hexokinase. Hexokinase contains two structurally similar domains represented by this family and PFAM:PF03727. Some members of the family have two copies of each of these domains	PF00349
Flavodoxin	PF00258
Enolase, N-terminal domain	PF03952
Glutamate-cysteine ligase. This family represents the catalytic subunit of glutamate-cysteine ligase (E.C. 6.3.2.2), also known as gamma-glutamylcysteine synthetase (GCS). This enzyme catalyses the rate limiting step in the biosynthesis of glutathione. T	PF03074
Phosphoglucomutase/phosphomannomutase, C-terminal domain	PF00408
Elongation factor 1 gamma, conserved domain	PF00647
Fumble. Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organization, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isofor	PF03630
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	PF00679
Ribosomal S3Ae family	PF01015
Eukaryotic protein kinase domain	PF00069
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 a protein which does not contain this domain. This domain is found	PF01595
Nuclear transport factor 2 (NTF2) domain. This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins	PF02136
RNA polymerase Rpb5, N-terminal domain. Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. The N-terminal domain is involved in DNA binding and is part of th	PF03871
Synaptogyrin. This family of proteins is distantly related to pfam01284	PF03218
DAN domain. This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerb	PF03045
pfam02947, flt3_lig, flt3 ligand. The flt3 ligand is a short chain cytokine with a 4 helical bundle fold	PF02947
TCP-1/cpn60 chaperonin family. This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family	PF00118
Retroviral aspartyl protease. Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein	PF00077
C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system	PF00386
V-type ATPase 116kDa subunit family	PF01496
MOSC N-terminal beta barrel domain. This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold	PF03476
Filamin/ABP280 repeat	PF00630
eRF1 domain 3. The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 is known.	PF03465
Glutamine synthetase, catalytic domain	PF00120
ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum m	PF03155
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	PF02237
ATP synthase subunit C	PF00137
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	PF00852
Non-repetitive/WGA-negative nucleoporin. This is a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and protein	PF03177
Aminotransferase class-V	PF00266
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 b	PF00096
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-phospha	PF00215
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	PF00530
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-oligomerisation	PF02023
Putative zinc finger in N-recognin	PF02207
ADP-ribosylglycohydrolase. This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisi	PF03747
ENT domain. This presumed domain is named after Emsy N Terminus (ENT). Emsy is a protein that is amplified in breast cancer and interacts with BRCA2. The N terminus of this protein is found to be similar to other vertebrate and plant proteins of unknown	PF03735
Senescence marker protein-30 (SMP-30). SMP-30, also known as regucalcin, seems to play a critical role in the highly differentiated functions of the liver and kidney and to exert a major impact on Ca2+ homeostasis	PF03758
BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not	PF00533
Protein prenyltransferase alpha subunit repeat	PF01239
RNA polymerases M/15 Kd subunit	PF02150
Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes	PF00338
Actin	PF00022
Fibronectin type III domain	PF00041
CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a	PF04103
RNA polymerase Rpb4	PF03874
Leo1-like protein. Members of this family are part of the Paf1/RNA polymerase II complex. The Paf1 complex probably functions during the elongation phase of transcription	PF04004
Tctex-1 family. Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction	PF03645
Phosphatidylinositol-specific phospholipase C, Y domain. This associates with pfam00388 to form a single structural unit	PF00387
FHIPEP family	PF00771
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 thi	PF00975
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	PF00179
Gamma-glutamyltranspeptidase	PF01019
GDNF receptor family. This family consists of Glial-cell-line-derived neurotrophic factor (GDNF) and neurturin (NTN) these receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuro	PF02351
GTP cyclohydrolase I. This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins	PF01227
Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to	PF03096
FMN-dependent dehydrogenase	PF01070
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	PF01454
Calreticulin family	PF00262
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. Th	PF01593
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	PF01846
Saccharopine dehydrogenase. This family comprised of three structural domains that can not be separated in the linear sequence. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF). The saccharopin	PF03435
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	PF01477
Met-10+ like-protein. The methionine-10 mutant allele of N. crassa codes for a protein of unknown function. However, homologous proteins have been found in yeast suggesting this protein may be involved in methionine biosynthesis, transport and/or utilizat	PF02475
MH2 domain. This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins	PF03166
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	PF00835
mRNA capping enzyme, catalytic domain. This family represents the ATP binding catalytic domain of the mRNA capping enzyme	PF01331
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 fac	PF01008
Fibrinogen beta and gamma chains, C-terminal globular domain	PF00147
Uncharacterised protein family (UPF0136). This family of short membrane proteins are as yet uncharacterised	PF03647
Asparagine synthase. This family is always found associated with pfam00310. Members of this family catalyse the conversion of aspartate to asparagine	PF00733
Sodium:solute symporter family	PF00474
Nucleoside diphosphate kinase	PF00334
ssDNA binding protein	PF00747
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	PF01546
Na+ dependent nucleoside transporter. This family consists of nucleoside transport proteins, like a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane, or a Na+-dependent nucleoside transporter selective for pyrimidin	PF01773
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, eithe	PF01725
Platelet activating factor acetylhydrolase. Platelet activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. At least three intracellul	PF02266
Proline dehydrogenase	PF01619
STAT protein, DNA binding 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. T	PF02864
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 in	PF02271
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 fol	PF02244
Oxysterol-binding protein	PF01237
CAAX amino terminal protease family. Members of this family are probably proteases. the family contains CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidin	PF02517
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 subun	PF02270
mbt repeat. The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino ter	PF02820
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 hydrog	PF01179
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	PF00573
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 b	PF00550
Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family	PF00249
Acyl-ACP thioesterase. This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolyzing an acyl group on a fatty acid	PF01643
Barrier to autointegration factor. The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration	PF02961
Rotavirus non-structural protein NSP3. This family consist of rotaviral non-structural RNA binding protein 34 (NS34 or NSP3). The NSP3 protein has been shown to bind viral RNA. The NSP3 protein consists of 3 conserved functional domains	PF01665
Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signaling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes,	PF03921
Gag P30 core shell protein. This protein is the viral core shell protein. P30 is essential for viral assembly	PF02093
Fumarylacetoacetate (FAA) hydrolase family. This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the ty	PF01557
Mitochondrial import inner membrane translocase subunit Tim17. The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim1	PF02466
Sulfotransferase proteins	PF00685
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 analog	PF01770
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 decad	PF01641
Sterol desaturase. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain many conserved histidine residues.	PF01598
Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the mo	PF03016
Uncharacterised protein family (UPF0131). This family of proteins are uncharacterised, however BtrG is part of a butirosin-biosynthetic gene cluster from Bacillus circulans	PF03674
CTF/NF-I family	PF00859
Prenylated rab acceptor (PRA1)	PF03208
pfam02882, THF_DHG_CYH_C, Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain	PF02882
von Willebrand factor type A domain	PF00092
GTP1/OBG family	PF01018
Phosphatidate cytidylyltransferase	PF01148
Dolichyl-phosphate-mannose-protein mannosyltransferase	PF02366
Mo25 protein family	PF03204
Arylesterase. This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyses organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity.	PF01731
Glutathione S-transferase, C-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but are not GSTs: * S-crystallins from squid. Similarity to GST previously noted. * Eukaryotic elongation	PF00043
Thymosin beta-4 family	PF01290
FERM domain (Band 4.1 family). This domain has been renamed the FERM domain, which stands for F for 4.1, E for Ezrin, R for radixin and M for moesin	PF00373
IMP dehydrogenase / GMP reductase. This family is involved in biosynthesis of guanosine nucleotide biosynthesis. Members of this family contain a TIM barrel structure. The alignment does not contain the whole TIM barrel domain. The alignment is truncated	PF00478
Transcription initiation factor IIA, gamma subunit, beta-barrel 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 multi	PF02751
Appr-1"-p processing enzyme family	PF01661
Phosphoribulokinase / Uridine kinase family	PF00485
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 involv	PF00098
MIZ zinc finger	PF02891
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 d	PF00665
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	PF01426
Herpesvirus glycoprotein D. Herpesviruses are dsDNA viruses with no RNA stage. This is a family consists of 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	PF01537
HCO3- transporter family. This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-	PF00955
Zinc finger, C3HC4 type (RING finger)	PF00097
Cation-dependent mannose-6-phosphate receptor	PF02157
Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold	PF02799
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 instan	PF02350
2-oxo acid dehydrogenases acyltransferase (catalytic domain). These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain	PF00198
Paralemmin	PF03285
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	PF00645
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	PF01380
Syndecan domain. Syndecans are transmembrane heparin sulfate proteoglycans which are implicated in the binding of extracellular matrix components and growth factors	PF01034
Cytochrome c oxidase subunit Vb	PF01215
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 metabolism, including nuclear transcription, pre mRNA	PF00270
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	PF00264
DNA repair protein Rad4	PF03835
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 ty	PF01507
Seven in absentia protein family. The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina result	PF03145
Copper amine oxidase, N2 domain. This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitou	PF02727
Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure	PF00023
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 d	PF01483
KH domain. KH motifs probably bind RNA directly. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia	PF00013
Vitelline membrane outer layer protein I (VOMI). VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furt	PF03762
NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossman fold	PF03446
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 p1	PF02229
TNFR/NGFR cysteine-rich region	PF00020
Low-density lipoprotein receptor domain class A	PF00057
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 at least one member, proteolysis has shown that the Peptid	PF01436
AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance	PF00873
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 utilise ATP others use GTP	PF00549
[2Fe-2S] binding domain	PF01799
WIF domain. The WIF domain is found in the RYK tyrosine kinase receptors and WIF the Wnt-inhibitory- factor. The domain is extracellular and and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it	PF02019
Fibroblast growth factor. Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. These growth factors cause dimerisation of their tyrosine kinase receptors leading to intracellular signaling.	PF00167
KCNQ1 voltage-gated potassium channel	PF03520
Raf-like Ras-binding domain	PF02196
Gpi16 subunit, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to new	PF04113
Dihydropyridine sensitive L-type calcium channel (Beta subunit)	PF00774
HYR domain. This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is unce	PF02494
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 cellu	PF01416
Phosphoenolpyruvate carboxykinase. Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate	PF00821
Nucleoporin interacting componentent	PF04097
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 c	PF02010
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	PF01400
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	PF01067
Elongation factor G, domain IV. This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold	PF03764
Rhabdovirus Non-virion protein. Infectious hematopoietic necrosis virus (IHNV) is a member of the family Rhabdoviridae. The non-virion protein (NV) is coded for by one of the six genes of the IHNV genome, but is absent in vesiculovirus -like rhabdovirus	PF02484
Interleukin 2	PF00715
Cell division protein. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP	PF00735
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 bacter	PF00149
Interleukin 4	PF00727
Interleukin 5	PF02025
3'5'-cyclic nucleotide phosphodiesterase	PF00233
Fumarylacetoacetate (FAA) hydrolase family. This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyr	PF01557
Lecithin:cholesterol acyltransferase. Lecithin:cholesterol acyltransferase (LACT) is involved in extracellular metabolism of plasma lipoproteins, including cholesterol	PF02450
Serpin (serine protease inhibitor). Structure is a multi-domain fold containing a bundle of helices and a beta sandwich	PF00079
Dihydroorotate dehydrogenase	PF01180
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	PF02359
Eukaryotic glutathione synthase	PF03199
Telomere-binding protein alpha subunit, N-terminal domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Al	PF02307
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 i	PF02271
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 invol	PF00098
Uncharacterized protein PaaI, COG2050	PF02584
Cytochrome P450. Cytochrome P450s are involved in the oxidative degradation of various compounds. Particularly well known for their role in the degradation of environmental toxins and mutagens. Structure is mostly alpha, and binds a heme cofactor	PF00067
2Fe-2S iron-sulfur cluster binding domain	PF00111
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 acti	PF01433
Clathrin adaptor complex small chain	PF01217
Phospholipase A2 inhibitor	PF02988
Thiamine monophosphate synthase/TENI. Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to y	PF02581
Rieske [2Fe-2S] domain. The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines	PF00355
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	PF01419
Starch binding domain	PF00686
Repeat in HS1/Cortactin. The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018	PF02218
RNA polymerase A/beta'/A" subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This family includ	PF01854
Dehydratase family	PF00920
Keratin, high sulfur B2 protein. High sulfur proteins are cysteine-rich proteins synthesized during the differentiation of hair matrix cells, and form hair fibers in association with hair keratin intermediate filaments. This family has been divided up in	PF01500
Phosphatidylinositol-specific phospholipase C, X domain. This associates with pfam00387 to form a single structural unit	PF00388
GAF domain. Domain present in phytochromes and cGMP-specific phosphodiesterases	PF01590
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 dimerisation	PF01342
Clp protease. The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. One member has lost all of these active site residues and is therefore inactive, others contain one or two l	PF00574
Transport protein particle (TRAPP) component, Bet3. TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is an 800kDa that contains at least 10 subunits	PF04051
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	PF02421
Fork head domain	PF00250
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	PF01729
Domain of unknown function DUF128. This archaebacterial protein family has no known function. The domain is found duplicated in some members	PF01995
Peptide hormone. This family contains glucagon, GIP, secretin and VIP	PF00123
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 metabolism. The ability of this widely distributed heterotrimeric enzym	PF01603
Alpha amylase, C-terminal all-beta 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 betwe	PF02806
Phosphatidyl serine synthase. Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyses the replacement of the head group of a phospholipid (phosp	PF03034
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	PF01597
Pyroglutamyl peptidase	PF01470
PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins	PF04012
B12 binding domain. This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle	PF02607
Actin interacting protein 3	PF03915
YT521-B-like family. This family of poorly characterised proteins contains YT521-B, a putative splicing factor from Rat. YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment	PF04146
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	PF02383
bZIP transcription factor	PF00170
Calcium-activated SK potassium channel	PF03530
Insulin/IGF/Relaxin family. Superfamily includes insulins	PF00049
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	PF01740
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	PF00730
Up-frameshift suppressor 2. Transcripts harboring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-actin	PF04050
Prenyltransferase and squalene oxidase repeat	PF00432
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	PF01429
Tetraspanin family	PF00335
CutA1 divalent ion tolerance protein. Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide vari	PF03091
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 analogu	PF01770
Uncharacterized ACR, COG2106	PF02598
Ribosomal prokaryotic L21 protein	PF00829
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 hav	PF01769
RNA polymerase Rpb8. Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits	PF03870
Rer1 family. RER1 family protein are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex	PF03248
pfam02898, NO_synthase, Nitric oxide synthase, oxygenase domain	PF02898
Core binding factor beta subunit. Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has b	PF02312
Villin headpiece domain	PF02209
Histidine acid phosphatase	PF00328
MOSC domain. The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutel	PF03473
Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active center disulfide bond. Some members with only the active site are not separated from the noise	PF00085
ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain	PF01388
Minor capsid protein VI. This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation	PF02993
Nuclear transition protein 2	PF01254
Polyphosphate kinase. Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules	PF02503
Granin (chromogranin or secretogranin)	PF01271
TruB family pseudouridylate synthase (N terminal domain)	PF01509
LGN motif, putative GEF specific for G-alpha GTPase	PF02188
Ribosomal family S4e	PF00900
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 GlcN	PF01762
ATP1G1/PLM/MAT8 family	PF02038
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. The family consists of various type I, II and III PIP5K enzymes. PIP5K cata	PF01504
Arylesterase. This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyses organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity. H	PF01731
MutS family, N-terminal putative DNA binding domain. This family consists of the N-terminal region of proteins in the mutS family of DNA mismatch repair proteins and is found associated with pfam00488 located in the C-terminal region. The mutS family of p	PF01624
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. T	PF01593
mbt repeat. The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino te	PF02820
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	PF01130
Cornichon protein	PF03311
Gpi16 subunit, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to ne	PF04113
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 famil	PF01400
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 ha	PF01429
Transcription factor TFIID (or TATA-binding protein, TBP)	PF00352
C.elegans Srg family integral membrane protein	PF02118
Putative diphthamide synthesis protein. One member is a candidate tumour 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 sy	PF01866
Dihydrofolate reductase	PF00186
Cytochrome c oxidase subunit VIIc. 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 cytochrome c oxidase subunit VIIc. The yeast member of this family	PF02935
pfam02897, Peptidase_S9_N, Prolyl oligopeptidase, N-terminal beta-propeller domain. This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see pfam00326), excluding larger peptides and proteins from proteolysi	PF02897
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	PF01417
Transcription initiation factor TFIID subunit A	PF03847
MAM domain. An extracellular domain found in many receptors	PF00629
Glycosyltransferase family 28 C-terminal domain. The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). Structural analysis suggests the C-terminal domain conta	PF04101
PTN/MK heparin-binding protein family	PF01091
Ras family. Includes sub-families Ras	PF00071
Gap junction alpha-8 protein (Cx50)	PF03509
Protein of unknown function DUF51. This family contains members in prokaryotes and eukaryotes. None of the members has a known function	PF01871
pfkB family carbohydrate kinase. This family includes a variety of carbohydrate and pyrimidine kinases. The family includes phosphomethylpyrimidine kinase EC:2.7.4.7. This enzyme is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an es	PF00294
ATP-sulfurylase	PF01747
homogentisate 1,2-dioxygenase. Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme	PF04209
Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the mos	PF03016
Competence protein. Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. These proteins may tran	PF03772
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	PF01974
YDG/SRA domain. The function of this domain is unknown, it contains a conserved motif YDG after which it has been named	PF02182
HesB-like domain. This family includes HesB which may be involved in nitrogen fixation	PF01521
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 i	PF01491
S-100/ICaBP type calcium binding domain. The S-100 domain is a subfamily of the EF-hand calcium binding proteins	PF01023
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 i	PF01812
'Cold-shock' DNA-binding domain	PF00313
Replication factor-A protein 1, N-terminal domain	PF04057
Phospholipid methyltransferase. The S. cerevisiae phospholipid methyltransferase (EC:2.1.1.16) has a broad substrate specificity of unsaturated phospholipids	PF04191
Porphobilinogen deaminase, C-terminal domain	PF03900
pfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain. This domain has a ferredoxin-like fold	PF02913
Phenylalanine and histidine ammonia-lyase	PF00221
Uncharacterized ACR, COG2135	PF02586
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	PF02267
Multicopper oxidase. Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain	PF00394
Beta-ketoacyl synthase, N-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone sythase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.	PF00109
CXXC zinc finger. This domain contains eight conserved cysteine residues that bind to zinc. The CXXC domain is found in proteins that methylate cytosine, proteins that bind to methyl cytosine and HRX related proteins	PF02008
Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking. In particular, Vps26 assembles into a retromer complex with at least four other proteins Vp	PF03643
RNA recognition motif. (a.k.a. RRM	PF00076
Glycosyl hydrolase family 1	PF00232
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	PF02026
Polysaccharide biosynthesis protein. This is a family of diverse bacterial polysaccharide biosynthesis proteins including the CapD protein, WalL protein mannosyl-transferase and several putative epimerases (e.g. WbiI)	PF02719
Phosphoribosyl transferase domain. This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyltransferase EC:2.4.2.7, Hypoxanthine-guanine-xanthine phosphoribosyltransferase, Hypoxanthine phosph	PF00156
Bunyavirus glycoprotein G1. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-struc	PF03557
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	PF00688
MHCK/EF2 kinase domain family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a	PF02816
K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly	PF02214
Phosphoenolpyruvate carboxykinase	PF01293
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 enzyme	PF02274
Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS)	PF00788
Sodium:neurotransmitter symporter family	PF00209
Ephrin	PF00812
Dip2/Utp12 Family. This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2	PF04003
Zinc finger, C2H2 type	PF00096
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	PF01765
pfam02892, zf-BED, BED zinc finger	PF02892
moaA / nifB / pqqE family	PF01444
Asparaginase	PF01112
C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function	PF02928
WAP-type (Whey Acidic Protein) 'four-disulfide core'	PF00095
mRNA capping enzyme, large subunit	PF03291
Exo70 exocyst complex subunit. The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae , Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocys	PF03081
Ubiquitin carboxyl-terminal hydrolase, family 1	PF01088
Urotensin II	PF02083
Transglutaminase family, C-terminal ig like domain	PF00927
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 euka	PF01248
Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain	PF03129
ICE-like protease (caspase) p20 domain	PF00656
NLP/P60 family. The function of this domain is unknown. It is found in several lipoproteins	PF00877
NADH-ubiquinone/plastoquinone oxidoreductase chain 4L	PF00420
CAP-Gly domain. CAP stands for cytoskeleton-associated proteins	PF01302
C2 domain	PF00168
Polyprenyl synthetase	PF00348
Fibrillarin	PF01269
CIDE-N domain. This domain is found in CAD nuclease, and ICAD, the inhibitor of CAD nuclease. The two proteins interact through this domain	PF02017
Thiamine pyrophosphate enzyme, N-terminal TPP binding domain	PF02776
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 func	PF01432
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	PF01119
Zinc finger C-x8-C-x5-C-x3-H type (and similar)	PF00642
bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region	PF00170
Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine s	PF01916
YT521-B-like family. This family of poorly characterised proteins contains YT521-B, a putative splicing factor from Rat. YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment f	PF04146
BRCA2 repeat. The alignment covers only the most conserved region of the repeat	PF00634
Rpp14 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	PF01900
Mpp10 protein. This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevi	PF04006
Cytochrome c oxidase subunit Va. 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 cytochrome c oxidase subunit Va	PF02284
Ubiquitin fusion degradation protein UFD1. Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family inclu	PF03152
Non-repetitive/WGA-negative nucleoporin. This is a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins	PF03177
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	PF01509
Elongation factor Tu C-terminal domain. Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts	PF03143
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	PF00651
Prothymosin/parathymosin family. Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation	PF03247
Uncharacterised protein family (UPF0143). This family of uncharacterised proteins are integral membrane proteins. They may contain 4 transmembrane helices. The family contains a conserved arginine and histidine that may be functionally important	PF03694
Alkaline phosphatase	PF00245
Sulfotransferase. Chondroitin 6-sulfotransferase catalyses the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin	PF03567
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	PF00779
Ferrochelatase	PF00762
Nuclear pore protein 84 / 107. Nup84p forms a complex with five proteins, of which Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis	PF04121
Herpesvirus UL6 like	PF01763
Corticotropin-releasing factor family	PF00473
Respiratory-chain NADH dehydrogenase 24 Kd subunit	PF01257
Zinc finger	PF00097
Glutamyl-tRNAGlu reductase. This family use NADPH as a cofactor	PF00745
MA3 domain. Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains	PF02847
Glycosyl transferase	PF00953
GHMP kinases putative ATP-binding protein	PF00288
Gaa1-like, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly s	PF04114
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	PF01138
Domain of unknown function DUF221. This family consists of hypothetical transmembrane proteins none of which have any function, the aligned region is at 538 residues at maximum length	PF02714
Rap/ran-GAP	PF02145
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	PF01064
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	PF01463
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	PF01248
bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Thus, this family is probably related to pfam00170	PF03131
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 bi	PF01565
Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate	PF00834
Domain of unknown function (DUF227). This family includes a large number of drosophila proteins of unknown function. The family also includes several C. elegans proteins. The alignment contains many histidines and aspartates that are conserved, suggesting	PF02958
Ribosomal protein L30p/L7e. This family includes prokaryotic L30 and eukaryotic L7	PF00327
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 nit	PF00190
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 va	PF01755
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	PF00795
pfam02885, Glycos_trans_3N, Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate	PF02885
Gastrin/cholecystokinin family	PF00918
Tubulin/FtsZ family	PF00091
ThiF family. This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family	PF00899
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	PF02186
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 lysop	PF01735
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 structur	PF00014
Taurine catabolism dioxygenase TauD, TfdA family. This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli is a alpha-ketoglutarate-dependent taurine dioxygenase. This enzyme catalyses the oxygenolytic release of	PF02668
LEM3 (ligand-effect modulator 3) family / CDC50 family. Members of this family have been predicted to contain transmembrane helices. The family member LEM3 is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in respo	PF03381
Uncharacterized ACR, YagE family COG1723	PF02582
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	PF01805
SH3 domain	PF00018
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	PF00096
Macrophage migration inhibitory factor (MIF)	PF01187
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 adenylylsulfate reductase	PF00890
Jun-like transcription factor. The c-Jun NH(2)-terminal kinase (JNK) is a member of an evolutionarily conserved sub-family of mitogen-activated protein (MAP) kinases	PF03957
Uncharacterised protein family (UPF0120)	PF03715
Domain of unknown function UPF0099. This domain has no known function	PF01981
Spectrin repeat. Spectrin repeats 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 spectri	PF00435
Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT)	PF03982
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	PF01566
Casein	PF00363
Transglycosylase SLT domain. This family is distantly related to pfam00062	PF01464
Autophagy protein Apg9. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targetin	PF04109
Insulinase (Peptidase family M16)	PF00675
Neurokinin B	PF03823
Transposase. This family includes the mariner transposase	PF01359
Heavy-metal-associated domain	PF00403
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	PF00903
TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediat	PF03073
Mitochondrial import inner membrane translocase subunit Tim17. The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim	PF02466
Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member 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 C-termin	PF02984
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 bacte	PF00149
DHH family. It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ	PF01368
Spumavirus gag protein	PF03276
Beta defensin	PF00711
DNA repair protein rad10	PF03834
Cornifin (SPRR) family. SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo.The most characteristic feature of	PF02389
pfam02888, CaMBD, Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-s	PF02888
Arginosuccinate synthase. This family contains a PP-loop motif	PF00764
Membrane protein of unknown function (DUF435). The members of this family are membrane proteins of unknown function. In some proteins this region is found associated with pfam02225	PF04258
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 a	PF00536
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-phosphat	PF00215
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 posit	PF01363
Autophagocytosis associated protein, N-terminal domain. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole	PF03986
Glycine cleavage T-protein (aminomethyl transferase). 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	PF01571
Ribosomal protein L13e	PF01294
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: Th	PF01833
Synaptobrevin	PF00957
ATP dependent DNA ligase domain. This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653	PF01068
Transcription initiation factor IID, 18kD subunit. This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone	PF02269
YjeF-related protein N-terminus	PF03853
Flavin-binding monooxygenase-like. This family includes FMO proteins and cyclohexanone monooxygenase	PF00743
DHHA2 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members. The domain is about 120 residues long and contains a conserved DXK motif at	PF02833
Transforming growth factor beta like domain	PF00019
F-actin capping protein, beta subunit	PF01115
Serine hydroxymethyltransferase	PF00464
Nebulin repeat	PF00880
Saposin A-type domain	PF02199
Adaptor complexes medium subunit family. This family also contains members which are coatomer subunits	PF00928
Inward rectifier potassium channel	PF01007
p53-associated protein (MDM2). 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 do	PF02279
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, hist	PF01702
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	PF01990
Glycosyl hydrolase family 14. This family are beta amylases	PF01373
Dihydrodipicolinate reductase	PF01113
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	PF00075
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 anc	PF00173
HIT family	PF01230
Interleukin-3	PF02059
Fatty acid desaturase	PF00487
XRCC1 N terminal domain	PF01834
Adenovirus minor core protein PV	PF03910
Delta serrate ligand	PF01414
Laminin B (Domain IV)	PF00052
Poly A polymerase family. 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	PF01743
Phosphomevalonate kinase. Phosphomevalonate kinase (EC:2.7.4.2) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. This family represents the animal typ	PF04275
S-adenosyl-L-homocysteine hydrolase	PF00670
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	PF00393
TT viral orf 1. TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in un	PF02956
Mannosyl oligosaccharide glucosidase. This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide	PF03200
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-ri	PF00644
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	PF00370
MaoC like domain. The MaoC protein is found to share similarity with a wide variety of enzymes	PF01575
SURF1 family	PF02104
Acetaldehyde dehydrogenase	PF02396
Enolase, C-terminal TIM barrel domain	PF00113
Intermediate filament proteins	PF00038
Kinesin motor domain	PF00225
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	PF02297
DedA family. This family combines the DedA related proteins and YIAN/YGIK family. Members of this family are not functionally characterised. These proteins contain multiple predicted transmembrane regions	PF00597
Protein of unknown function (DUF390). This family of long proteins are currently only found in the rice genome. They have no known function. However they may be some kind of transposable element	PF04094
Nucleotide-sensitive chloride conductance regulator (ICln)	PF03517
Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes	PF00380
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 transmembra	PF01490
Somatotropin hormone family	PF00103
Glycosyl transferase family 11. This family contains several fucosyl transferase enzymes	PF01531
Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-oct	PF02348
FecCD transport family	PF01032
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	PF00536
Acyl-CoA dehydrogenase, N-terminal domain. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain	PF02771
Deoxyribonuclease II	PF03265
SCAMP family. In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cy	PF04144
Uncharacterized ACR, COG1565	PF02636
Thyroglobulin type-1 repeat	PF00086
Core histone H2A/H2B/H3/H4	PF00125
CRAL/TRIO, N-terminus. This all-alpha domain is found to the N-terminus of pfam00650	PF03765
Cytidylyltransferase. This family includes: Cholinephosphate cytidylyltransferase, Glycerol-3-phosphate cytidylyltransferase	PF01467
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	PF00068
ADP-ribosylglycohydrolase. This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisin	PF03747
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 relate	PF01713
IQ calmodulin-binding motif. Calmodulin-binding motif	PF00612
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	PF02296
Angiotensin-converting enzyme. Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid	PF01401
Importin-beta N-terminal domain	PF03810
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 positi	PF01363
Ribosomal protein L9, N-terminal domain	PF01281
DnaB-like helicase C 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 dup	PF03796
Sodium/hydrogen exchanger family. Na/H antiporters are key transporters in maintaining the pH of actively metobolizing cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminu	PF00999
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 acti	PF01588
NADH dehydrogenase	PF00146
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,	PF00078
Fructose-bisphosphate aldolase class-I	PF00274
Aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding domain	PF02738
Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars	PF00483
Uncharacterized ACR, COG1579	PF02591
Calsequestrin	PF01216
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 defor	PF00551
Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel	PF02932
PWI domain	PF01480
Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold	PF01233
Glycosyl hydrolase family 20, domain 2. This domain has a zincin-like fold	PF02838
Isocitrate/isopropylmalate dehydrogenase	PF00180
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 f	PF01758
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	PF01082
CoA binding domain. This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases	PF02629
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 baculoviruse	PF01607
Armadillo/beta-catenin-like repeat	PF00514
MH1 domain. This is the MH1 (MAD homology 1) domain found at the amino terminus of MAD related proteins. This domain can bind to DNA. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain s	PF03165
Sorting nexin, N-terminal domain. These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2	PF03700
O-Glycosyl hydrolase family 30	PF02055
Tropomyosin	PF00261
LIF / OSM family	PF01291
Signal recognition particle, alpha subunit, N-terminal. SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of	PF04086
Cytochrome oxidase assembly protein. This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus subtilis. COX15 is required for cytochrome c oxidase assembly in yeast	PF02628
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 p	PF00651
Mago nashi protein. This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene. The human homologue has been shown to interact with an RNA binding protein. An RNAi knockout of the C	PF02792
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 assembl	PF01823
Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II	PF02879
Retinoblastoma-associated protein B domain. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserve	PF01857
Retinal pigment epithelial membrane protein. This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequenc	PF03055
Cytochrome D1 heme domain. Cytochrome cd1 (nitrite reductase) catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme i	PF02239
Prephenate dehydrogenase. Members of this family are prephenate dehydrogenases EC:1.3.1.12 involved in tyrosine biosynthesis	PF02153
Stromal antigen (SA/STAG) protein	PF03365
Flavivirus glycoprotein, central and dimerisation domains	PF00869
Defensin propeptide	PF00879
K+ potassium transporter. This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members	PF02705
Uncharacterized ACR, COG1590	PF02676
Ctr copper transporter family. The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of hi	PF04145
Dynamin central region. This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169	PF01031
Cytosolic long-chain acyl-CoA thioester hydrolase. This family consist of various cytosolic long-chain acyl-CoA thioester hydrolases including human and rat. The aligned region is repeated with in the sequence of human and rat cytosolic long-chain acyl-C	PF01662
Phosphomannose isomerase type I	PF01238
Guanylate kinase	PF00625
Sodium/hydrogen exchanger family. Na/H antiporters are key transporters in maintaining the pH of actively metobolizing cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus	PF00999
Ribosomal protein L19e	PF01280
Vacuolar protein sorting 55. Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase. Both Vps55 and obesity receptor gene-related protein	PF04133
Cyclin	PF00134
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 s	PF01509
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 sandwi	PF00037
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	PF03054
Translation initiation factor SUI1	PF01253
Domain of unknown function (DUF298). Members of this family contain a basic helix-loop-helix leucine zipper motif	PF03556
Chromo shadow domain. This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain	PF01393
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	PF01403
e3 binding domain. This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit	PF02817
Aminotransferase class I and II	PF00155
Squalene/phytoene synthase	PF00494
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 act	PF01433
Fibroblast growth factor. Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. These growth factors cause dimerisation of their tyrosine kinase receptors leading to intracellular signaling	PF00167
Neuregulin family	PF02158
Virulence determinant. The UK protein is an African swine fever virus (ASFV) protein that is highly conserved amongst strains, and is an important viral virulence determinant for domestic pigs	PF02512
emp24/gp25L/p24 family. Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains	PF01105
ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum	PF03155
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 assemb	PF01823
cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of	PF02827
RhoGAP domain	PF00620
Plus-3 domain. This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively c	PF03126
Kappa casein. Kappa-casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para kappa-casein) and a soluble hydrophilic glycopeptide (caseinomacro	PF00997
Ubiquitin carboxyl-terminal hydrolase family 2	PF00443
tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases	PF01411
Pox virus Ag35 surface protein	PF03286
Glycosyltransferase family 43	PF03360
Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors	PF00104
Tim10/DDP family zinc finger. Putative zinc binding domain with four conserved cysteine residues. This domain is found in X-linked deafness dystonia protein. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Membe	PF02953
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	PF01658
Biotin/lipoate A/B protein ligase family. This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to for	PF03099
SART-1 family. This family of proteins appear to contain a leucine zipper and may therefore be a family of transcription factors	PF03343
Apoptosis regulator proteins, Bcl-2 family	PF00452
Strictosidine synthase. Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyses the condensation of tryptamine with secologanin to form strictosidine	PF03088
Ferredoxin-fold anticodon binding domain. This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold	PF03147
ARD/ARD' family. The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be e	PF03079
TIP41-like family. The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway	PF04176
CBS domain. CBS domains are small intracellular modules of unknown function. They are mostly found in 2 or four copies within a protein. Pairs of CBS domains dimerise to form a stable globular domain. Two CBS domains are found in inosine-monophosphate deh	PF00571
Eukaryotic porin	PF01459
Microtubule associated protein (MAP65/ASE1 family)	PF03999
Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin	PF01825
MraW methylase family. Members of this family are probably SAM dependent methyltransferases. This family appears to be related to pfam01596	PF01795
Glycerophosphoryl diester phosphodiesterase family. E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has be	PF03009
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	PF01564
Tudor domain. Domain of unknown function present in several RNA-binding proteins. copies in the Drosophila Tudor protein. Slight ambiguities in the alignment	PF00567
Permease family. This family includes permeases for diverse substrates such as xanthine, uracil and vitamin C. However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predict	PF00860
Integrins, beta chain. Sequences cut off at repeats due to overlap with EGF	PF00362
Phosphate transporter family. This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukemia virus receptor	PF01384
Cobalt transport protein	PF02361
Synaptophysin / synaptoporin	PF01284
RNA polymerase Rpb6. Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. The bacterial equivalent to Rpb6 is the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly	PF01192
TNF(Tumor Necrosis Factor) family	PF00229
Eukaryotic initiation factor 1A	PF01176
Fanconi anaemia group A protein	PF03511
Plus-3 domain. This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively ch	PF03126
Elongation factor TS	PF00889
Catalase	PF00199
Citrate synthase	PF00285
Roadblock/LC7 domain. This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dyne	PF03259
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	PF01839
Myosin head (motor domain)	PF00063
ATP-sulfurylase. This family consists 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 PA	PF01747
Phosphotyrosine interaction domain (PTB/PID)	PF00640
Putative 5'-3' exonuclease domain. This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be nec	PF03159
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 t	PF01454
BAR domain. The BAR domain is found in amphiphysin and clathrin binding protein. However the function of this domain is unknown	PF03114
CBL proto-oncogene N-terminus, EF hand-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily co	PF02761
Biotin-requiring enzyme. This alignment covers two families, the conserved lysine residue binds biotin in one group and lipoic acid in the other	PF00364
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	PF01049
Cobalamin synthesis protein/P47K. This family of proteins contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans	PF02492
Uracil DNA glycosylase superfamily	PF03167
Dephospho-CoA kinase. This family catalyzes 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	PF01121
Glucuronate isomerase. This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyses the reactions: D-glucuronate <=> D-fructuronate and	PF02614
Peptidase C13 family. This family of peptidases is known as the hemoglobinase family because it contains a globin degrading enzyme from blood parasites. However relatives are found in plants and other organisms that have other functions. Members of this	PF01650
STAT protein, protein interaction 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 fa	PF02865
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	PF02234
TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta and joins t	PF02002
Ribosomal protein S7p/S5e. This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes	PF00177
Beta/Gamma crystallin. The alignment comprises two Greek key motifs since the similarity between them is very low	PF00030
Uncharacterized protein family (ORF7) DUF. Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized function	PF03112
Cdc37 family. In the budding yeast Saccharomyces cerevisiae, Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90	PF03234
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 cle	PF01663
Suppressor Mra1. The suppressor Mra1 is found in high-copy-number when Ras1 is mutated, that recovers the mating deficiency caused by the decrease of Ras1 activity. Mutational analysis in yeast suggests that the suppressor Mra1 is essential for cell grow	PF03587
Tissue inhibitor of metalloproteinase. Members of this family are common in extracellular regions of vertebrate species	PF00965
Glycosyltransferase family 28 C-terminal domain. The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). Structural analysis suggests the C-terminal domain contai	PF04101
Uncharacterized protein family, UPF0065	PF03401
MORN repeat. The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000	PF02493
Glycosyl hydrolases family 2, TIM barrel domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities	PF02836
FAD binding domain of DNA photolyase	PF03441
Ependymin	PF00811
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 subu	PF02270
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-	PF01391
Platelet activating factor acetylhydrolase. Platelet activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. At least three intracellu	PF02266
UBA domain	PF00627
HYR domain. This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is unc	PF02494
Nucleosome assembly protein (NAP). It is thought that NAPs may be involve in regulating gene expression as a result of histone accessibility	PF00956
Galactoside-binding lectin	PF00337
Phosphoribosyl transferase domain. This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyltransferase EC:2.4.2.7, Hypoxanthine-guanine-xanthine phosphoribosyltransferase, Hypoxanthine phosp	PF00156
Ubiquinol-cytochrome C chaperone	PF03981
MCM2/3/5 family	PF00493
Vitamin B12 dependent methionine synthase, activation domain	PF02965
pfam02888, CaMBD, Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-	PF02888
Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene	PF01553
Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I	PF02878
Peridinin-chlorophyll A binding protein	PF02429
dUTPase. dUTPase hydrolyses dUTP to dUMP and pyrophosphate	PF00692
Eukaryotic protein of unknown function, DUF284. Members of this family have no known function. They have been predicted to contain transmembrane helices	PF03381
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase comp	PF00562
Ribosomal protein S5, N-terminal domain	PF00333
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	PF01545
Trypsin	PF00089
START domain	PF01852
Growth-Arrest-Specific Protein 2 Domain	PF02187
CutC family. Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are be	PF03932
Transcription initiation factor IIA, gamma subunit, beta-barrel domain	PF02751
Phosphorylase family 2	PF00896
AIR synthase related protein, C-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 function of the C-terminal domain of AIR synt	PF02769
Interphotoreceptor retinoid-binding protein. Interphotoreceptor retinoid-binding protein (IRBP) mediates retinoid trafficking between the photoreceptors and pigmented epithelium. This Pfam family represents a repeat domain found four times in the mammalia	PF02692
Runt domain	PF00853
RPEL repeat. The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that one member contains a pfam02037 domain that is also impl	PF02755
Ubiquitin carboxyl-terminal hydrolases family 2	PF00442
Oxidoreductase FAD-binding domain	PF00970
Glutathione S-transferase, C-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but are not GSTs: * S-crystallins from squid. Similarity to GST previously noted. * Eukaryotic elongation f	PF00043
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 eukary	PF01496
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	PF02394
Eukaryotic initiation factor 4E	PF01652
L1 transposable element	PF02994
Cation transporter/ATPase, N-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport	PF00690
MAPEG family. This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism)	PF01124
AICARFT/IMPCHase bienzyme. This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-	PF01808
Organic Anion Transporter Polypeptide (OATP) family, N-terminus. This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution	PF03132
Peptidase C13 family. This family of peptidases is known as the hemoglobinase family because it contains a globin degrading enzyme from blood parasites. However relatives are found in plants and other organisms that have other functions. Members of this f	PF01650
Gap junction alpha-1 protein (Cx43)	PF03508
Tropomodulin. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two doma	PF03250
RIO1/ZK632.3/MJ0444 family	PF01163
ubiE/COQ5 methyltransferase family	PF01209
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 dihydrou	PF01207
Ferritin-like domain. This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins	PF00210
Vacuolar protein sorting-associated protein 35. Vacuolar protein sorting-associated protein (Vps) 35 is one of around 50 proteins involved in protein trafficking. In particular, Vps35 assembles into a retromer complex with at least four other proteins Vp	PF03635
Gag P30 core shell protein. According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly	PF02093
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 regio	PF01576
pfam02939, UcrQ, UcrQ family. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This family represents the 9.5 kDa subunit of the complex	PF02939
Reovirus viral attachment protein sigma 1. This family consists of the reovirus sigma 1 hemagglutinin, cell attachment protein. This glycoprotein is a minor capsid protein and also determins the serotype-specific humoral immune response. Sigma 1 consist o	PF01664
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	PF00554
CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conser	PF02762
pfam02935, COX7C, Cytochrome c oxidase subunit VIIc. 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 cytochrome c oxidase subunit VIIc. The yeast me	PF02935
alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes	PF00561
3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-termin	PF01612
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	PF00631
IBR domain. The IBR (In Between Ring fingers) domain is found to occur between pairs of ring fingers (pfam00097). The function of this domain is unknown. This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain	PF01485
Glutaminyl cyclase. Glutaminyl cyclase catalyses the formation of the pyroglutamyl residue present at the amino terminus of numerous secretory peptides and proteins. Glutaminyl cyclase posses a zinc aminopeptidase domain in which the four functionally imp	PF03565
Domain of unknown function (DUF341)	PF03959
S-adenosylmethionine synthetase, N-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold	PF00438
Alanine dehydrogenase/pyridine nucleotide transhydrogenase. This family now also contains the lysine 2-oxoglutarate reductases	PF01262
Porphobilinogen deaminase, dipyromethane cofactor binding domain	PF01379
Domain of unknown function UPF0086. This small conserved archaeal protein has no known function	PF01868
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:- D	PF02366
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 b	PF01067
Succinate dehydrogenase cytochrome b subunit	PF01127
2-hydroxychromene-2-carboxylate isomerase family. 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 HCC	PF03046
CCR4-Not complex component, Not1. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID	PF04054
Insulin/IGF/Relaxin family	PF00049
Respiratory-chain NADH dehydrogenase, 49 Kd subunit	PF00346
Cystine-knot domain	PF00007
Pou domain - N-terminal to homeobox domain	PF00157
YbaK / prolyl-tRNA synthetases associated domain. This domain of unknown function is found in numerous prokaryote organisms. The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes.	PF04073
Lysyl oxidase	PF01186
Animal haem peroxidase	PF03098
Kringle domain. Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta	PF00051
Ribosomal Proteins L2, C-terminal domain	PF03947
Fructosamine kinase. This family includes eukaryotic fructosamine-3-kinase enzymes. The family also includes bacterial members that have not been characterised but probably have a similar or identical function	PF03881
jmjN domain	PF02375
MAPEG family	PF01124
Sybindin-like family. Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses	PF04099
pfam02948, Amelogenin, Amelogenin. Amelogenins play a role in biomineralization. They seem to regulate the formation of crystallites during the secretory stage of tooth enamel development. thought to play a major role in the structural organization and m	PF02948
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 a	PF02347
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 are confirmed as DnaJ con	PF00226
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	PF01476
Protein of unknown function DUF100. This prokaryotic family has no known function	PF01950
Hydroxymethylglutaryl-coenzyme A reductase	PF00368
Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165	PF01610
pfam02889, Sec63, Sec63 domain	PF02889
CPSF A subunit region. This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in p	PF03178
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	PF00797
Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH	PF01053
Ribosomal protein S11	PF00411
Matrix protein (MA), p15. The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity	PF01140
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. The high cutoff is so high to avoid overlaps with related families	PF00071
7TM chemoreceptor. This large family of proteins are related to pfam00001. They are 7 transmembrane receptors. This family does not include all known members, as there are problems with overlapping specificity with pfam00001. This family is greatly expand	PF01461
Ribosomal protein S12	PF00164
pfam02871, Octopine_DH_N, NAD/NADP octopine/nopaline dehydrogenase, NAD binding 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 f	PF02871
Sas10/Utp3 family. This family contains Sas10 which hash been identified as a regulator of chromatin silencing. The family also contains Utp3 a component of the U3 ribonucleoprotein complex. The exact molecular function of this family is unknown	PF04000
Ribosomal protein S15	PF00312
Ribosomal protein S16	PF00886
Pyruvate kinase, alpha/beta domain	PF02887
Ribosomal protein S17	PF00366
Ribosomal protein S18	PF01084
Ribosomal protein S19	PF00203
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 multimeri	PF02268
Nerve growth factor family	PF00243
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	PF01297
Hedgehog amino-terminal signaling domain. For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation	PF01085
Amiloride-sensitive sodium channel	PF00858
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 no	PF01562
Domain of unknown function (DUF383). domo keywords :chromosome c26f1.12c 41.3	PF04063
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	PF01592
NLI interacting factor. This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase	PF03031
RNase P subunit p30. This protein is part of the RNase P complex that is involved in tRNA maturation	PF01876
pfam02883, Alpha_adaptinC2, Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site.	PF02883
Lipoate synthase. Lipoate synthase (or lipoic acid synthetase) catalyses the formation of alpha-(+)-lipoic acid, required for lipoate biosynthesis	PF02546
Protein of unknown function DUF101. The members of this family are uncharacterised. The alignment of these proteins contains several conserved polar residues that might be potential catalytic residues	PF01951
F-box associated region. Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. One member is involved in binding to N-glycosylate	PF04300
P53	PF00870
P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB)	PF00786
Putative replicase 1 (ORF2)	PF02122
Late embryogenesis abundant protein. Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown	PF02987
DNA polymerase epsilon subunit B. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme con	PF04042
Possible metal-binding domain in RNase L inhibitor, RLI. Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often fou	PF04068
Insulin-like growth factor binding protein	PF00219
Ribosomal protein S27	PF01667
DnaJ central domain (4 repeats). 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	PF00684
Protein of unknown function, DUF258	PF03193
Protein of unknown function, DUF259	PF03194
Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion ta	PF03623
Latrophilin Cytoplasmic C-terminal region. This family consists of the cytoplasmic C-terminal region in latrophilin. Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein cou	PF02354
Dihydrodipicolinate synthetase family. This family has a TIM barrel structure	PF00701
Leucine carboxyl methyltransferase. Family of leucine carboxyl methyltransferases EC:2.1.1.- . This family may need divides a the full alignment contains a significantly shorter mouse sequence	PF04072
CAS/CSE protein, C-terminus. Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis	PF03378
Domain of unknown function. This putative domain is found in members of the Dicer protein family. This protein is a dsRNA nuclease that is involved in RNAi and related processes. This domain of about 100 amino acids has no known function, but does contai	PF03368
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	PF00769
D12 class N6 adenine-specific DNA methyltransferase	PF02086
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	PF00171
Protein of unknown function (DUF396). A family of conserved eukaryotic transmembrane proteins	PF04148
D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.2	PF03894
tRNA pseudouridine synthase	PF01416
pfam02878, PGM_PMM_I, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I	PF02878
CAAX amino terminal protease family. Members of this family are probably proteases. the family contains CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidi	PF02517
Phosphoglycerate mutase family. Y019_MYCTU and YK23_YEAST are significantly similar and contain identical active site residues	PF00300
Lyase	PF00206
DNA-dependent RNA polymerase. This is a family of single chain RNA polymerases	PF00940
Protein of unknown function, DUF265	PF03266
GMC oxidoreductase. This family of proteins bind FAD as a cofactor	PF00732
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 cata	PF01336
Xanthomonas avirulence protein, Avr/PthA	PF03377
Nitroreductase family. Members of this family utilise FMN as a cofactor	PF00881
Adenylylsulfate kinase. Enzyme that catalyses the phosphorylation of adenylylsulfate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif	PF01583
ST7 protein. The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain	PF04184
Inositol monophosphatase family	PF00459
Tim10/DDP family zinc finger. Putative zinc binding domain with four conserved cysteine residues. This domain is found in X-linked deafness dystonia protein. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Memb	PF02953
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	PF01712
BAF60b domain of the SWIB complex	PF02201
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	PF00883
Leishmanolysin	PF01457
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 ha	PF00554
XPA protein	PF01286
Alpha-L-fucosidase	PF01120
Adenosine-deaminase (editase) domain	PF02137
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 are confirmed as DnaJ cont	PF00226
Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OA	PF01053
Transient receptor	PF02164
Delta-aminolevulinic acid dehydratase	PF00490
Conserved nucleoporin domain	PF04096
Protein of unknown function, DUF270	PF03189
Scramblase. Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involve	PF03803
DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold	PF03104
Diacylglycerol kinase accessory domain (presumed). 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	PF00609
Smg-4/UPF3 family. This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3	PF03467
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 typi	PF00036
Formamidopyrimidine-DNA glycosylase	PF01149
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	PF01079
Peptidase family M41	PF01434
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	PF01534
Phosphoribosylglycinamide synthetase, B 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-phosph	PF02842
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 e	PF02005
RNA polymerases L / 13 to 16 kDa subunit	PF01193
Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase	PF00481
Ribonucleotide reductase, small chain	PF00268
Regulatory subunit of type II PKA R-subunit	PF02197
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 transmembran	PF01169
Sorbin homologous domain	PF02208
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 involv	PF00047
Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA s	PF04135
Peptidase family M48	PF01435
DNA polymerase family A	PF00476
AMP-binding enzyme	PF00501
Peptidase family M49	PF03571
Glutamate/Leucine/Phenylalanine/Valine dehydrogenase	PF00208
PQ loop repeat. Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localization of cystinosin to lysosomes. How	PF04193
SRF-type transcription factor (DNA-binding and dimerisation domain)	PF00319
Thi4 family. This family includes a putative thiamine biosynthetic enzyme	PF01946
NOL1/NOP2/sun family	PF01189
Plectin repeat. This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen	PF00681
Sec7 domain. The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the pfam00025 family	PF01369
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 catalyzes the removal of two reducing equivalents from the cy	PF02441
Sodium:sulfate symporter transmembrane region. There are also some members in this family that belong to the subfamily SODIT1	PF00939
Per1-like. A member of this family has been implemented in protein processing in the endoplasmic reticulum	PF04080
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	PF02368
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	PF00683
PXA domain. This domain is associated with PX domains pfam00787	PF02194
'chromo' (CHRromatin Organization MOdifier) domain	PF00385
Peptidase family M50	PF02163
Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization	PF00711
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. Th	PF01922
Keratin, high sulfur B2 protein. High sulfur proteins are cysteine-rich proteins synthesized during the differentiation of hair matrix cells, and form hair fibers in association with hair keratin intermediate filaments. This family has been divided up int	PF01500
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	PF00004
Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this r	PF02295
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	PF01099
Agrin NtA domain. Agrin is a multidomain heparan sulphate proteoglycan, that is a key organizer for the induction of postsynaptic specializations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domai	PF03146
Granulin	PF00396
Ribosomal protein L1p/L10e family. This family includes prokaryotic L1 and eukaryotic L10	PF00687
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 t	PF00627
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	PF01413
ATP synthase	PF00231
PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation	PF02562
Phosphorylase family. Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)	PF01048
Zn-finger in ubiquitin-hydrolases and other protein	PF02148
pfkB family carbohydrate kinase. This family includes a variety of carbohydrate and pyrimidine kinases. The family includes phosphomethylpyrimidine kinase EC:2.7.4.7. This enzyme is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an ess	PF00294
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	PF00163
ZIP Zinc transporter. The ZIP family consists of zinc transport proteins and many putative metal transporters. The main contribution to this family is from the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the	PF02535
NADH-ubiquinone/plastoquinone oxidoreductase, chain 3	PF00507
TRAF-type zinc finger	PF02176
Mandelate racemase / muconate lactonizing enzyme, C-terminal domain. C-terminal domain is TIM barrel fold, dehydratase-like domain. Manganese is associated with this domain	PF01188
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	PF02170
Fragilysin metallopeptidase (M10C) enterotoxin	PF02051
V-ATPase subunit C	PF03223
60Kd inner membrane protein	PF02096
pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel	PF02932
PTB domain (IRS-1 type)	PF02174
Arrestin (or S-antigen)	PF02752
GNT-I family. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) EC:2.4.1.101 transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis o	PF03071
V-ATPase subunit H	PF03224
Perilipin family	PF03036
Mer11 DNA-binding domain. The Mre11 complex is a multisubunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 o	PF04152
Citrate transporter	PF03600
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), whic	PF00026
Arv1-like family. Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis	PF04161
7 transmembrane receptor (Secretin family)	PF00002
ATPase family associated with various cellular activities (AAA)	PF00004
Peptidase C1-like family. This family is closely related to the Peptidase_C1 family pfam00112, containing several prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases	PF03051
Signal recognition particle, alpha subunit, N-terminal. SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of t	PF04086
1,3-beta-glucan synthase component. This family consists of various 1,3-beta-glucan synthase components including Gls1, Gls2 and Gls3 from yeast. 1,3-beta-glucan synthase EC:2.4.1.34 also known as callose synthase catalyses the formation of a beta-1,3-glu	PF02364
Inner centromere protein, ARK binding region. This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregatio	PF03941
Tumor protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction a	PF04201
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 recombina	PF01028
Immunoglobulin domain	PF00047
Sec8 exocyst complex component specific domain	PF04048
RolB/RolC glucosidase family. This family of proteins includes RolB and RolC. RolC releases cytokinins from glucoside conjugates. Whereas RolB hydrolyses indole glucosides	PF02027
pfam02902, Peptidase_C48, Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn	PF02902
N-acetylglucosamine-6-phosphate deacetylase. This family are predicted to adopt a TIM barrel fold. This is family of N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=>	PF02612
Zona pellucida-like domain	PF00100
Uncharacterized ACR, YfiH family COG1496	PF02578
von Hippel-Lindau disease tumor suppressor protein. VHL forms a ternary complex with the elonginB and elonginC proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor mRNA	PF01847
Intermediate filament protein	PF00038
Gamma interferon inducible lysosomal thiol reductase (GILT). This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similarit	PF03227
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 some members, proteolysis has shown that the Peptidyl-alph	PF01436
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 transmembr	PF01490
Protein kinase A anchor	PF03832
Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions	PF00583
Branched-chain amino acid transport system / permease component. This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH and LivM both of which are form the LIV-I transport system. Also f	PF02653
Zn-finger in Ran binding protein and others	PF00641
Ribosomal protein S6e	PF01092
Macrophage scavenger receptor	PF03523
DIL domain. The DIL domain has no known function	PF01843
Scramblase. Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved	PF03803
Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member 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-termi	PF00134
Pterin 4 alpha carbinolamine dehydratase. Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerisation cofactor of hepatocyte nuclear factor 1-alpha)	PF01329
Sec20. Sec20 is a membrane glycoprotein associated with secretory pathway	PF03908
TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold	PF02969
Cytochrome C oxidase subunit II, periplasmic domain	PF00116
Serum amyloid A protein	PF00277
Paramyxovirus P/V phosphoprotein. Paramyxoviral P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural protei	PF03210
Kv2 voltage-gated K+ channel	PF03521
Acyltransferase family. This family includes a range of acyltransferase enzymes. This domain is found in many as yet uncharacterised C. elegans proteins and it is approximately 300 amino acids long	PF01757
Putative methyltransferase. This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity	PF02390
Conserved hypothetical protein 95	PF03602
Thiolase, C-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase	PF02803
MtN3/saliva family. This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these p	PF03083
F-actin capping protein alpha subunit	PF01267
Interleukin 7/9 family. IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-9 is a multi-functional cytokine that, although originally described as a T-cell growth factor, its function in T-cell res	PF01415
Ribosomal protein S7e	PF01251
Transposase	PF01526
Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site	PF02404
Histone-like transcription factor (CBF/NF-Y) and archaeal histone. This family includes archaebacterial histones and histone like transcription factors from eukaryotes	PF00808
Ubiquitin fusion degradation protein UFD1. Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includ	PF03152
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 biosynthesi	PF01042
Disintegrin	PF00200
Cadherin domain	PF00028
Diacylglycerol kinase catalytic domain (presumed). 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	PF00781
dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be si	PF03455
Notch (DSL) domain. The Notch domain is also called the 'DSL' domain. The notch proteins are transmembrane proteins with extracellular domains of repeated EGF domains and the notch (or DSL) domain N-terminal to that. These proteins are generally involved	PF00066
FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif	PF00498
wnt family	PF00110
Actinobacillus constitutively-expressed outer membrane lipoprotein A	PF03346
Chromosome condensation protein 3, C-terminal region. Cnd3 is a Member of the five subunit condensin complex. Each subunit is essential for mitotic condensation	PF04154
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 that may be involved in RNA stabilisation. Thi	PF01535
Fatty acid hydroxylase	PF04116
pfam02891, zf-MIZ, MIZ zinc finger	PF02891
FAT domain. The FAT domain is named after FRAP, ATM and TRRAP	PF02259
3-oxo-5-alpha-steroid 4-dehydrogenase. This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalysed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-ster	PF02544
Ribosomal L22e protein family	PF01776
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 i	PF02186
Ribosomal protein S8e	PF01201
Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle	PF02689
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 u	PF00176
MAS20 protein import receptor	PF02064
LacY proton/sugar symporter. This family is closely related to the sugar transporter family	PF01306
Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member 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-termin	PF00134
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 do	PF00665
Interleukin-6/G-CSF/MGF family	PF00489
POT family. The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters	PF00854
Leucine rich repeat N-terminal domain	PF01462
Retroviral GAG p10 protein. This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated	PF02337
Glucocorticoid receptor	PF02155
pfam02938, GAD, GAD domain. This domain is found in some members of the GatB and aspartyl tRNA synthetases	PF02938
Transcription factor AP-2	PF03299
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	PF00575
Uncharacterised protein family (UPF0160). This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368	PF03690
Platelet-activating factor acetylhydrolase, plasma/intracellular isoform II. Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl	PF03403
Exonuclease. This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III	PF00929
Ribosomal protein L10	PF00466
LEM3 (ligand-effect modulator 3) family / CDC50 family. Members of this family have been predicted to contain transmembrane helices. The family member LEM3 is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in resp	PF03381
Cytochrome c oxidase subunit VIa	PF02046
Ribosomal protein L13	PF00572
XPG I-region	PF00867
NADH:flavin oxidoreductase / NADH oxidase family	PF00724
Ribosomal protein L15	PF00256
Ribosomal protein L16	PF00252
Ribosomal protein L17	PF01196
pfam02910, succ_DH_flav_C, Fumarate reductase/succinate dehydrogenase flavoprotein C-terminal domain. This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases	PF02910
Ribosomal protein L19	PF01245
Got1-like family. Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins, Sed5, present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events	PF04178
Calcium-activated BK potassium channel alpha subunit	PF03493
Interphotoreceptor retinoid-binding protein. Interphotoreceptor retinoid-binding protein (IRBP) mediates retinoid trafficking between the photoreceptors and pigmented epithelium. This Pfam family represents a repeat domain found four times in the mammali	PF02692
Hydratase/decarboxylase. This family consist of various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase encoded by mhpD i	PF01689
QXW lectin repeat	PF00652
Tryptophan 2,3-dioxygenase	PF03301
Choline/Carnitine o-acyltransferase	PF00755
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	PF00637
Ribosomal L29 protein	PF00831
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 transmem	PF02009
Ribosomal protein L20	PF00453
Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in proka	PF02787
Organic Anion Transporter Polypeptide (OATP) family, C-terminus. This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution	PF03137
CPSF A subunit region. This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pr	PF03178
Ribosomal protein L23	PF00276
ERCC4 domain. This domain is predicted to be a nuclease domain	PF02732
Phosphoglycerate kinase	PF00162
Fumarate reductase/succinate dehydrogenase flavoprotein C-terminal domain. This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases	PF02910
Isoprenylcysteine carboxyl methyltransferase (ICMT) family. The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboyxl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this met	PF04140
Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is unknown	PF02171
F5/8 type C domain. This domain is also known as the discoidin (DS) domain family. The bacterial examples are not yet included in the SEED alignment and are only found with low scores	PF00754
Colipase, C-terminal domain. SCOP reports duplication of common fold with Colipase N-terminal domain	PF02740
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	PF01909
Laminin G domain	PF00054
Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29	PF00777
Adenylate and Guanylate cyclase catalytic domain	PF00211
B-box zinc finger	PF00643
Glutamine amidotransferases class-II	PF00310
Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes	PF00253
WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mG	PF00568
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	PF00519
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 r	PF02221
PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown	PF00855
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	PF02005
Protein of unknown function (DUF342). This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length	PF03961
Domain of unknown function DUF71. This family of proteins have no known function. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.In some members of this family, this domain is associated with pfam01042	PF01902
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	PF01410
TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochae	PF02824
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. Tr	PF02386
Ribosomal protein L34	PF00468
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	PF00361
Ribosomal protein L36	PF00444
Intermediate filament tail domain	PF00932
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	PF02347
Translation initiation factor IF-3	PF00707
Cystatin domain	PF00031
Pyridoxal-dependent decarboxylase conserved domain	PF00282
Glucose inhibited division protein. This is a family of bacterial Glucose inhibited division proteins these are probably involved in the regulation of cell devision	PF02527
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	PF00616
Wilm's tumour protein	PF02165
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	PF01394
Protein-tyrosine phosphatase	PF00102
Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase, EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-octu	PF02348
p53-associated protein (MDM2). 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 dom	PF02279
FAD linked oxidases, C-terminal domain. This domain has a ferredoxin-like fold	PF02913
Cation-independent mannose-6-phosphate receptor repeat. The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat	PF00878
NNMT/PNMT/TEMT family	PF01234
Mouse mammary tumor virus superantigen. The mouse mammary tumor virus (MMTV) is a milk-transmitted type B retrovirus. The superantigen (SAg) is encoded by the long terminal repeat. The SAgs are also called PR73	PF01054
Thymidine kinase	PF00265
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)	PF01135
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	PF00978
ENV polyprotein (coat polyprotein)	PF00429
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 synt	PF00587
Yippee putative zinc-binding protein	PF03226
Ribosomal protein L44	PF00935
BED zinc finger	PF02892
WSC domain. This domain may be involved in carbohydrate binding	PF01822
WWE domain. The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems	PF02825
Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine	PF01916
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 dimerisation. E	PF00958
Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold	PF00619
Choline/ethanolamine kinase. Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway	PF01633
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 fa	PF01758
3-beta hydroxysteroid dehydrogenase/isomerase family. The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursor	PF01073
UBA/TS-N domain	PF00627
RNA polymerase alpha subunit	PF00623
Translocation protein Sec62	PF03839
Anp1. The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins colocalize within the cis Golgi, and that they are physically associated in two distinct complexes	PF03452
Presenilin	PF01080
Spectrin repeat. Spectrin repeats 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 spectr	PF00435
tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included	PF00133
Uncharacterised protein family (UPF0183). This family of proteins includes Lin-10 from C. elegans	PF03676
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	PF02142
Flagellar hook-associated protein 2. The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria	PF02465
Glu-tRNAGln amidotransferase C subunit. This is a family of Glu-tRNAGln amidotransferase C subunits. The Glu-tRNA Gln amidotransferase enzyme itself is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correc	PF02686
Choloylglycine hydrolase. This family of choloylglycine hydrolases includes conjugated bile acid hydrolase (CBAH) EC:3.5.1.24, penicillin acylase EC:3.5.1.11 and acid ceramidase EC:3.5.1.23 which cleave carbon-nitrogen bonds, other than peptide bonds, in	PF02275
Ocular albinism type 1 protein	PF02101
Aconitase family (aconitate hydratase)	PF00330
Cyclophilin type peptidyl-prolyl cis-trans isomerase	PF00160
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	PF02141
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 doma	PF00012
Ribosomal L40e family. Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein	PF01020
Hyaluronidase	PF01630
Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokar	PF02787
MSP (Major sperm protein) domain	PF00635
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 galactosyl	PF01501
Phosphatidylethanolamine-binding protein	PF01161
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 n	PF00307
Aldose 1-epimerase	PF01263
MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases	PF01853
Peptidyl-tRNA hydrolase 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 cons	PF00472
MutS family, N-terminal putative DNA binding domain. This family consists of the N-terminal region of proteins in the mutS family of DNA mismatch repair proteins and is found associated with pfam00488 located in the C-terminal region. The mutS family of	PF01624
Spin/Ssty Family. Spindlin (Spin) is a novel maternal transcript present in the unfertilized egg and early embryo. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members	PF02513
Sulfate transporter family. Mutations may lead to several human diseases	PF00916
Class I Histocompatibility antigen, domains alpha 1 and 2	PF00129
Galactosyltransferase	PF02709
DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, whic	PF03184
Occludin/ELL family	PF02168
Phosducin	PF02114
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	PF01483
GDNF receptor family. This family consists of Glial-cell-line-derived neurotrophic factor (GDNF) and neurturin (NTN) these receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuron	PF02351
Oligosaccharyl transferase STT3 subunit. This family consists of the oligsacharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosccharyl transferase (OTase) complex of proteins and is required for its activity. OTase	PF02516
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 family is difficult to model due to many similar but different sub-types o	PF00008
Ribosomal protein L21e	PF01157
ADP-ribosylation factor family	PF00025
PMP-22/EMP/MP20/Claudin family	PF00822
Cytochrome b(C-terminal)/b6/petD	PF00032
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	PF02290
DOMON domain. The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with 7-8 strands. The domain may mediate extracellular adhesive interactions	PF03351
Mago nashi protein. This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene. The human homologue has been shown to interact with an RNA binding protein. An RNAi knockout of the	PF02792
Prismane/CO dehydrogenase family. This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centers - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster. Th	PF03063
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	PF01676
Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit. Acetyl co-enzyme A carboxylase carboxyltransferase is composed of an alpha and beta subunit	PF03255
Synuclein. There are three types of synucleins in humans, these are called alpha, beta and gamma. Alpha synuclein has been found mutated in families with autosomal dominant Parkinson's disease. A peptide of alpha synuclein has also been found in amyloid	PF01387
TILa domain. This cysteine rich domain occurs along side the TIL pfam01826 domain and is likely to be a distantly related relative. This domain is found five to twenty-five times in zonadhesins. The TILa domain is also found twice in an IGG FC binding pr	PF02345
ROK family	PF00480
Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges	PF01927
High molecular weight glutenin subunit. Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin	PF03157
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)	PF01532
Uricase	PF01014
Proliferating cell nuclear antigen, C-terminal domain. N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA	PF02747
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	PF00105
Ribosomal protein L6e	PF01159
Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities	PF00703
Aminopeptidase I zinc metalloprotease (M18)	PF02127
Phospholipase D. Active site motif. Phosphatidylcholine-hydrolyzing 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 certa	PF00614
Ankyrin repeat. Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure	PF00023
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	PF01813
Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair	PF03962
C2 domain. Phosphoinositide 3-kinase region postulated to contain a C2 domain. Outlier of pfam00168 family	PF00792
Putative diphthamide synthesis protein.One member is a candidate tumour suppressor gene. DPH2 from yeast1, which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein sy	PF01866
Herpesvirus transcription activation factor (transactivator). This family includes EBV BRLF1 and similar ORF 50 proteins from other herpesviruses	PF03326
Glycosyl transferases group 1. Mutations in this domain may lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharid	PF00534
Interleukin-12 alpha subunit. Interleukin 12 (IL-12) is a disulphide-bonded heterodimer consisting of a 35kDa alpha subunit and a 40kDa beta subunit. It is involved in the stimulation and maintenance of Th1 cellular immune responses, including the normal	PF03039
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 trypt	PF00605
PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretin	PF04012
Apolipoprotein A1/A4/E family. These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein E	PF01442
Glucose inhibited division protein A	PF01134
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 fun	PF01432
Protein kinase C terminal domain	PF00433
Poly-adenylate binding protein, unique domain	PF00658
Thrombospondin type 1 domain	PF00090
Vertebrate endogenous opioids neuropeptide	PF01160
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 galactosylt	PF01501
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	PF01170
Vacuolar protein sorting 55. Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase. Both Vps55 and obesity receptor gene-related protei	PF04133
Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin Putative zinc finger	PF00569
Groucho/TLE N-terminal Q-rich domain. The N-terminal domain of the Grouch/TLE co-repressor proteins are involved in oligomerisation	PF03920
SKI/SNO/DAC family. This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and	PF02437
Glycosyltransferase family 6	PF03414
Thiamine pyrophosphate enzyme, central domain. The central domain of TPP enzymes contains a 2-fold Rossman fold	PF00205
Antitermination protein	PF03589
Putative GTP-ase 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	PF01412
Furin-like cysteine rich region	PF00757
Platelet-derived growth factor (PDGF)	PF00341
Ribonuclease T2 family	PF00445
Acyl CoA binding protein	PF00887
RPEL repeat. The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that one member contains a pfam02037 domain that is also impli	PF02755
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	PF01763
Octicosapeptide repeat. Short motif that may bind Ca2+	PF00564
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, corri	PF00809
Myc amino-terminal region. The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes invol	PF01056
Prolyl oligopeptidase family	PF00326
Lipocalin / cytosolic fatty-acid binding protein family	PF00061
Mov34/MPN/PAD-1 family. 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. It has b	PF01398
tRNA synthetases class I (E and Q), anti-codon binding 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 a	PF03950
SPX domain. We have named this region the SPX domain after (SYG1, Pho81 and XPR1). This 180 residue length 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 sub	PF03105
Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	PF01315
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 one member is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet	PF01344
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 sy	PF01693
Transaldolase	PF00923
Galactose binding lectin domain	PF02140
Ribosomal protein L24e	PF01246
ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activ	PF02597
HMG (high mobility group) box	PF00505
Matrix metalloprotease, N-terminal domain. This family is found N-terminal to the catalytic domain of matrixin	PF03933
ORMDL family. Evidence form suggests that ORMDLs are involved in protein folding in the ER	PF04061
Glycoprotein hormone	PF00236
Tesmin/TSO1-like CXC domain. This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin and TSO1. This family is called a CXC domain in	PF03638
LCCL domain	PF03815
Polyribonucleotide nucleotidyltransferase, RNA binding domain. This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction	PF03726
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	PF01569
Copper amine oxidase, N3 domain. This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous	PF02728
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 p	PF01602
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	PF01066
Uncharacterised protein family (UPF0185). This family contains a number of small uncharacterised proteins including BM-002	PF03671
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 in	PF01428
Protein of unknown function (DUF425). Family member HYNA is the product of a novel gene expressed in human liver cancer tissue	PF04243
mRNA capping enzyme, C-terminal domain	PF03919
Flotillin family. Flotillins are integral membrane proteins that have been shown to be present in several subcellular components, including caveolae (invaginated plasma membrane microdomains), lipid rafts (sphingolipid and cholesterol-rich, detergent-res	PF03149
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	PF00378
Gamma-butyrobetaine hydroxylase. Members of this family are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1	PF03322
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 spermid	PF01536
Chitinase	PF00192
Putative methyltransferase	PF02390
Na+ dependent nucleoside transporter. This family consists of nucleoside transport proteins. One member is a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane. One member is a a Na+-dependent nucleoside transporter se	PF01773
Mechanosensitive ion channel. Two members of this protein family of M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp	PF00924
Phosphofructokinase	PF00365
GCM motif protein	PF03615
Methyl-accepting chemotaxis protein (MCP) signaling domain. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs	PF00015
Mitosis protein DIM1	PF02966
Thiamine biosynthesis protein (ThiI). ThiI is required for thiazole synthesis, required for thiamine biosynthesis	PF02568
recA bacterial DNA recombination protein	PF00154
Arp2/3 complex, 34kD subunit p34-Arc. Arp2/3 protein complex has been implicated in the control of actin polymerization in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p	PF04045
HELP domain. The HELP (Hydrophobic ELP) domain is found in EMAP and EMAP-like proteins (ELPs). Although called a domain it contains a predicted transmembrane helix and may not form a globular domain. It is also not clear if these proteins localize to memb	PF03451
EF hand	PF00036
CO dehydrogenase flavoprotein C-terminal domain	PF03450
Amyloid A4 extracellular domain	PF02177
GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins	PF02893
Death domain	PF00531
PBX domain. The PBX domain is a bipartite acidic domain	PF03792
Allantoicase repeat. This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)	PF03561
FAD binding domain. This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase	PF00667
ATP synthase A chain	PF00119
HAT (Half-A-TPR) repeat. The HAT (Half A TPR) repeat is found in several RNA processing proteins	PF02184
Zinc carboxypeptidase	PF00246
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	PF00174
Ribosome-binding factor A	PF02033
TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermedia	PF03073
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	PF00189
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 eukaryo	PF01496
Coatomer WD associated domain	PF04053
Ribosomal S17	PF00833
Proliferating cell nuclear antigen, N-terminal domain. N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA	PF00705
2-nitropropane dioxygenase. Members of this family catalyse the denitrification of a number of nitroalkanes using either FAD or FMN as a cofactor	PF03060
O-methyltransferase. This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine	PF00891
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	PF01699
SKIP/SNW domain. This domain is found in chromatin proteins	PF02731
Translocon-associated protein (TRAP), alpha subunit. The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across	PF03896
Hexokinase. Hexokinase contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains	PF03727
Roadblock/LC7 domain. This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dyn	PF03259
Phosphoribosylglycinamide synthetase, C 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-phosph	PF02843
DMRTA motif. This region is found to the C-terminus of the pfam00751. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown	PF03474
Elongation factor Tu domain 2. Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in ot	PF03144
UbiA prenyltransferase family	PF01040
Bacterial extracellular solute-binding protein, family 7. This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein	PF03480
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-semialdehyd	PF00171
Virulence factor MVIN. The MVIN protein is a putative integral membrane protein. The function is unknown	PF03023
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 no	PF00307
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	PF01404
Utp11 protein. This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This	PF03998
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 involve	PF00047
Hsp90 protein	PF00183
Domain of unknown function (DUF323). This presumed domain is found in bacterial proteins. In some cases these proteins also contain a protein kinase domain. The function of this domain is unknown	PF03781
2-hydroxychromene-2-carboxylate isomerase family. 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	PF03046
Ergosterol biosynthesis ERG4/ERG24 family	PF01222
Phospholamban. The regulation of calcium levels across the membrane of the sarcoplasmic reticulum involves the interplay of many membrane proteins. Phospholamban is a 52 residue integral membrane protein that is involved in reversibly inhibiting the Ca(2	PF04272
Inorganic pyrophosphatase	PF00719
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	PF00622
Zinc finger, C2HC type. This is a DNA binding zinc finger domain	PF01530
Ku70/Ku80 N-terminal alpha/beta domain. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino	PF03731
AMOP domain. This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges	PF03782
Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion inter	PF02330
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	PF01488
Carbon-nitrogen hydrolase. This family contains hydrolases that break carbon-nitrogen bonds. The family includes: Nitrilase EC:3.5.5.1	PF00795
Glycosyl hydrolases family 38. Glycosyl hydrolases are key enzymes of carbohydrate metabolism	PF01074
Lipase (class 3)	PF01764
Prepro-orexin	PF02072
Paf1. Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i	PF03985
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	PF00520
Ribosomal protein S27a. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis o	PF01599
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	PF02222
Alpha amylase, C-terminal all-beta 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 betwee	PF02806
R3H domain	PF01424
Endothelin family	PF00322
Disulfide bond formation protein DsbB. This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidizes the periplasmic protein DsbA which in turn oxidizes cysteines in other periplasmic proteins in order to make disu	PF02600
Isoprenylcysteine carboxyl methyltransferase (ICMT) family. The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboyxl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this meth	PF04140
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 o	PF01225
MH1 domain. This is the MH1 (MAD homology 1) domain found at the amino terminus of MAD related proteins. This domain can bind to DNA. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain sh	PF03165
Legume-like lectin family. Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first recognized members of a family of animal lectins similar (19-	PF03388
CUB domain	PF00431
EF-1 guanine nucleotide exchange domain. This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains	PF00736
PQ loop repeat. Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localization of cystinosin to lysosomes. Howe	PF04193
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	PF01424
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 prot	PF01437
PSP. Proline rich domain found in numerous spliceosome associated proteins	PF04046
Hydroxymethylglutaryl-coenzyme A synthase	PF01154
Cytochrome c oxidase subunit VIc. 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 cytochrome c oxidase subunit VIc	PF02937
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 aminoacyla	PF00749
UTP--glucose-1-phosphate uridylyltransferase. This family consists of UTP--glucose-1-phosphate uridylyltransferases, EC:2.7.7.9. Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate urid	PF01704
Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12	PF03154
DDHD domain. The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoester	PF02862
DJ-1/PfpI family. The family includes the protease PfpI. This domain is also found in transcriptional regulators. This family appears to be distantly related to Glutamine amidotransferases pfam00117	PF01965
Tuberin	PF03542
CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B di	PF04218
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 b	PF01566
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-f	PF01821
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 observa	PF00794
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 endo	PF01421
Protein of unknown function (DUF423). Potential integral membrane protein	PF04241
Extracellular link domain	PF00193
SAP domain. The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins	PF02037
Arsenical pump membrane protein	PF02040
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 anch	PF00173
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	PF02403
Sulfotransferase protein	PF00685
Luciferase-like monooxygenase	PF00296
Nucleoside transporter. This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their o	PF01733
P21-ARC (ARP2/3 complex 21 kDa subunit). The seven component ARP2/3 actin-organizing complex is involved in actin assembly and function	PF04062
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 one member is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet.	PF01344
DNA gyrase/topoisomerase IV, subunit A	PF00521
Erythropoietin/thrombopoietin	PF00758
ATP synthase, Delta/Epsilon chain, beta-sandwich domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunits are called delta and epsilon in human and metazoan species but in bacterial species the del	PF02823
Tektin family. Tektins are cytoskeletal proteins. They have been demonstrated in such cellular sites as centrioles, basal bodies, and along ciliary and flagellar doublet microtubules. Tektins form unique protofilaments, organized as longitudinal polymers	PF03148
RasGAP C-terminus	PF03836
MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA a	PF02854
ABC1 family. This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytoc	PF03109
Utp21 specific WD40 associated domain. Utp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA	PF04192
Domain of unknown function (DUF380). Domain of unknown function, present in a ribonuclease P subunit in humans. Possibly a metal-binding domain	PF04067
Guanylate-kinase-associated protein (GKAP) protein	PF03359
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	PF01491
Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-oc	PF02348
T-box. The T-box encodes a 180 amino acid domain that binds to DNA	PF00907
Type IV secretion system CagX conjugation protein	PF03524
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	PF00898
MtN3/saliva family. This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these pr	PF03083
Maf-like protein. Maf is a putative inhibitor of septum formation in eukaryotes, bacteria, and archaea	PF02545
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 n	PF01592
Golgi 4-transmembrane spanning transporter	PF03821
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	PF02135
Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family	PF01527
POLO box duplicated region	PF00659
Ribosomal protein L11, N-terminal domain. The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain	PF03946
Rotavirus major capsid protein VP6. Rotaviruses consist of three concentric protein shells. The intermediate (middle) protein layer consists 260 trimers of VP6. VP6 in the most abundant protein in the virion. VP6 is also involved in virion assembly, and p	PF00980
Respiratory-chain NADH dehydrogenase, 30 Kd subunit	PF00329
Granulocyte-macrophage colony-stimulating factor	PF01109
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	PF00613
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	PF02423
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	PF00009
Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold	PF02784
Uncharacterised protein family (UPF0139)	PF03669
Nuclear movement protein. The nuclear movement protein or NudC, was first identified as a nuclear distribution (nud) gene that regulates nuclear movement in the filamentous fungus. The mammalian homologue of NudC interacts with Lis1, a neuronal migration	PF03593
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 spermi	PF01536
Peptidyl-tRNA hydrolase	PF01195
Cellulose synthase. Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that	PF03552
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 aminoacyl	PF00749
CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B d	PF04218
lactate/malate dehydrogenase, alpha/beta C-terminal 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 membe	PF02866
DTW domain. This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after	PF03942
Eukaryotic aspartyl protease	PF00026
WD domain, G-beta repeat	PF00400
Androgen receptor	PF02166
Peptidase family U34	PF03577
lactate/malate dehydrogenase, alpha/beta C-terminal 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 member	PF02866
Dynamin family	PF00350
Transcription initiation factor IIA, gamma subunit, helical domain	PF02268
Riboflavin kinase / FAD synthetase. This family consists part of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activitys. They catalyse the 5'-phos	PF01687
Hepatic lectin, N-terminal domain	PF03954
Male specific sperm protein. This family of drosophila proteins are typified by the repetitive motif C-G-P	PF03940
CUE domain. Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2	PF02845
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 carbox	PF00594
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	PF00062
Uroporphyrinogen decarboxylase (URO-D)	PF01208
Leptin	PF02024
Triosephosphate isomerase	PF00121
NAD(P) transhydrogenase beta subunit. This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes. The domain is often found in conjunction with pfam01262. Pyridine nucleotide	PF02233
Kelch motif	PF01344
Annexin. This family of annexins also includes giardin that has been shown to function as an annexin	PF00191
PCRF domain. This domain is found in peptide chain release factors	PF03462
Transcription factor E2F/dimerisation partner (TDP). This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in associa	PF02319
RNA 3'-terminal phosphate cyclase	PF01137
Peroxin 13, N-terminal domain. Both termini of the Peroxin-13 are oriented to the cytosol. Peroxin-13 is required for peroxisomal association of peroxin-14	PF04088
Progesterone receptor	PF02161
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	PF00635
GrpE	PF01025
Cofilin/tropomyosin-type actin-binding protein. Severs actin filaments and binds to actin monomers	PF00241
Sp100 domain. The function of this domain is unknown. It is about 105 amino acid residues in length and is predicted to be predominantly alpha helical. This domain is usually found at the amino terminus of protein that contain a SAND domain pfam01342	PF03172
Acyl transferase domain	PF00698
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	PF01462
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 alternati	PF00076
Mitochondrial import inner membrane, translocase subunit TIM44. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids o	PF04280
pfam02894, GFO_IDH_MocA_C, Oxidoreductase family, C-terminal alpha/beta domain. This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family	PF02894
Eukaryotic initiation factor 5A hypusine, DNA-binding OB fold	PF01287
Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain	PF00763
Double-stranded RNA binding motif. 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 localization of at least five different mRNAs in the e	PF00035
Sec23/Sec24 family. 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/2	PF04105
Bacterial regulatory helix-turn-helix protein, lysR family	PF00126
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 embryo	PF00806
VHS domain. Domain present in VPS-27, Hrs and STAM	PF00790
S-adenosylmethionine synthetase, C-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold	PF02773
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 deca	PF01641
Ribosomal protein S5, C-terminal domain	PF03719
Phosphatidyl serine synthase. Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyses the replacement of the head group of a phospholipid (phos	PF03034
short chain dehydrogenase. This family contains a wide variety of dehydrogenases	PF00106
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	PF01133
ADP-ribosylation factor family. Pfam combines a number of different Prosite families together	PF00025
PAS domain. CAUTION. This family does not currently match all known examples of PAS domains. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels	PF00989
NADH-ubiquinone/plastoquinone oxidoreductase chain 6	PF00499
Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA	PF04135
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	PF01756
Neurohypophysial hormones, C-terminal Domain. N-terminal Domain is in hormone5	PF00184
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	PF00849
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 f	PF00056
Pectinacetylesterase	PF03283
BTB/POZ domain. The BTB (for BR-C	PF00651
Arenavirus glycoprotein	PF00798
PCI domain	PF01399
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 t	PF01064
Hsp20/alpha crystallin family	PF00011
Lipocalin / cytosolic fatty-acid binding protein family. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. Structure is an eight-stranded beta barrel	PF00061
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	PF00045
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 com	PF02321
Arginase family	PF00491
Anaphase promoting complex subunit 8 / cdc23. The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8)	PF04049
Glycosyl hydrolase family 79, N-terminal domain. Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular	PF03662
Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity	PF03029
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	PF02263
Interleukin-1 / 18. This family includes interleukin-1 and interleukin-18	PF00340
Uncharacterised protein family (UPF0171)	PF03666
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 biosyn	PF00289
Isoflavone reductase. This is a family of isoflavone reductases from plants. Isoflavone reductase enzymes EC:1.3.1.45 catalyse the penultimate step in the synthesis of the phytoalexin medicarpin	PF02716
Interleukin 7/9 family. IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-9 is a multi-functional cytokine that, although originally described as a T-cell growth factor, its function in T-cell resp	PF01415
WH2 motif. The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP and Scar1 (mammalian homolog) to interact via their WH2 motifs with actin	PF02205
ATP synthase, Delta/Epsilon chain, beta-sandwich domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunits are called delta and epsilon in human and metazoan species but in bacterial species the de	PF02823
Hexokinase. Hexokinase contains two structurally similar domains represented by this family and PFAM:PF00349. Some members of the family have two copies of each of these domains	PF03727
Spc97 / Spc98 family. The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin	PF04130
Biopterin-dependent aromatic amino acid hydroxylase. This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein	PF00351
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	PF01030
Repeat in ubiquitin-activating (UBA) protein	PF02134
WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro	PF00397
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	PF00136
Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure	PF02931
ATP:guanido phosphotransferase, N-terminal domain. The N-terminal domain has an all-alpha fold	PF02807
Collagen triple helix repeat (20 copies)	PF01391
Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated	PF03089
Radical SAM superfamily	PF04055
Uncharacterised protein family (UPF0172)	PF03665
NeuB family. NeuB is the prokaryotic N-acetylneuraminic acid (Neu5Ac) synthase. It catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only	PF03102
pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB	PF02173
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	PF02225
MyTH4 domain. Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins	PF00784
Tubulin binding cofactor A	PF02970
Calponin family repeat	PF00402
Oxidoreductase family, NAD-binding Rossmann fold. This family of enzymes utilise NADP or NAD	PF01408
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 i	PF01803
Ribosomal L10	PF00826
Monooxygenase. This family includes diverse enzymes that utilise FAD	PF01360
Formate--tetrahydrofolate ligase	PF01268
Ribosomal L15	PF00827
HD domain. HD domains are metal dependent phosphohydrolases	PF01966
Indole-3-glycerol phosphate synthase	PF00218
KIX domain. CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun	PF02172
Alphaherpesvirus glycoprotein E. Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) (pfam01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation	PF02480
Recombination protein O. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination	PF02565
GDP dissociation inhibitor	PF00996
Mo-co oxidoreductase dimerisation domain. This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure	PF03404
S-adenosylmethionine synthetase, central domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold	PF02772
Ribosomal protein S19e	PF01090
Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This	PF03133
Synapsin, ATP binding domain. Ca dependent ATP binding in this ATP grasp fold. Function unknown	PF02750
eRF1 domain 3. The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 is known	PF03465
RanBP1 domain	PF00638
DNA polymerase delta, subunit 4	PF04081
Sodium:sulfate symporter transmembrane region	PF00939
Up-frameshift suppressor 2. Transcripts harboring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acti	PF04050
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 Glc	PF01762
Eukaryotic-type DNA primase, large subunit. DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa	PF04104
Tissue factor	PF01108
Ribosomal protein L35Ae	PF01247
Bombesin-like peptide	PF02044
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	PF00467
ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella	PF00006
Monocarboxylate transporter	PF01587
Dehydrogenase E1 component	PF00676
GH3 auxin-responsive promoter	PF03321
Adenylate cyclase. One member was found to complement mutants of E. coli. cya. This protein has been shown to be an adenylate kinase	PF01928
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 initiate	PF01642
Vacuolar protein sorting 36. Vps36 is involved in Golgi to endosome trafficking	PF04132
Coronavirus nucleocapsid protein	PF00937
FAD binding domain in molybdopterin dehydrogenase	PF00941
Integral membrane protein DUF106. This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins	PF01956
ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems	PF03308
Mab-21 protein	PF03281
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	PF01896
Tellurite resistance protein TehB	PF03848
Peptidase C16 family	PF01831
Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found	PF02883
Peptidase family C25	PF01364
4-hydroxybenzoyl-CoA thioesterase. This enzyme (EC 3.1.2.23) catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3	PF03061
Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signaling proteins that contain pfam00169, rasGEF, rhoGEF, rhoGAP, pfam00615, pfam00595 domains	PF00610
Low molecular weight phosphotyrosine protein phosphatase	PF01451
Amidase	PF01425
Transcription factor E2F/dimerisation partner (TDP). This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in associ	PF02319
PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)	PF01399
RNase3 domain	PF00636
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 contai	PF01591
Domain of unknown function	PF03619
Plectin/S10 domain. This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding	PF03501
Glutaredoxin	PF00462
TIR domain. The TIR domain is an intracellular signaling domain found in MyD88, interleukin 1 receptor and the Toll receptor. Called TIR (by SMART?) for Toll - Interleukin - Resistance	PF01582
Cell differentiation family, Rcd1-like. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes	PF04078
Folate receptor family. This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anc	PF03024
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	PF01409
PH domain. PH stands for pleckstrin homology	PF00169
Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is	PF03095
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 tropom	PF00992
tRNA synthetases class I (C). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only cysteinyl tRNA synthetases	PF01406
Deoxyribose-phosphate aldolase. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function	PF01791
SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet	PF00588
Phosphatidylinositol transfer protein	PF02121
UDP-glucose/GDP-mannose dehydrogenase family, UDP binding 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 re	PF03720
Papain family cysteine protease	PF00112
Eukaryotic-type carbonic anhydrase	PF00194
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. EL	PF01448
Oestrogen receptor	PF02159
RHO protein GDP dissociation inhibitor	PF02115
CENP-B protein. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding domain, which binds to a corresponding 17bp CENP-B box sequence. In the C-terminal 59 residues,	PF03184
Laminin EGF-like (Domains III and V). This family is like pfam00008 but has 8 conserved cysteines instead of 6	PF00053
Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function	PF00596
Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking. In particular, Vps26 assembles into a retromer complex with at least four other proteins Vps	PF03643
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90	PF02518
D-ala D-ala ligase. This family contains D-alanine--D-alanine ligase enzymes EC:6.3.2.4	PF01820
Second step splicing factor 1. SSF is thought to bind rRNA and similarity with peter pan in Drosophila suggests a role in cell proliferation	PF03877
Retroviral GAG p10 protein. This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated w	PF02337
Corticotropin ACTH domain	PF00976
L27 domain. The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7	PF02828
Single-strand binding protein family	PF00436
BTB/POZ domain	PF00651
Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known t	PF03096
Calcium-activated potassium channel, beta subunit	PF03185
Rad17 cell cycle checkpoint protein	PF03215
Dynein light chain type 1	PF01221
Fibroblast growth factor	PF00167
Transthyretin precursor (formerly prealbumin). Transthyretin is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. Mutations in the human transthyretin are associated with several genetic disorders	PF00576
Eukaryotic initiation factor 3, gamma subunit. eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit if eIF3	PF04189
Polypeptide deformylase	PF01327
ParA family ATPase	PF00991
EAP30. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of tr	PF04157
Fes/CIP4 homology domain	PF00611
HSF-type DNA-binding	PF00447
Immunoglobulin A1 protease. This family consists of immunoglobulin A1 protease proteins. The immunoglobulin A1 protease cleaves immunoglobulin IgA and is found in pathogenic bacteria such as Neisseria gonorrhoeae. Not all of the members of this family are	PF02395
Glycosyl hydrolases family 31. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases	PF01055
Rad9. Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage	PF04139
Bacterial surface antigen. This entry includes the following surface antigens	PF01103
EPTP domain. Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. This presumed domain has no known function, b	PF03736
Auxin Efflux Carrier	PF03547
Glycosyl hydrolase family 26	PF02156
Peptidase family C50	PF03568
Adenylosuccinate synthetase	PF00709
Peptidase family C54	PF03416
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase com	PF00562
SPFH domain / Band 7 family. This family includes proteins with high blast scores to known Band 7 protein: HflC from E. coli, HflK from E. coli, Prohibitin family members	PF01145
Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain	PF02729
Paxillin family	PF03535
u-PAR/Ly-6 domain	PF00021
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 ar	PF01534
Autophagy protein Apg6. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either assoc	PF04111
Fasciclin domain. This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria	PF02469
pfam02946, GTF2I, GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain	PF02946
Carbohydrate phosphorylase. The members of this family catalyse the formation of glucose 1-phosphate from one of the following polyglucoses	PF00343
Programmed cell death protein 2, C-terminal domain	PF04194
OAR domain	PF03826
Ezrin/radixin/moesin family	PF00769
MIT domain	PF04212
FATC domain. The FATC domain is named after FRAP, ATM, TRRAP C-terminal	PF02260
Sulfatase	PF00884
pfam02928, zf-C5HC2, C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function	PF02928
Interleukin 15. Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses	PF02372
Ribonuclease HII	PF01351
Plexin repeat	PF01437
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	PF00910
Protein of unknown function (DUF410). Family of conserved eukaryotic proteins with undetermined function	PF04190
DNA photolyase. This domain binds a light harvesting cofactor	PF00875
TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta and joins	PF02002
LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins	PF03466
Pentaxin family. Pentaxins are also known as pentraxins	PF00354
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	PF01968
Adaptin N terminal region	PF01602
Myogenic Basic domain. This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates	PF01586
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	PF01191
Vps53-like, N-terminal domain. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events	PF04100
DIX domain. The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerisation. It is involved in the homo- oligomerisation of mouse axin. The axin DIX domain also interacts with the disheveled DIX domain. The	PF00778
Palmitoyl protein thioesterase	PF02089
Cathelicidin. A novel protein family, showing a conserved proregion and a variable carboxyl-terminal antimicrobial domain. This region shows similarity to cystatins	PF00666
S25 ribosomal protein	PF03297
Sodium:dicarboxylate symporter family	PF00375
Fic protein family. This family consists of the Fic (filamentation induced by cAMP) protein and its relatives. The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein	PF02661
3-hydroxyacyl-CoA dehydrogenase, C-terminal domain. This family also includes lambda crystallin. Some proteins include two copies of this domain	PF00725
K-Cl Co-transporter type 1 (KCC1)	PF03522
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 tand	PF00050
FKBP-type peptidyl-prolyl cis-trans isomerases	PF00254
Patched family. The transmembrane protein Patched is a receptor for the morphogene Sonic Hedgehog. This protein associates with the smoothened protein to transduce hedgehog signals	PF02460
Uncharacterized membrane protein family UPF0013. These proteins are integral membrane proteins of unknown function	PF01554
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-che	PF01078
Helix-hairpin-helix motif	PF00633
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	PF01555
Periodic tryptophan protein 2 WD repeat associated domain	PF04047
Saccharopine dehydrogenase. This family comprised of three structural domains that can not be separated in the linear sequence. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF). The saccharopine	PF03435
NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions	PF01370
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 c	PF00805
Autophagy protein Apg12. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg12 is covalently bound to Apg5	PF04110
Protein-arginine deiminase (PAD). Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes EC:3.5.3.15 catalyse the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-	PF03068
Sir2 family	PF02146
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 i	PF02142
Glutathione S-transferase, N-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but are not GSTs: * S-crystallins from squid. Similarity to GST previously noted. * Eukaryotic elongation	PF02798
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 barr	PF02219
Adaptin N terminal region. This family consists of the N terminal region of various alpha	PF01602
Glutathione peroxidase	PF00255
Topoisomerase DNA binding C4 zinc finger	PF01396
Glycosyl hydrolase family 59	PF02057
WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGl	PF00568
FAD binding domain. This domain is involved in FAD binding in a number of enzymes	PF01494
Aminotransferase class-III	PF00202
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	PF00664
Folate receptor family. This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anch	PF03024
Autophagy protein Apg9. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeti	PF04109
Renal dipeptidase	PF01244
Glutamine synthetase, beta-Grasp domain	PF03951
SMC family, C-terminal domain. This Pfam family represents a conserved domain towards the C-terminus of the SMC family proteins. A second conserved domain is found at the N-terminus (pfam02463). The SMC (structural maintenance of chromosomes) superfamily	PF02483
Permease family. This family includes permeases for diverse substrates such as xanthine, uracil and vitamin C. However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predic	PF00860
ATP-sulfurylase. This family consists 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 P	PF01747
Stanniocalcin family	PF03298
3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-termi	PF01612
3' exoribonuclease family, domain 2. 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	PF03725
Beta-amyloid peptide (beta-APP)	PF03494
ribosomal L5P family C-terminus. This region is found associated with pfam00281	PF00673
Nrap protein. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap	PF03813
Endo/excinuclease amino terminal domain. This domain has no known function it is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE	PF01541
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 center around conserved cysteine, histidine,	PF01841
PDZ domain (Also known as DHR or GLGF). PDZ domains are found in diverse signaling proteins	PF00595
SET domain. 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 doma	PF00856
u-PAR/Ly-6 domain. This extracellular disulphide bond rich domain is related to pfam00087	PF00021
Myb-like DNA-binding domain	PF00249
Putative transcriptional regulator. Members of this family range in length from 140-180 amino acids. One member interacts with c-Myc and represses its transcriptional activity. Suggesting that other members of this family may also regulate transcription	PF02996
Protein kinase domain	PF00069
pfam02936, COX4, Cytochrome c oxidase subunit IV. 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 cytochrome c oxidase subunit IV. The Dictyostelium	PF02936
High molecular weight glutenin subunit. Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, gluteni	PF03157
Stathmin family	PF00836
Inhibitor of Apoptosis domain. BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat' Also known as IAP repeat	PF00653
DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which	PF03184
Cytidine and deoxycytidylate deaminase zinc-binding region	PF00383
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	PF01826
Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain	PF00130
Synuclein. There are three types of synucleins in humans, these are called alpha, beta and gamma. Alpha synuclein has been found mutated in families with autosomal dominant Parkinson's disease. A peptide of alpha synuclein has also been found in amyloid p	PF01387
Phosphoglycerate mutase family	PF00300
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 carboxy	PF00594
Beige/BEACH domain	PF02138
Uncharacterized ACR, COG1354	PF02616
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 a	PF00430
FlhB HrpN YscU SpaS Family	PF01312
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 in Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans	PF01437
NSF attachment protein	PF02071
pfam02926, THUMP, THUMP domain. The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. It is predicted that this domain is an RNA-binding domain that adopts an alpha/b	PF02926
Electron transfer flavoprotein beta subunit. This protein is distantly related to and forms a heterodimer with pfam00766	PF01012
Nicotinate phosphoribosyltransferase (NAPRTase). Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyses the first reaction in the NAD salvage synthesis	PF04095
Transcription initiation factor IID, 31kD subunit. This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated tran	PF02291
Daxx Family. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remians to be determined	PF03344
Glycophorin A	PF01102
Uncharacterised protein family (UPF0121). Uncharacterised integral membrane protein family	PF03661
Sodium:alanine symporter family	PF01235
Fungal specific domain of unknown function (DUF391). A family of uncharacterised fungal proteins	PF04125
Ku70/Ku80 beta-barrel domain. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bin	PF02735
Cullin family	PF00888
Cytochrome b561	PF03188
Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca	PF02888
Leucine rich repeat C-terminal domain	PF01463
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	PF00581
ab-hydrolase associated lipase region	PF04083
Alpha-2-macroglobulin family N-terminal region. This family includes the N-terminal region of the alpha-2-macroglobulin family	PF01835
Domain of unknown function DUF130. This family has no known function, it consists of C. elegans proteins and is present as a repeat in some members. The aligned region has 4 conserved cysteine residues and is a maximum of 175 residues long	PF02343
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	PF01562
Prp18 domain. The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequ	PF02840
mTERF. This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein	PF02536
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 is related to this family	PF00031
BolA-like protein. This family consist of the morpho-protein BolA from E. coli and its various homologs. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems	PF01722
haloacid dehalogenase-like hydrolase. This family are 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 tw	PF00702
MMPL family. Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, alth	PF03176
Orbivirus VP3 (T2) protein. The orbivirus VP3 protein is part of the virus core and makes a 'subcore' shell made up of 120 copies of the 100K protein. VP3 particles can also bind RNA and are fundamental in the early stages of viral core formation. Also fo	PF01700
Gag polyprotein, inner coat protein p12. The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus	PF01141
C-5 cytosine-specific DNA methylase	PF00145
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 lack	PF00179
Lipid-A-disaccharide synthetase. This is a family of lipid-A-disaccharide synthetases	PF02684
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 grou	PF01597
Supt5 repeat. This short region of similarity is found in two tandem copies in Supt5 proteins that are involved in chromatin regulation. The function of this region is unknown	PF03439
Thrombospondin N-terminal -like domain	PF02210
Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI	PF01381
Alpha amylase	PF00128
Phosphomevalonate kinase. Phosphomevalonate kinase (EC:2.7.4.2) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. This family represents the animal ty	PF04275
Galactose-1-phosphate uridyl transferase, C-terminal domain. SCOP reports fold duplication with N-terminal domain. Both involved in Zn and Fe binding	PF02744
7 transmembrane receptor (metabotropic glutamate family)	PF00003
Vomeronasal organ pheromone receptor family, V1R. This family represents one of two known vomeronasal organ receptor families, the V1R family (after)	PF03402
ATP synthase delta (OSCP) subunit. The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family pfam00401	PF00213
Major royal jelly protein. Royal jelly is the food of queen bee larvae, and is responsible for the high reproductive ability of the queen. Major royal jelly proteins make up around 90% of larval jelly proteins. This family also the sequence-related yellow	PF03022
Ribosomal protein S27a. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of	PF01599
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. T	PF01242
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 yea	PF01479
Guanylin precursor	PF02058
tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes	PF01921
Low temperature viability protein	PF04180
Reeler domain	PF02014
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 re	PF02221
Trefoil (P-type) domain	PF00088
'Paired box' domain	PF00292
Domain of unknown function (DUF315). Family of plant hypothetical proteins	PF03759
Vinculin family	PF01044
Acyl-CoA dehydrogenase, middle domain. Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold	PF02770
HSF-type DNA-binding domain	PF00447
HEAT repeat. The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). CAUTION: This family does not contain all known HEAT repeats	PF02985
Transposase, Mutator family	PF00872
Prion/Doppel alpha-helical domain. The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the no	PF00377
O-methyltransferase	PF01596
pfam02906, Fe_hyd_lg_C, Iron only hydrogenase large subunit, C-terminal domain	PF02906
Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1	PF00240
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	PF01992
haloacid dehalogenase-like hydrolase	PF00702
BRICHOS domain. The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer	PF04089
TCL1/MTCP1 family. Two related oncogenes, TCL-1 and MTCP-1, are overexpressed in T cell prolymphocytic leukemias as a result of chromosomal rearrangements that involve the translocation of one T cell receptor gene to either chromosome 14q32 or Xq28	PF01840
pfam02893, GRAM, GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins	PF02893
SAC3/GANP family. This family of eukaryotic proteins brings together the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localization of MCM3, a protein that associates with chromatin in the G1 p	PF03399
Anp1. The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localize within the cis Golgi, and that they are physically associated in two distinct complexes	PF03452
NAD:arginine ADP-ribosyltransferase	PF01129
Protein of unknown function DUF52. This family contains members from all branches of life. The function of this protein is unknown	PF01875
FKBP-type peptidyl-prolyl cis-trans isomerase	PF00254
Reovirus viral attachment protein sigma 1. This family consists of the reovirus sigma 1 hemagglutinin, cell attachment protein. This glycoprotein is a minor capsid protein and also determins the serotype-specific humoral immune response. Sigma 1 consist	PF01664
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 fact	PF01008
Trehalase	PF01204
Cell cycle protein. This entry includes the following members	PF01098
Lysosome-associated membrane glycoprotein (Lamp)	PF01299
Uncharacterized ACR, YneC family COG1359	PF02619
Cytochrome C1 family	PF02167
Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain	PF02752
Uncharacterised protein family (UPF0041)	PF03650
Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossman NAD(P) binding fold	PF00044
Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	PF02775
Adenylate kinase	PF00406
Doublecortin	PF03607
Hexon-associated protein (IIIa)	PF02455
Adenine deaminase. Adenine deaminase EC:3.5.4.2 hydrolyses adenine to form hypoxanthine and ammonia. The enzyme is part of a large metal dependent hydrolase superfamily. Adenine deaminases reaction is important for adenine utilization as a purine and also	PF01979
pfam02877, PARP_reg, Poly(ADP-ribose) polymerase, regulatory 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 affini	PF02877
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 con	PF00082
SCO1/SenC. This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c o	PF02630
Putative transcriptional regulator. Members of this family range in length from 140-180 amino acids. One member interacts with c-Myc and represses its transcriptional activity. Suggesting that other members of this family may also regulate transcription b	PF02996
Sushi domain (SCR repeat)	PF00084
Presenilin. Mutations in presenilin-1 are a major cause of early onset Alzheimer's disease. It has been found that presenilin-1 binds to beta-catenin in-vivo. This family also contains SPE proteins from C.elegans	PF01080
Core-2/I-Branching enzyme. This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme. I-branching enzyme is responsible for the production of the blood group I-antigen during embryo	PF02485
Class II histocompatibility antigen, alpha domain	PF00993
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 unknow	PF01469
Ribosomal Proteins L2	PF00181
CRAL/TRIO domain. The original profile has been extended to include the carboxyl domain from the known structure of Sec14	PF00650
Iron/manganese superoxide dismutases, alpha-hairpin domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one	PF00081
Putative phosphatase regulatory subunit. This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein has been shown to interact with glycogen synthase,	PF03370
Seven in absentia protein family. The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results	PF03145
PH domain	PF00169
MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a small domain that may have a ligand transferase function	PF02815
Uncharacterised protein family (UPF0108)	PF03656
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	PF00217
Casein kinase II regulatory subunit	PF01214
RNA polymerase A/beta'/A" subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This family inclu	PF01854
CAIB/BAIF family. This is a family of enzymes with diverse function, including fatty-acid CoA racemase enzymes such as arylpropionyl-CoA epimerase a key enzyme in the inversion metabolism of ibuprofen, carnitine dehydratase (CAIB) (EC 4.2.1.89) and bile a	PF02515
Sec63 domain	PF02889
ATP-NAD kinase. Members of this family are ATP-NAD kinases EC:2.7.1.23. Catalyses the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus	PF01513
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 typ	PF01507
N-terminal domain	PF02078
Transcription initiation factor IID, 18kD subunit. This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histon	PF02269
Transketolase, pyridine binding domain. This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases	PF02779
SCAMP family. In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a c	PF04144
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	PF00058
Ribosomal Proteins L2, RNA binding domain	PF00181
Beta type Zein	PF02054
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 pi	PF01602
Bacteriophage lysis protein. This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database	PF03245
CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of precorrin-2 to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chloroph	PF02514
EB1-like C-terminal motif. This motif is found at the C-terminus of proteins that are related to the EB1 protein. The EB1 proteins contain an N-terminal CH domain pfam00307. The human EB1 protein was originally discovered as a protein interacting with the	PF03271
dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be sim	PF03455
Structure-specific recognition protein	PF03531
Retinoblastoma-associated protein B domain. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved	PF01857
Apoptosis regulator proteins	PF00452
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	PF02229
SAC3/GANP family. This family of eukaryotic proteins brings together the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localization of MCM3, a protein that associates with chromatin in the G1	PF03399
Phosphotriesterase family	PF02126
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 tropomy	PF00992
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 su	PF02109
3-beta hydroxysteroid dehydrogenase/isomerase family. The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precurso	PF01073
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	PF02036
Regulator of chromosome condensation (RCC1)	PF00415
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	PF00007
Gaa1-like, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly	PF04114
Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase	PF01182
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 d	PF02272
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	PF00560
Spin/Ssty Family. Spindlin (Spin) is a novel maternal transcript present in the unfertilized egg and early embryo. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members o	PF02513
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	PF01585
5'-3' exonuclease, C-terminal SAM fold	PF01367
Copper amine oxidase, N2 domain. This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous	PF02727
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 in Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans p	PF01437
Fusion glycoprotein F0	PF00523
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.	PF00008
Aldo/keto reductase family	PF00248
Tc5 transposase	PF03221
MHCK/EF2 kinase domain family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a b	PF02816
Protein of unknown function (DUF431)	PF04252
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. E	PF01448
EAP30. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of t	PF04157
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-rib	PF00644
Autophagy protein Apg6. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either asso	PF04111
ATP-dependent protease La (LON) domain	PF02190
HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus	PF00632
GNS1/SUR4 family	PF01151
CBF/Mak21 family	PF03914
Tropomodulin. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two domai	PF03250
Uncharacterised protein family (UPF0100). This family of proteins are periplasmic binding proteins that includes ModA the molybdate-binding protein. Some members of this family are in the UPF0100 family	PF03697
HpcH/HpaI aldolase family. This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase	PF03328
Retinal pigment epithelial membrane protein. This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence	PF03055
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 (prefere	PF01510
Vacuolar (H+)-ATPase G subunit. This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins	PF03179
Skp1 family, tetramerisation domain	PF03931
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. STA	PF01017
Ribonucleotide reductase, barrel domain	PF02867
MYND finger	PF01753
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	PF00801
Cation transporting ATPase, C-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport	PF00689
Ribosomal protein L31e	PF01198
UBX domain. Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p	PF00789
Glucose-6-phosphate dehydrogenase, NAD binding domain	PF00479
Arginyl tRNA synthetase N terminal domain. This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA re	PF03485
NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation	PF02540
CBL proto-oncogene N-terminal domain 1. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and	PF02262
Vitelline membrane outer layer protein I (VOMI). VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furth	PF03762
Ets-domain	PF00178
NOT2 / NOT3 / NOT5 family. NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5	PF04153
Transcription initiation factor TFIID 23-30kDa subunit	PF03540
Lipase	PF00151
Domain of unknown function (DUF384). domo keywords :chromosome c26f1.12c 41.3	PF04064
OTU-like cysteine protease. This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine	PF02338
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 formati	PF02320
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 releas	PF00984
DNA mismatch repair proteins, mutS family	PF00488
Cytochrome c/c1 heme lyase	PF01265
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	PF01266
Protein of unknown function DUF124. This prokaryotic protein family has no known function	PF01987
Tryptophan/tyrosine permease family	PF03222
5'-nucleotidase	PF01009
von Willebrand factor type D domain	PF00094
pfam02921, UCR_TM, Ubiquinol cytochrome reductase transmembrane region. Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex	PF02921
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 var	PF01755
Nucleoside diphosphate kinases	PF00334
RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated	PF02463
Early E1A protein. This is a family of adenovirus early E1A proteins. The E1A protein is 32 kDa it can however be cleaved to yield the 28 kDa protein. The E1A protein is responsible for the transcriptional activation of the early genes with in the viral g	PF02703
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 metabolism. The ability of this widely distributed heterotrimeric enzy	PF01603
Helicase conserved C-terminal domain. 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	PF00271
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	PF01017
Nucleotide-sugar transporter. This family of membrane proteins transport nucleotide sugars from the cytoplasm into golgi vesicles. Individual members transport CMP-sialic acid, UDP-galactose, and UDP-GlcNAc	PF04142
ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella	PF02874
Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine	PF00439
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	PF02376
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 relat	PF01713
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	PF00204
Molybdopterin oxidoreductase	PF00384
Hormone receptor domain. This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain	PF02793
Domain of unknown function DUF28. This domain is found in bacterial and yeast proteins it compromises the entire length or central region of most of the proteins in the family, all of which are hypothetical with no known function. The average length of th	PF01709
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 dihydrour	PF01207
pfam02881, SRP54_N, SRP54-type protein, helical bundle domain	PF02881
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), whi	PF00026
Glycosyl hydrolase family 20, catalytic domain. This domain has a TIM barrel fold	PF00728
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 r	PF01842
Eukaryotic protein of unknown function, DUF279	PF03357
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	PF01922
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 le	PF01394
tRNA synthetases class I (W and Y)	PF00579
Galanin	PF01296
Cornifin (SPRR) family	PF02389
Glycosyl transferases group 1. Mutations in this domain may lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysacchari	PF00534
DNA/RNA non-specific endonuclease	PF01223
Phospholipase/Carboxylesterase. This family consists of both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases pfam00561	PF02230
TMS membrane protein/tumour differentially expressed protein (TDE)	PF03348
F-box associated region. Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. One member is involved in binding to N-glycosylated	PF04300
3'-5' exonuclease	PF01612
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	PF00930
Uncharacterized ACR, YdiU/UPF0061 family	PF02696
Mitochondrial carrier protein	PF00153
Ribosomal protein L34e	PF01199
Dishevelled specific domain. This domain is specific to the signaling protein dishevelled. The domain is found adjacent to the PDZ domain pfam00595, often in conjunction with DEP (pfam00610) and DIX (pfam00778)	PF02377
Sec1 family	PF00995
Protein of unknown function (DUF409). Family of eukaryotic membrane proteins with unknown function	PF04188
Domain of unknown function DUF60. The proteins in this family have no known function. Two proteins have been annotated as phosphotransferases, however this is not supported experimentally, and should be viewed with caution	PF01885
Thiolase, N-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase	PF00108
Plasmid Maintenance Protein. The SMP protein has been implemented in plasmid stability	PF03901
Bacterial surface antigen. This entry includes the following surface antigens; D15 antigen from H.influenzae	PF01103
Ribosomal protein L6, N-terminal domain	PF03868
Neuromedin U	PF02070
Poxvirus D5 protein. This protein is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase	PF03288
Transcription factor IIA, alpha/beta subunit. Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are repr	PF03153
Bacterial extracellular solute-binding proteins, family 3	PF00497
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 mou	PF01794
Transferring receptor-like dimerisation domain. This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure	PF04253
Glycosyl hydrolase family 79, N-terminal domain. Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular m	PF03662
Transketolase, C-terminal domain. The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site	PF02780
Dynamin GTPase effector domain	PF02212
Borrelia outer surface protein D (OspD)	PF03207
Clusterin	PF01093
Eukaryotic protein of unknown function, DUF292	PF03398
Uncharacterized ACR, YggU family COG1872	PF02594
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	PF01365
Nucleoside transporter. This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their	PF01733
pfam02919, Topoisomer_I_N, Eukaryotic DNA topoisomerase I, DNA binding fragment. 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 replicat	PF02919
Orn/Lys/Arg decarboxylase, major domain	PF01276
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 b	PF02251
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 f	PF00645
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	PF01812
HlyD family secretion protein	PF00529
Ribosomal protein L15 amino terminal region. This family is always associated with pfam00256. This family is diagnostic of ribosomal L15 proteins	PF01305
NADP oxidoreductase coenzyme F420-dependent	PF03807
SAM dependent carboxyl methyltransferase. This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step meth	PF03492
Microtubule associated protein 1A/1B, light chain 3. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity	PF02991
Env gp36 protein (HERV/MMTV type). This family includes the GP36 protein from retroviruses such as mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs). The GP36 protein is an envelope protein that has a predicted transmembrane heli	PF03056
Uncharacterised protein family (UPF0123). This family of proteins are uncharacterised, they contain five CXXC motifs	PF03660
WHEP-TRS domain	PF00458
Rabaptin	PF03528
RNA polymerase Rpb5, N-terminal domain. Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. The N-terminal domain is involved in DNA binding and is part of t	PF03871
Uncharacterised protein family (UPF0169). Members of this family are predicted to be lipoproteins. The function of these proteins is unknown	PF03696
Metallo-beta-lactamase superfamily	PF00753
Legume-like lectin family. Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first recognized members of a family of animal lectins similar (19-2	PF03388
uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain	PF03456
Ribosomal L39 protein	PF00832
Glypican	PF01153
Alpha crystallin A chain, N terminal	PF00525
Dor1-like family. Dor1 is involved in vesicle targeting to the yeast Golgi apparatus and complexes with a number of other trafficking proteins, which include Sec34 and Sec35	PF04124
Ribosomal protein L36e	PF01158
Somatomedin B domain	PF01033
HEC/Ndc80p family. Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle	PF03801
Uncharacterized BCR, YhhW family COG1741	PF02678
Glutaminyl cyclase. Glutaminyl cyclase catalyses the formation of the pyroglutamyl residue present at the amino terminus of numerous secretory peptides and proteins. Glutaminyl cyclase posses a zinc aminopeptidase domain in which the four functionally im	PF03565
NUDIX domain	PF00293
K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly r	PF02214
Syntaxin	PF00804
E1-E2 ATPase	PF00122
eIF4-gamma/eIF5/eIF2-epsilon. This domain of unknown function is found at the C-terminus of several translation initiation factors	PF02020
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	PF01106
Thioredoxin	PF00085
Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes	PF00237
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 tryp	PF00605
Putative membrane protein. This family called family 8 in, may be a transmembrane protein The specific function of this protein is unknown	PF01062
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 i	PF01428
PAC motif. PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold	PF00785
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	PF00091
DDT domain. This domain is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors)	PF02791
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)	PF00839
CDC45-like protein. CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human, mouse and smut fungus among others	PF02724
CBL proto-oncogene N-terminus, EF hand-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily con	PF02761
Malic enzyme, N-terminal domain	PF00390
Tau and MAP protein, tubulin-binding repeat	PF00418
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 metallopeptidase	PF00045
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	PF01777
Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activate	PF03089
Chaperonin 10 Kd subunit	PF00166
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 initiat	PF01642
Retrotransposon gag protein. Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved	PF03732
RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signaling pathways	PF02759
Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this re	PF02295
pfam02911, formyl_trans_C, Formyl transferase, C-terminal domain	PF02911
Uncharacterised protein family (UPF0080)	PF03651
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	PF00782
NTR/C345C module. We have not included the related pfam00965 family. It has been suggested that the common function of these modules is binding to metzincins. A subset of this family is known as the C345C domain because it occurs in complement C3, C4 and	PF01759
Eukaryotic ribosomal protein L18	PF00828
pfam02926, THUMP, THUMP domain. The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. It is predicted that this domain is an RNA-binding domain that adopts an alpha/	PF02926
Ciliary neurotrophic factor	PF01110
F-box domain	PF00646
Transcription factor Tfb2	PF03849
Glycoprotease family	PF00814
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	PF01505
Ctr copper transporter family. The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of hig	PF04145
Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyse the reaction: Phosphatidyl-L-serine <=> phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in t	PF02666
Transcription factor Tfb4	PF03850
Glutamate-cysteine ligase. This family represents the catalytic subunit of glutamate-cysteine ligase (E.C. 6.3.2.2), also known as gamma-glutamylcysteine synthetase (GCS). This enzyme catalyses the rate limiting step in the biosynthesis of glutathione. Th	PF03074
Homeobox domain	PF00046
Na+ dependent nucleoside transporter. This family consists of nucleoside transport proteins, like a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane, or a Na+-dependent nucleoside transporter selective for pyrimidine	PF01773
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	PF01522
Cytosol aminopeptidase family, N-terminal domain	PF02789
pfam02887, PK_C, Pyruvate kinase, alpha/beta domain	PF02887
RPEL repeat	PF02755
pfam02877, PARP_reg, Poly(ADP-ribose) polymerase, regulatory 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 affinit	PF02877
Deuterolysin metalloprotease (M35) family	PF02102
Ribosomal protein S21e	PF01249
RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases	PF00620
ZPR1 zinc-finger domain. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localized to the cytoplasm. But in proliferating cells treated with EGF or with othe	PF03367
GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain	PF02946
MmgE/PrpD family. This family includes 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle	PF03972
FYVE zinc finger	PF01363
Vacuolar protein sorting-associated protein 35. Vacuolar protein sorting-associated protein (Vps) 35 is one of around 50 proteins involved in protein trafficking. In particular, Vps35 assembles into a retromer complex with at least four other proteins Vps	PF03635
Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signaling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, d	PF03921
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 domai	PF00552
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 f	PF01694
RasGEF domain. Guanine nucleotide exchange factor for Ras-like small GTPases	PF00617
Nuf2 family. Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein h	PF03800
Sigma-54 interaction domain	PF00158
Marek's disease glycoprotein A	PF02124
Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is only found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family	PF01637
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 o	PF01734
Uncharacterized protein family UPF0001	PF01168
Ribosomal L28e protein family	PF01778
Galactosyltransferase. This is a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activitys	PF02709
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	PF00070
Uncharacterized protein family UPF0005	PF01027
Hr1 repeat	PF02185
Glutathione S-transferase, N-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but are not GSTs: * S-crystallins from squid. Similarity to GST previously noted. * Eukaryotic elongation f	PF02798
Glutamine amidotransferase class-I	PF00117
Uncharacterized protein family UPF0007	PF01128
Telomere-binding protein alpha subunit, N-terminal domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. A	PF02307
Integral membrane protein DUF92. Members of this family have several predicted transmembrane helices. The function of these prokaryotic proteins is unknown	PF01940
Iron-containing alcohol dehydrogenase	PF00465
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	PF00230
Tumor protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction	PF04201
Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold	PF02800
Calx-beta domain	PF03160
Cytochrome c oxidase subunit VIIa. Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the heart and liver isoforms of cytochrome c oxidase subunit VIIa	PF02238
Mpp10 protein. This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerev	PF04006
FG-GAP repeat	PF01839
Mob1/phocein family. Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known struc	PF03637
Bcl-2 homology region 4	PF02180
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 lyso	PF01735
Protein of unknown function (DUF343). This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest	PF03966
6-O-methylguanine DNA methyltransferase, DNA binding domain. This domain is a 3 helical bundle	PF01035
pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure	PF02931
Connexin	PF00029
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	PF00621
SAND family protein. Members of this family are uncharacterised proteins that have been called SAND proteins. These protein do not contain a SAND domain. The members of this family are 500-600 amino acids long and contain several conserved motifs	PF03164
Giardia variant-specific surface protein	PF03302
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 act	PF01588
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.	PF01242
Profilin	PF00235
SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins	PF00448
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 cont	PF00082
Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-	PF02606
Phage maturation protein	PF03863
Hydantoinase B/oxoprolinase. This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase EC:3.5.2.9 which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the ox	PF02538
Melibiase	PF02065
Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex	PF04056
CNH domain. Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations	PF00780
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	PF00538
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	PF01026
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 bind	PF02252
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	PF00024
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 t	PF01909
Pancreatic ribonuclease. Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices	PF00074
Peptidyl-tRNA hydrolase 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 con	PF00472
ZPR1 zinc-finger domain. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localized to the cytoplasm. But in proliferating cells treated with EGF or with other	PF03367
Uncharacterised protein family (UPF0083)	PF03654
Iodothyronine deiodinase	PF00837
Putative methyltransferase. Members of this family of hypothetical plant proteins are probably methyltransferases: several of the aligned sequences either match methyltransferase profiles, or contain a SAM-binding motif. One member contains both	PF03141
Phosphorylase family	PF01048
Rabphilin-3A effector domain. This is a family of proteins involved in protein transport in synaptic vesicles. Rabphilin-3A has been shown to contact Rab3A, a small G protein important in neurotransmitter release, in two distinct areas	PF02318
Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion inte	PF02330
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	PF00224
DIX domain. The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerisation. It is involved in the homo- oligomerisation of mouse axin. The axin DIX domain also interacts with the disheveled DIX domain. The D	PF00778
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 tande	PF00050
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	PF02274
Mov34/MPN/PAD-1 family. 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. It has	PF01398
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	PF01803
BSD domain. This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function	PF03909
Riboflavin kinase / FAD synthetase. This family consists part of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activitys. They catalyse the 5'-pho	PF01687
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 possibly related to the pfam00135 family	PF00756
Uncharacterized protein family UPF0021	PF01171
Clathrin light chain	PF01086
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 conta	PF01591
Sec61beta family. This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG	PF03911
Uncharacterized protein family UPF0023	PF01172
AFG1-like ATPase. This family of proteins contains a P-loop motif and are predicted to be ATPases	PF03969
Class II histocompatibility antigen, beta domain	PF00969
Uncharacterized protein family UPF0024	PF01142
Ribosomal protein S24e	PF01282
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	PF00627
Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity	PF00248
Uncharacterized protein family UPF0027	PF01139
Uncharacterized protein family UPF0029	PF01205
YEATS family. We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity	PF03366
TSC-22/dip/bun family	PF01166
MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans	PF00917
Domain of unknown function DUF143. This domain has no known function nor do any of the proteins that possess it. The aligned region is approximately 100 amino acids long	PF02410
PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline	PF00639
eIF-6 family. This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues	PF01912
D-Ala-D-Ala carboxypeptidase 3 (S13) family	PF02113
impB/mucB/samB family. These proteins are involved in UV protection	PF00817
Coenzyme A transferase	PF01144
Eukaryotic phosphomannomutase. This enzyme EC:5.4.2.8 is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions	PF03332
Sterol desaturase. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain many conserved histidine residues. M	PF01598
KE2 family protein. The function of members of this family is unknown, although they have been suggested to contain a DNA binding leucine zipper motif	PF01920
Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones	PF02525
pfam02879, PGM_PMM_II, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II	PF02879
Not1 N-terminal domain, CCR4-Not complex component	PF04065
Transcription factor TFIIB repeat	PF00382
Statherin. Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N-terminus of statherin is highly charge, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite	PF03875
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 i	PF02421
Uncharacterized protein family UPF0034	PF01207
Uncharacterized protein family UPF0036	PF02147
Herpes virus major capsid protein. This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and th	PF03122
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	PF01749
Putative transcriptional regulator. Members of this family range in length from 140-180 amino acids, some interacts with c-Myc and repress its transcriptional activity. Suggesting that other members of this family may also regulate transcription by intera	PF02996
Guanylate-binding protein, C-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	PF02841
DNA polymerase epsilon subunit B. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme cons	PF04042
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 cytop	PF00584
ER lumen protein retaining receptor	PF00810
ARD/ARD' family. The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be	PF03079
Protein of unknown function (DUF229). Members of this family are uncharacterised. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains	PF02995
CG-1 domain. CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are ass	PF03859
Autophagocytosis associated protein, C-terminal domain. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole	PF03987
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 mous	PF01794
PI3-kinase family, p85-binding domain	PF02192
GDA1/CD39 (nucleoside phosphatase) family	PF01150
Myosin N-terminal SH3-like domain. This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown	PF02736
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 th	PF00975
Slow voltage-gated potassium channel	PF02060
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 thi	PF00977
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	PF00730
Glucose-6-phosphate dehydrogenase, C-terminal domain	PF02781
BRO1-like domain. This functionally uncharacterised domain is found in a number of signal transduction proteins, including Rhophilin and BRO1	PF03097
Structural protein 2. This family represents structural protein 2 of the hepatitis E virus. The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation	PF03014
Ribosomal protein S26e	PF01283
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	PF00514
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 Kelch is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Sev	PF01344
Glycyl-tRNA synthetase beta subunit	PF02092
Bacterial dnaA protein	PF00308
DNA polymerase alpha subunit B. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner	PF04058
STAT protein, DNA binding 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. Th	PF02864
PRP38 family. Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about	PF03371
Phosphoglucose isomerase. Phosphoglucose isomerase catalyses the interconversion of glucose-6-phosphate and fructose-6-phosphate	PF00342
Sm protein	PF01423
pfam02922, isoamylase_N, Isoamylase N-terminal domain. This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase	PF02922
Sema domain	PF01403
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 lipovitelli	PF01347
Cytochrome c oxidase subunit III	PF00510
Pyridoxal-dependent decarboxylase, C-terminal sheet domain. These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates	PF00278
Fanconi anaemia group C protein	PF02106
Zinc-binding dehydrogenase	PF00107
Integral membrane protein DUF110. This archaebacterial protein family has no known function. Some members of this family are annotated as FlaJ, however we can find no supporting evidence for this annotation	PF01961
Putative phosphatase regulatory subunit. This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein has been shown to interact with glycogen synthase, p	PF03370
Uncharacterized protein family UPF0054	PF02130
Ribosomal protein L3	PF00297
Sodium:sulfate symporter transmembrane region. Some members in this family belong to the subfamily SODIT1	PF00939
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 str	PF00128
4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family	PF00142
Ribosomal protein L5	PF00281
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	PF00048
CLN3 protein. This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease)	PF02487
Ribosomal protein L6	PF00347
Copper amine oxidase, N3 domain. This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitou	PF02728
TAP42-like family. The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 (PFAM:PF04176) interacts with TAP42 and negatively regulates the TOR signaling pathway	PF04177
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 Pfam family consists of putative competence-damaged proteins from	PF02464
SCO1/SenC. This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c ox	PF02630
HIN-200/IF120x domain. This domain has no know function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain pfam02758	PF02760
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 modi	PF01472
Protein phosphatase 2A regulatory B subunit (B56 family)	PF01603
Vacuolar sorting protein 9 (VPS9) domain	PF02204
Shikimate kinase	PF01202
Insulin-like growth factor binding proteins	PF00219
Endoplasmic Reticulum Oxidoreductin 1 (ERO1). Members of this family are required for the formation of disulphide bonds in the ER	PF04137
Domain of unknown function DUF59. This family includes prokaryotic proteins of unknown function. The family also includes PhaH from Pseudomonas putida. PhaH forms a complex with PhaF, PhaG and PhaI, which hydroxylates phenylacetic acid to 2-hydroxyphenyla	PF01883
Copper type II ascorbate-dependent monooxygenase, C-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold	PF03712
Hantavirus glycoprotein G2. The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins. G1 and G2, as a precursor protein in the complementary sense RNA	PF01561
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	PF01576
LIM domain. This family represents two copies of the LIM structural domain	PF00412
Anaphase-promoting complex, subunit 10 (APC10)	PF03256
Ribosomal L27 protein	PF01016
Proteasome A-type and B-type	PF00227
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	PF00731
Ribosomal protein S28e	PF01200
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	PF01465
Arrestin (or S-antigen), N-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain	PF00339
Calcitonin / CGRP / IAPP family	PF00214
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	PF00014
Paired amphipathic helix repeat. This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-lo	PF02671
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 o	PF00797
Myogenic Basic domain. This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates s	PF01586
3-oxo-5-alpha-steroid 4-dehydrogenase. This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalysed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-stero	PF02544
Atrial natriuretic peptide	PF00212
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, threoni	PF00291
Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits	PF00615
Cytidylyltransferase. This family includes: Cholinephosphate cytidylyltransferase. Glycerol-3-phosphate cytidylyltransferase	PF01467
TPR Domain	PF00515
Skp1 family, dimerisation domain	PF01466
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 utilise thiamine pyrophosphate as a cofacto	PF00456
Antifreeze-like domain. This family contains type III antifreeze proteins as well as a variety of enzymes. This domain is presumed to be involved in sugar binding in the enzyme proteins	PF01354
Cytosolic long-chain acyl-CoA thioester hydrolase. This family consist of various cytosolic long-chain acyl-CoA thioester hydrolases including human and rat. The aligned region is repeated with in the sequence of human and rat cytosolic long-chain acyl-Co	PF01662
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 d	PF00320
Protein of unknown function DUF84. The function of this prokaryotic protein family is unknown	PF01931
Fumble. Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organization, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoform	PF03630
Somatostatin/Cortistatin family. Members of this family are hormones. Somatostatin inhibits the release of somatotropin. Cortistatin is a peptide that is related to the Somatostatins that is found to depresses neuronal electrical activity but, unlike som	PF03002
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 fo	PF01865
Cyclic nucleotide-binding domain	PF00027
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.	PF01352
Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1	PF03142
DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions	PF01529
Peptide methionine sulfoxide reductase. This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine	PF01625
Heme oxygenase	PF01126
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 fami	PF00031
PX domain. PX domains bind to phosphoinositides	PF00787
MOSC domain. The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely	PF03473
Calpain family cysteine protease	PF00648
Fes/CIP4 homology domain. Alignment extended from. Highly alpha-helical	PF00611
Ribosomal protein L14. This family includes the eukaryotic ribosomal protein L14	PF01929
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 fo	PF02244
Olfactomedin-like domain	PF02191
KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels	PF03520
Inositol polyphosphate kinase. ArgRIII has has been demonstrated to be an inositol polyphosphate kinase	PF03770
Fructose-1-6-bisphosphatase	PF00316
Electron transfer flavoprotein alpha subunit. This protein is distantly related to and forms a heterodimer with pfam01012	PF00766
Protein of unknown function DUF122. This protein family has no known function	PF01984
Mak10 subunit, NatC N(alpha)-terminal acetyltransferase. NatC N(alpha)-terminal acetyltransferases contains Mak10p, Mak31p and Mak3p subunits. All three subunits are associated with each other to form the active complex	PF04112
Endomembrane protein 70	PF02990
Ribosomal L29e protein family	PF01779
Ammonium Transporter Family	PF00909
2OG-Fe(II) oxygenase superfamily. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2	PF03171
EXS family. We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisae, and sequences that are thought to be	PF03124
Na+/Pi-cotransporter. This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotranspor	PF02690
Josephin	PF02099
Uncharacterised protein family (UPF0184)	PF03670
Cyclin-dependent kinase 5 activator protein	PF03261
2-hydroxychromene-2-carboxylate isomerase family. 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 HC	PF03046
Transcription factor S-II (TFIIS)	PF01096
Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle	PF00441
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. These proteins contain two pfam00571 domains	PF00654
TB2/DP1, HVA22 family. This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein, which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological	PF03134
Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes	PF00416
Oxygen-independent Coproporphyrinogen III oxidase. This family of bacterial enzymes catalyses the anaerobic transformation of coproporphyrinogen III to protoporphyrinogen IX required for porphyrin biosynthesis	PF02473
Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors	PF00060
Integrin alpha cytoplasmic region. This family contains the short intracellular region of integrin alpha chains	PF00357
SRP54-type protein, helical bundle domain	PF02881
RNA polymerase Rpb7, N-terminal domain. Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during Pol II elongation	PF03876
Interferon alpha/beta domain	PF00143
AhpC/TSA family. This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA)	PF00578
Glycosyl hydrolases family 15	PF00723
Integral membrane protein DUF6. This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region	PF00892
Glycosyl hydrolases family 18	PF00704
O-methyltransferase. Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase, caffeoyl-CoA O-methyltransferase and a family of bacterial O-methyltransferases that may be involved in antibiotic production	PF01596
SURF4 family	PF02077
SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel	PF00018
3-hydroxyacyl-CoA dehydrogenase, NAD binding domain. This family also includes lambda crystallin	PF02737
HORMA domain. The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise 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	PF02301
Cytochrome oxidase c subunit VIII. 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 cytochrome c oxidase subunit VIII	PF02285
ICE-like protease (caspase) p10 domain	PF00655
Cytochrome c. The cytochrome 556 and cytochrome c' families are not included	PF00034
Protein of unknown function DUF52	PF01875
CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserv	PF02762
GTPase of unknown function	PF01926
ATP synthase (E/31 kDa) subunit. This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit	PF01991
Dynein heavy chain. This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is	PF03028
Family 4 glycosyl hydrolase	PF02056
Rabphilin-3A effector domain	PF02318
TEA/ATTS domain family	PF01285
Translationally controlled tumor protein	PF00838
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 t	PF00024
Fimbrial Usher protein. This protein is involved in biogenesis of gram negative bacterial pili	PF00577
Glycosyl hydrolase family 65 central catalytic domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic pho	PF03632
Sm protein. 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 spli	PF01423
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 a	PF00086
Lectin C-type domain. This family includes both long and short form C-type	PF00059
Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DN	PF03372
Glu/Leu/Phe/Val dehydrogenase, dimerisation domain	PF02812
Copper/zinc superoxide dismutase (SODC). superoxide dismutases (SODs) 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	PF00080
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 compl	PF01728
Integrin, beta chain. Sequences cut off at repeats due to overlap with EGF	PF00362
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	PF00503
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 homolog. The region contains a putative zinc binding C4 finger	PF01873
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	PF02310
Translin family. Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes a protein that was found to interact with translin by yeast two-hybrid screen	PF01997
Guanine nucleotide exchange factor for Ras-like GTPases	PF00618
Alpha-2-macroglobulin family. This family includes the C-terminal region of the alpha-2-macroglobulin family	PF00207
PAP/25A associated domain	PF03828
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 o	PF02359
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	PF01392
Steroid binding domain	PF03001
Cache domain	PF02743
BAG domain. Domain present in Hsp70 regulators	PF02179
jmjC domain	PF02373
NB-ARC domain	PF00931
Glycosyl hydrolases family 35	PF01301
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	PF01608
STAT protein, protein interaction 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 fac	PF02865
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	PF02254
Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain	PF00185
Glycosyl hydrolases family 39	PF01229
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	PF01431
SPO11 homologue	PF03533
Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain	PF02882
Gelsolin repeat	PF00626
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	PF00876
Small cytokines (intecrine/chemokine)	PF00048
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 t	PF00068
C. elegans Sre G protein-coupled chemoreceptor. Caenorhabditis elegans Sre proteins are candidate chemosensory receptors. There are four main recognized groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre (this family), Sra pfam02117 and Srb pfam0217	PF03125
pfam02935, COX7C, Cytochrome c oxidase subunit VIIc. 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 cytochrome c oxidase subunit VIIc. The yeast mem	PF02935
Ribosomal protein S2	PF00318
IMP dehydrogenase / GMP reductase C terminus. This family is involved in biosynthesis of guanosine nucleotide biosynthesis. Members of this family contain a TIM barrel structure. The alignment does not contain the whole TIM barrel domain. The alignment is	PF00478
Ribosomal protein S6	PF01250
PUA domain	PF01472
Ribosomal protein S8	PF00410
Signal peptidase I	PF00461
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389	PF02826
Rad52/22 family double-strand break repair protein	PF04098
Exocyst complex subunit Sec15-like	PF04091
Myc amino-terminal region. The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes invo	PF01056
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	PF00552
AP endonuclease family 1	PF01260
Ribosomal protein L14p/L23e	PF00238
Uroporphyrinogen-III synthase HemD. This family consists of uroporphyrinogen-III synthase HemD EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea. This enzyme catalyses the reaction: Hydroxymethylbil	PF02602
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 fa	PF01694
CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit,	PF04103
Helix-loop-helix DNA-binding domain	PF00010
Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48kD subunit. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as	PF03345
Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc	PF01780
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 pfam01119	PF00204
Caveolin	PF01146
Lipase/Acylhydrolase with GDSL-like motif	PF00657
GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilizes membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins	PF03127
Chlorophyll A-B binding protein	PF00504
DNA directed RNA polymerase, 7 kDa subunit	PF03604
Transcription initiation factor IID, 31kD subunit. This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated tra	PF02291
Amino acid permease	PF00324
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 co	PF02010
haloacid dehalogenase-like hydrolase. This family are 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 t	PF00702
tRNA synthetases class II (D, K and N). Other tRNA synthetase sub-families are too dissimilar to be included	PF00152
ATP synthase alpha/beta chain, C terminal domain	PF00306
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 s	PF02109
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	PF00389
Domain of unknown function (DUF367)	PF04034
sic protein. Serotype M1 group A Streptococcus strains cause epidemic waves of human infections. This family includes the sic protein an extracellular protein (streptococcal inhibitor of complement) that inhibits human complement	PF03482
LBP / BPI / CETP family, N-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar	PF01273
MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA	PF02854
Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion tar	PF03623
Oxidoreductase NAD-binding domain. Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity	PF00175
LEM domain. The LEM domain is 50 residues long and is composed of two parallel alpha helices. This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2, Emerin and Man1	PF03020
PRP38 family. Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is abou	PF03371
TBC domain. Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, imply that these domains are GTPase activator proteins of Rab-like small GTPases	PF00566
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 st	PF00128
Nop14-like family. Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production	PF04147
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	PF02213
DDHD domain. The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoestera	PF02862
Longevity-assurance protein (LAG1). Members of this family are involved in determining life span. The molecular mechanisms by which LAG1 determines longevity are unclear, although some evidence suggest a participation in ceramide synthesis	PF03798
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 domai	PF00751
Ornithine decarboxylase antizyme	PF02100
Death effector domain	PF01335
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 dimerisation.	PF00958
Dehydrogenase E1 component. This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase	PF00676
HMGL-like. This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase	PF00682
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 aci	PF01063
Fibronectin type I domain	PF00039
Uncharacterised protein family (Hly-III / UPF0073). Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It is not clear if all the members of this family are hemolysins. It ha	PF03006
Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p	PF03154
Mpv17 / PMP22 family. The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is	PF04117
Cyclin-dependent kinase regulatory subunit	PF01111
Nuf2 family. Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein ha	PF03800
Sodium transport protein	PF02386
Core-2/I-Branching enzyme. This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme. I-branching enzyme is responsible for the production of the blood group I-antigen during embryon	PF02485
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 do	PF00320
Latrophilin Cytoplasmic C-terminal region. This family consists of the cytoplasmic C-terminal region in latrophilin. Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein coup	PF02354
RNB-like protein. The function of this region of similarity is uncertain	PF00773
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	PF01958
SEA domain. Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains	PF01390
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	PF02245
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 phosphotran	PF01636
RNA polymerases N / 8 kDa subunit	PF01194
Pancreatic hormone peptide	PF00159
Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member 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 C-termi	PF02984
Acylphosphatase	PF00708
Hrf1 family. This family includes a number of eukaryotic proteins. It is an integral membrane protein, conserved in at least 1 copy in all sequenced eukaryotes. The gene name in S. pombe is hrf1+ for Heavy metal Resistance Factor 1	PF03878
Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins	PF00748
von Willebrand factor type C domain. The high cutoff was used to prevent overlap with pfam00094	PF00093
Glycerophosphoryl diester phosphodiesterase family. E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has b	PF03009
Urea transporter. Members of this family transport urea across membranes. The family includes a bacterial homologue	PF03253
Thiamin pyrophosphokinase, catalytic domain. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TP	PF04263
HMG14 and HMG17	PF01101
Carboxyl transferase domain. All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction	PF01039
Peptidase family M3	PF01432
MutT-like domain	PF00293
TILa domain. This cysteine rich domain occurs along side the TIL pfam01826 domain and is likely to be a distantly related relative. This domain is found five to twenty-five times in zonadhesins. The TILa domain is also found twice in an IGG FC binding pro	PF02345
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	PF00176
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 alternativ	PF00076
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 dom	PF00012
Huntingtin	PF03541
Male sterility protein. This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included	PF03015
Quinolinate phosphoribosyl transferase, N-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	PF02749
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 cell	PF01699
VPS28 protein	PF03997
DAN domain. This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerbe	PF03045
Cytochrome C and Quinol oxidase polypeptide I	PF00115
Eukaryotic glutathione synthase, ATP binding domain	PF03917
Putative metallopeptidase (SprT family). This family of uncharacterised proteins may be zinc metallopeptidases	PF03926
Ku70/Ku80 C-terminal arm. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C terminal arm. Thi	PF03730
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 shoul	PF01594
Perilipin family. The perilipin family includes lipid droplet-associated protein (perilipin) and adipose differentiation-related protein (adipophilin)	PF03036
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family. This family includes: Ribosomal L7A from metazoa	PF01248
14-3-3 protein	PF00244
Adenylylsulfate kinase	PF01583
Dynein heavy chain. This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is a	PF03028
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 d	PF00586
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 bi	PF02251
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 formatio	PF02320
Domain of unknown function DUF34. One member of this family NIF3 (NGG1p interacting factor 3) interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex the exact function of this interaction is unknown	PF01784
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 clea	PF01663
IncA protein. Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation	PF04156
Parathyroid hormone family	PF01279
Appr-1"-p processing enzyme family. This domain is found in a number of otherwise unrelated proteins. This domain 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 vi	PF01661
Iron/manganese superoxide dismutases, C-terminal domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one.	PF02777
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	PF01094
Transcription factor IIA, alpha/beta subunit. Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are rep	PF03153
pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella	PF02874
Mitochondrial import inner membrane, translocase subunit TIM44. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of	PF04280
Repair protein Rad1/Rec1/Rad17	PF02144
Eukaryotic cobalamin-binding protein	PF01122
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 bacteria	PF00091
SAICAR synthetase. Also known as Phosphoribosylaminoimidazole-succinocarboxamide synthase	PF01259
Isochorismatase family. This family are hydrolase enzymes	PF00857
Mob1/phocein family. Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known stru	PF03637
Transferrin	PF00405
Helicase conserved C-terminal domain	PF00271
HELP motif. The HELP (Hydrophobic ELP) motif is found in EMAP and EMAP-like proteins (ELPs). The HELP motif contains a predicted transmembrane helix so probably does not form a globular domain. It is also not clear if these proteins localize to membranes.	PF03451
eubacterial secY protein	PF00344
Myelin basic protein	PF01669
Interleukin 10	PF00726
Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48kD subunit. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known a	PF03345
RNA polymerase A/beta'/A" subunit	PF01854
BTG1 family. A novel family of anti-proliferative proteins	PF01211
Sugar (and other) transporter	PF00083
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 s	PF02391
EXS family. We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisae, and sequences that are thought to be m	PF03124